CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application Ser. No. 14/461,306, filed Aug. 15, 2014, which claims priority to U.S. provisional application No. 61/903,268, filed Nov. 12, 2013, all of which are incorporated herein by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing, which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. The Sequence Listing, labeled “059545.000016_SequenceListing_May2019_ST25.txt,” was created on May 30, 2019, and is 7 KB.

BACKGROUND OF THE INVENTION

A significant challenge facing testing laboratories is quality control. Some reports have indicated that mutations in cancer genes were correctly identified by only 70% of testing laboratories (Bellon, et al. External Quality Assessment for KRAS Testing Is Needed: Setup of a European Program and Report of the First Joined Regional Quality Assessment Rounds. Oncologist. 2011 April; 16(4): 467-478). Questions have been raised regarding how to monitor next generation sequencing and assays as well as the concordance of variant calls across multiple platforms, library preparation methods, and bioinformatic pipelines. Compositions and methods providing a flexible, single reagent representing a large number of genetic variants are desired by those of ordinary skill in the art and are described herein.

SUMMARY OF THE INVENTION

The disclosure provides compositions, controls, plasmids, cells, methods and kits comprising nucleic acid molecules.

In one embodiment, a nucleic acid molecule comprising multiple variants of a reference is disclosed. In other embodiments, a mixture or combination of nucleic acid molecules comprising variants of the reference sequence are disclosed.

In certain embodiments, the nucleic acid molecule or mixture of nucleic acid molecules comprise one or more variants present at a high or low-frequency.

In certain embodiments, the disclosure provides a control reagent comprising multiple nucleic acid molecules.

In yet another embodiment, a kit comprising at least one nucleic acid molecule or mixture of nucleic acid molecules comprising variants is disclosed

In another embodiment, a method for confirming the validity of a sequencing reaction is disclosed. The method comprises including a known number of representative sequences and/or variants thereof in a mixture comprising a test sample potentially comprising a test nucleic acid sequence, and sequencing the nucleic acids in the mixture, wherein detection of all of the representative sequences and/or variants in the mixture indicates the sequencing reaction was accurate.

The disclosure also provides a composition comprising multiple nucleic acid species wherein the nucleic acid sequence of each species differs from its neighbor species by a predetermined percentage.

In certain embodiments, a method is provided that comprises sequencing a nucleic acid species in order to calibrate a sequencing instrument.

In yet other embodiments, the disclosure provides plasmids and cells encoding the nucleic acids or mixture of nucleic acids disclosed herein.

The disclosure also provides a plasmid and/or a cell comprising multiple nucleic acid species wherein the nucleic acid sequence of each species differs from its neighbor species by a predetermined percentage.

The disclosure further provides a frequency ladder. The frequency ladder comprises a plurality of variants at different frequencies.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Exemplary EGFR amplicon selection.

FIG. 2 is a graph showing variant frequency at each nucleotide position as well as percentage A and G content. Sequences 1-5 are the same and are used to dilute out sequences 6-10. Each sequence is found in its own cassette, and all cassettes are found in the same plasmid. This design provides an absolute truth—e.g., there is 10% sequence 6 in this design. In contrast to mixing with genomic sequence, this provides the most precision when making a 10% mix. This could be used to calibrate assays.

FIG. 3 is a schematic of an exemplary plasmid with 10 sequences and restriction sites, leading to equal ratios of each sequence.

FIG. 4 is a graph showing the frequency percentage per run comprising Panel A (FLT3, PDGFRA, FGFR3, CSF1R, EGFR, HRAS, and TP53).

FIG. 5 is a graph showing the frequency percentage per run of Panel A and Panel B (TP53, PIK3CA, GNA11, VHL, FBXW7, RET, HNF1A, and STK11)

FIG. 6 is a graph showing the frequency percentage per run of Panel A, Panel B, and Panel C (RB1, EGFR, ABL1, ERBB2, and ATM).

FIG. 7 is a graph showing the frequency percentage per run of Panel A, Panel B, Panel C, and Line D, which represents the number of reads (i.e., coverage)

FIG. 8 is a graph showing the number of variants (deletions, insertions, complex, multiple nucleotide variants (MNV), and single nucleotide variants (SNV)) and average number of variants detected across multiple sites using CHPv2 (AMPLISEQ™ Cancer Hotspot Panel version 2), TSACP(TRUSEQ™ Amplicon Cancer Panel), and TSTP (TRUSIGHT™ Tumor Panel).

FIG. 9 is a graph showing analysis conducted with data from sites that tested two lots of the control at least once or one lot at least twice. Detection is indicated in dark squares and absence light squares.

FIG. 10 is a graph showing the mean number and mean percentage SNPs detected for CHPv2 and TTP.

FIG. 11 is a graph showing the mean number and mean percentage of SNPs detected for CHPv2 and TACP.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein are compositions, methods, kits, plasmids, and cells comprising nucleic acid reference sequences and variants of a reference sequence. The compositions disclosed herein have a variety of uses, including but not limited to, assay optimization, validation, and calibration; peer-to-peer comparison; training and PT/EQA, QC monitoring, reagent QC, and system installation assessment.

There is a recognized need in the market for flexible, reliable control materials for NGS testing (see Assuring the Next Quality of Next-Generation Sequencing in Clinical Laboratory Practice; Next Generation Sequencing: Standardization of Clinical Testing (Nex-SToCT) Working group Principles and Guidelines, Nature Biotechnology, doi:10.1038/nbt.2403; and ACMG Clinical laboratory standards for next generation sequencing, American College of Medical Genetics and Genomics,doi: 10.1038/gim.2013.92). This disclosure provides such control materials.

This disclosure relates to control reagents representing reference sequences and/or variants thereof (e.g., mutations) that may be used for various purposes such as, for instance, assay validation/quality control in sequencing reactions (e.g., next generation sequencing (NGS) assays). Traditional metrics used to characterize the quality of a sequencing reaction include, for instance, read length, minimum quality scores, percent target-mapped reads, percent pathogen-specific reads, percent unique reads, coverage levels, uniformity, percent of non-covered targeted bases and/or real-time error rate. Parameters that may affect quality include, for instance, the types and/or number of analytes being monitored (e.g., the types and number of polymorphisms (single or multiple nucleotide polymorphisms (SNPs, MNPs)), insertions and/or deletions, amplicons, assay contexts and/or limits of detection), sample type (e.g., mammalian cells, infectious organism, sample source), commutability (e.g., validation across multiple technology platforms and/or types of screening panels being utilized), sample preparation (e.g., library preparation type/quality and/or type of sequencing reaction (e.g., run conditions, sequence context)), and/or other parameters. Those of ordinary skill in the art realize, for instance, that the quality of such reactions may vary between laboratories due to subtle differences in guidelines, the metrics and parameters mentioned above, the reference standards used, and the fact that many NGS technologies are highly complex and evolving. This disclosure provides quality control reagents that may be used in different laboratories, under different conditions, with different types of samples, and/or across various technology platforms to confirm that that assays are being carried out correctly and that results from different laboratories may be reliably compared to one another (e.g, that each is of suitable quality). In some embodiments, the problem of confirming the quality of a sequencing reaction is solved using a multiplex control comprising multiple nucleic acid fragments, each representing a different variant of a reference sequence.

In certain embodiments, a control reagent for use in sequencing reactions is provided. The control reagent may comprise one or more components that may be used alone or combined to assess the quality of a particular reaction. For instance, some assays are carried out to identify genetic variants present within a biological sample. The control reagents described herein may also provide users with the ability to compare results between laboratories, across technology platforms, and/or with different sample types. For instance, in some embodiments, the control reagent may represent a large number of low percentage (e.g., low frequency) variants of different cancer-related genes that could be used to detect many low percentage variants in a single assay and/or confirm the reliability of an assay. The control reagent could be used to generate numerous data points to compare reactions (e.g., run-to-run comparisons). The control reagent may be used to determine the reproducibility of variant detection over time across multiple variables. The control reagent may be used to assess the quality of a sequencing run (i.e., that the instrument has sufficient sensitivity to detect the included variants at the given frequencies). The control reagent may also be used to differentiate between a proficient and a non-proficient user by comparing their sequencing runs, and/or to differentiate the quality of reagents between different lots. The control reagent may also aid in assay validation studies, as many variants are combined in one sample material. This obviates the need for multiple samples containing one or two variants each, and greatly shortens the work and time required to validate the assay.

The control reagent typically comprises one or more nucleic acid (e.g., DNA, RNA, circular RNA, hairpin DNA and/or RNA) fragments containing a defined reference sequence of a reference genome (defined as chromosome and nucleotide range) and/or one or more variants of the reference sequence. The source material for the variants may be genomic DNA, synthetic DNA, and combinations thereof. A variant typically includes nucleotide sequence variations relative to the reference sequence. The variant and reference sequence typically share at least 50% or about 75-100% (e.g., any of about 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99%) sequence identity. In some embodiments, however, the identity shared may be significantly less where, for example, the variant represents a deletion or insertion mutation (either of which may be up to several kilobases or more). An exemplary deletion may be, for instance, recurrent 3.8 kb deletion involving exons 17a and 17b within the CFTR gene as described by Tang, et al. (J. Cystic Fibrosis, 12(3): 290-294 (2013) (describing a c.2988+1616_c.3367+356de13796ins62 change, flanked by a pair of perfectly inverted repeats of 32 nucleotides)). In some embodiments, variants may include at least one of a single nucleotide polymorphism (SNP), one or more multiple nucleotide polymorphism(s) (MNV), insertion(s), deletion(s), copy number variation(s), gene fusion(s), duplication(s), inversion(s), repeat polymorphism(s), homopolymer(s), non-human sequence(s), or any combination thereof. Such variants (which may include by reference any combinations) may be included in a control reagent as part of the same or different components. The reference sequence(s) and/or variants may be arranged within a control reagent as cassettes.

Cassettes contains a reference sequence or variant adjoined and/or operably linked to one or more restriction enzyme site(s), sequencing primer(s) site, and/or hairpin-forming site(s). In some embodiments, it may be useful to include different types of sequences adjacent to each cassette; for instance, it may be useful to design one cassette to be adjacent to a restriction enzyme and/or a hairpin sequence. Doing so may help prevent problems such as cross-amplification between adjacent fragments/cassettes. As such, each reference sequence and/or variant may be releasable and/or detectable separate from any other reference sequence and/or variant. The typical cassette may be about 400 bp in length but may vary between 50-20,000 bp (e.g., such as about any of 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 800, 900, 1000, 2500, 5000, 7500, 10000, 12500, 15000, 17500, or 20000 bp). Each control reagent may comprise one or more cassettes, each representing one or more reference sequence(s) and/or variant(s) (e.g., each being referred to as a “control sequence”). Each reference sequence and/or variant may be present in a control sequence and/or control reagent at percentage of about any of 0.1% to 100% (e.g., about any 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2.5, 5, 7.5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%). For instance, a control sequence or control reagent that is 100% reference sequence or variant would be a reagent representing only one reference sequence or variant. Similarly, a control sequence or control reagent comprising 50% of a variant would be a control reagent representing only up to two reference sequences and/or variants. The remaining percentage could consist of other sequences such as control sequences and the like.

In certain embodiments a T7 or other promoter can be present upstream of each cassette. This allows for massively parallel transcription of many gene regions. This technique facilitates construction of a control containing equivalent amounts of each target sequence. When there are equivalent amounts of many targets, ease of use of the control is increased. For example, contamination in a control in a patient sample would be easier to detect because all transcripts would show up in the contaminated sample. It is highly unlikely for patient samples to contain, e.g., a large number of fusion transcripts, such an assay result would signal the user that that a contamination issue is present. This is in contrast to a situation in which only one transcript is present at a much higher abundance in a contaminated sample—which could lead to the contaminant being mistaken for a true positive signal. The ability to construct a control with equivalent amounts of each target sequence eliminates the potential for this type of error.

In certain embodiments, the reference sequence(s) and/or variants may be adjoined and/or operably linked to one or more different restriction enzyme sites, sequencing primer site(s), and/or hairpin-forming sites. As described above, certain designs may be used to prevent problems such as cross-amplification between reference sequences and/or variants. In some embodiments, the control sequences and/or cassettes may optionally be arranged such that the same are releasable from the control reagent. This may be accomplished by, for instance, including restriction enzyme (RE) sites at either end of the control sequence. A control reagent may therefore be arranged as follows: RE site/control sequence/RE site. The RE sites may be the same and/or different from one another. The RE sites in one cassette may also be the same and/or different to those present in any other cassette. As such, the control sequences may be released from the cassette as desired by the user by treating the control sequence with one or more particular restriction enzymes.

In some embodiments, the control reagent may comprise multiple components that may be used together. In certain embodiments, the multiple components comprise a first and a second component which may be plasmids comprising different control sequences and/or different arrangements of the same control sequences. Thus, the components may represent the same or different reference sequences and/or variants. Such components may be used together as a panel, for instance, such that a variety of reference sequences and/or variants may be assayed together. Where the reference sequences and/or variants are the same, each component may include those variants in different cassette arrangements and/or forms. In some embodiments, the multiple components may comprise a first component representing one or more SNP variants and a second component representing one or more multiple nucleotide polymorphism(s), insertion(s), deletion(s), copy number variation(s), gene fusion(s), duplication(s), inversion(s), repeat polymorphism(s), homopolymer(s), and/or non-human sequence(s). The components may be the same or different types of nucleic acids such as plasmids, with each comprising the same or different variants of one or more reference sequences arranged as described herein or as may be otherwise determined to be appropriate by one of ordinary skill in the art. In some embodiments, different types of plasmids may be combined to provide a multi-component control reagent representing many different reference sequences and/or variants.

Plasmids can be quantified by any known means. In one embodiment, quantitation of each plasmid is performed using a non-human ‘xeno’ digital PCR target sequence. The exact copy number of the plasmid is determined. The exact copy number of genomic DNA is also determined (obtained by quantification of genomic target site(s)). With this information, controls can be accuratley and reproducibly developed that contain all targets/variants within a tight frequency range.

The variants may be contained within the control reagent as DNA fragments, each containing a defined sequence derived from a reference genome (defined as chromosome and nucleotide range) with one or more variations (e.g., nucleotide differences) introduced into the fragment. A variant may be, for instance, a sequence having one or more nucleotide sequence differences from the defined sequence (e.g., a reference sequence). For instance, an exemplary reference sequence may comprise “hostpots” suitable for modification. Such hotspots may represent nucleotides and/or positions in a reference sequence that occur in nature (e.g., mutations observed in cancer cells). One or more of such hotspots may be modified by changing one or more nucleotides therein to produce a control sequence (or portion thereof) that may be incorporated into a control reagent. For example, modification of the exemplary epidermal growth factor receptor (EGFR) Ex19 reference sequence to produce control sequences (Hotspots 1, 2, 3, 4, 5) is shown below (see also, FIG. 1):

Wild Type (e.g., EGFR Ex19) CCAAGCTC (SEQ ID NO: 1) . . . AGGATCTTGA (SEQ ID NO: 2) . . . AACTGAATTC (SEQ ID NO: 3) . . . AAAAAG (SEQ ID NO: 4) . . . ATCAAAGTGC (SEQ ID NO: 5) (400 bp)

Hotspot ID 1 CCAATCTC (SEQ ID NO: 6) . . . AGGATCTTGA (SEQ ID NO: 2) . . . AACTGAATTC (SEQ ID NO: 3) . . . AAAAAG (SEQ ID NO: 4) . . . ATCAAAGTGC (SEQ ID NO: 5)

Control Sequence Contains Multiple Hotspots

CCAATCTC (SEQ ID NO: 6; HOTSPOT ID 1) . . . AGGAACTTGA (SEQ ID NO: 7; HOTSPOT ID 2) . . . AACTCAATTC (SEQ ID NO: 8; HOTSPOT ID 3) . . . ATAAAG (SEQ ID NO: 9; HOTSPOT ID 4) . . . ATGAAAGTGC (SEQ ID NO: 10; HOTSPOT ID 5). This exemplary control sequence thereby represents multiple EGFR variants (e.g., Hotspot IDs 1, 2, 3, 4, 5, etc.) A control reagent may comprise multiple control sequences, each representing one or more variants of the same or different reference sequences. Any number of variants may be represented by a control sequence, and any number of control sequences may be included in a control reagent. A control reagent may comprise, for instance, a number of variants such that the all possible variants of a particular reference sequence are represented by a single control reagent. For instance, the control reagent may comprise multiple SNPs, MNPs, deletions, insertions and the like, each representing a different variant of the reference sequence. Additional, exemplary, non-limiting variants are shown in Tables 1A and 1B and Table 6.

Control reagents may also be designed to represent multiple types of control sequences. For instance, control reagents may be designed that represent multiple types of reference sequences and/or variants thereof (which may be found in control sequences alone or in combination). Exemplary categories of control sequences for which the control reagents described herein could have relevance include not only the aforementioned cancer-related areas but also fields of inherited disease, microbiology (e.g., with respect to antibiotic resistance mutations, immune-escape related mutations), agriculture (e.g. plant microbe and/or drug resistance-related mutations), livestock (e.g., mutations related to particular livestock traits), food and water testing, and other areas. Exemplary combinations (e.g., panels) of cancer-related reference sequences that may be represented by a particular control reagent (or combinations thereof) are shown in Table 2.

The control reagents and methods for using the same described herein may provide consistent control materials for training, proficiency testing and quality control monitoring. For instance, the control reagents may be used to confirm that an assay is functioning properly by including a specific number of representative sequences and/or variants thereof that should be detected in an assay and then calculating the number that were actually detected. This is exemplified by the data presented in Table 3:

As illustrated in Table 3, a “bad run” is identified where the number of variants detected does not match the number of variants expected to be detected (e.g., included in the assay). As shown in the exemplary assay of Table 3, if a particular control reagent (or combination thereof) used in an assay includes 15 representative sequences and/or variants thereof, all 15 should be detected if the assay is properly carried out. If less than 15 of these control sequences are not detected, the assay is identified as inaccurate (e.g., a “Bad Run”). If all 15 of the sequences are detected, the assay is identified as accurate (e.g., a “Good Run”). Variations of this concept are also contemplated herein, as would be understood by those of ordinary skill in the art.

In certain embodiments, the control reagent may be prepared by mixing variant DNA fragments (e.g., as may be incorporated into a plasmid) with genomic DNA or synthesized DNA comprising “wild-type” (e.g., non-variant) sequence. Such sequence may be obtained from or present in control cells (e.g., naturally occurring or engineered/cultured cell lines). In some embodiments, the wild-type sequence may be included on a DNA fragment along with the variant sequence, or the variant sequences may be transfected into and/or mixed with cells (e.g., control cells). In certain embodiments, such mixtures may be used to prepare formalin-fixed, paraffin-embedded (FFPE) samples (e.g., control FFPE samples), for example. For instance, in some embodiments, the control reagent may be prepared and tested by designing a control sequence (e.g., an amplicon) comprising a representative sequence and/or variant thereof; designing restriction sites to surround each amplicon; synthesizing a nucleic acid molecule comprising a cassette comprising the amplicon and the restriction sites; and, incorporating the cassette into a plasmid backbone. The construct may then be tested by sequencing it alone (e.g, providing an expected frequency of 100%) or after mixing the same with, for example, genomic DNA at particular expected frequencies (e.g., 50%). Such constructs may also be mixed with cells for various uses, including as FFPE controls.

In certain embodiments, the control reagents described herein can also be used to provide a frequency ladder. A frequency ladder is composed of many variants at different frequencies. In some embodiments, the control reagent could be used to provide an “ladder” in, for example, 5% increments of abundance (e.g., about any of 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% abundance). For example, the ladder could be constructed by taking a single sample with many different variants present at high (e.g., 80% allele frequency) and making dilutions down to low frequencies. Alternatively, the ladder could be a single sample containing variants at different frequencies. The ladder could be used as a reference for many sample types, including somatic variants at low abundance (e.g., tumor single nucleotide polymorphisms), or germline variants present at, as a non-limiting example, about 50% abundance. Such a ladder may also be used to determine instrument limits of detection for many different variants at the same time. This saves users time in finding materials containing one to a few variants and resources for testing because all variants are present in a single sample rather than many. An example is provided in Table 8:

As shown in Table 8, a ladder was constructed by diluting a sample containing 555 variants starting at approximately 50% frequency down to ˜3% frequency. The ladder was tested in duplicate using the Ion AMPLISEQ® Cancer Hotspot Panel v2 using the Ion Torrent PERSONAL GENOME MACHINE® (PGM). The frequencies for 35 of the variants are reported for each sample tested. The shaded cells indicate that the variant was not detected. Such data could be used to establish the limit of detection for each variant.

The ladder could be used across many platforms, including Sanger sequencing and next generation platforms, and both RUO and IVD applications could benefit from use of this standard. The frequency ladder could also serve as internal controls in sequencing reactions, much like the 1 kb DNA ladder serves as a reference in almost every agarose gel. As an example, one design would provide five unique and five identical sequences as shown in FIGS. 2 and 3. As shown therein, in one sequence position, there is a variant present in only one of these ten sequences. At a second position, the variant is present in two of the ten sequences. At the third position, the variant is present in three of the sequences, and so on. This would yield variants at 10% frequency increments from 0-100%. This is a simplified example and random intervening sequences may be necessary to prevent sequencing artifacts. The product could take any suitable form such as an oligonucleotide (e.g., PCR fragment or synthetic oligonucleotide), plasmids, or one plasmid with concatenated sequences separated by identical restriction enzyme sites (FIG. 3). An advantage of having all sequence variants on one plasmid is that the relative levels of all ten sequences within a mixture would be well controlled; during manufacturing, the plasmid could be cleaved between each sequence with the same enzyme, giving rise to ten fragments at equal ratios. As would be understood by those of ordinary skill in the art, derivations of such a ladder could include different variant types (e.g., insertions and/or deletions), every nucleotide change could be incorporated into the design (e.g., A->C, A->T, etc.), and/or smaller increments could provide fine-tuned measurement at abundances lower than 10%. For instance, a second plasmid with other mutations could be added to the initial plasmid at a one to nine ratio, yielding variants at even lower frequencies. Such a low frequency sequencing ladder could be an essential control when measuring somatic mutations that appear, for example, at <10% abundance. In some embodiments, such a sequencing ladder may comprise multiple nucleic acid species wherein the nucleic acid sequence of each species differs from its neighbor species by a predetermined percentage (e.g., about any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10% or more). Each species may comprise, for instance, any suitable number of nucleotides (e.g., about any of 5, 10, 20, 40, 50, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, or 500). Each species may also comprise a homopolymer sequence of at least 3 nucleotides. In some embodiments, the nucleic acid of the species is DNA, and these may be encoded on vectors such as plasmids and/or by and/or within cells. In some embodiments, each species may comprise a nucleic acid bar code that may be unique to each species. Methods comprising sequencing the nucleic acid species to calibrate a sequencing instrument, to obtain data for sequencing instrument development work, including algorithm development, base calling, variant calling, and/or verify that an instrument is functioning properly (e.g., IQ/OQ/PQ) are also contemplated.

One of ordinary skill in the art would understand that the control reagents described herein are broadly useful in a variety of sequencing systems and/or platforms. For instance, the control reagents described herein may be used in any type of sequencing procedure including but not limited to Ion Torrent semiconductor sequencing, Illumina MISEQ®, capillary electrophoresis, microsphere-based systems (e.g., Luminex), Roche 454 system, DNA replication-based systems (e.g., SMRT by Pacific Biosciences), nanoball- and/or probe-anchor ligation-based systems (Complete Genomics), nanopore-based systems and/or any other suitable system.

One of ordinary skill in the art would also understand that the control reagents described herein are broadly useful in a variety of nucleic acid amplification-based systems and/or platforms. The control reagents described herein may used in and/or with any in vitro system for multiplying the copies of a target sequence of nucleic acid, as may be ascertained by one of ordinary skill in the art. Such systems may include, for instance, linear, logarithmic, and/or any other amplification method including both polymerase-mediated amplification reactions (such as polymerase chain reaction (PCR), helicase-dependent amplification (HDA), recombinase-polymerase amplification (RPA), and rolling chain amplification (RCA)), as well as ligase-mediated amplification reactions (such as ligase detection reaction (LDR), ligase chain reaction (LCR), and gap-versions of each), and combinations of nucleic acid amplification reactions such as LDR and PCR (see, for example, U.S. Pat. No. 6,797,470). Such systems and/or platforms may therefore include, for instance, PCR (U.S. Pat. Nos. 4,683,202; 4,683,195; 4,965,188; and/or 5,035,996), isothermal procedures (using one or more RNA polymerases (see, e.g., PCT Publication No. WO 2006/081222)), strand displacement (see, e.g., U.S. Pat. No. RE39007E), partial destruction of primer molecules (see, e.g., PCT Publication No. WO 2006/087574)), ligase chain reaction (LCR) (see, e.g., Wu, et al., Genomics 4: 560-569 (1990)), and/or Barany, et al. Proc. Natl. Acad. Sci. USA 88:189-193 (1991)), Qβ RNA replicase systems (see, e.g., PCT Publication No. WO 1994/016108), RNA transcription-based systems (e.g., TAS, 3SR), rolling circle amplification (RCA) (see, e.g., U.S. Pat. No. 5,854,033; U.S. Patent Application Publication No. 2004/265897; Lizardi et al. Nat. Genet. 19: 225-232 (1998); and/or Bailer et al. Nucleic Acid Res., 26: 5073-5078 (1998)), and/or strand displacement amplification (SDA) (Little, et al. Clin. Chem. 45:777-784 (1999)), among others. These systems, along with the many other systems available to the skilled artisan, may be suitable for use with the control reagents described herein.

In one embodiment, a control reagent may be designed and tested using one or more of the steps below:

- designing a control sequence (e.g., an amplicon) comprising a representative sequence of a particular gene of interest and/or variants thereof (e.g., those targeted by commercially-available NGS tests such as the AMPLISEQ Cancer Hotspot Panel v2, and/or the TRUSEQ Amplicon Cancer Panel);
- identifying sequence from a genome reference source (e.g., Genome Reference Consortium Human Reference 37 (GRCh37)) encompassing the amplicon;
- designing a cassette comprising an ˜400 bp sequence comprising the amplicon surrounded by (e.g., 5′ and 3′) the genomic sequence identified in step b);
- designing restriction sites to surround each cassette prepared in step c) (e.g., where one version may additionally include sequences that create a hairpin when the DNA is single-stranded);
- synthesizing a nucleic acid molecule comprising the cassette of step c) and restriction sites of step d) using a common vector (e.g., pUC57) (e.g., “plasmid V1”);
- preparing a second plasmid (e.g., “plasmid V2”) comprising multiple fragments of the gene of interest (and/or variants thereof) with a hairpin structure and a restriction site between each region;
- optionally, linearizing the variant sequences contained within plasmids V1 and/or V2 with a restriction enzyme;
- mixing the variants with genomic DNA (e.g., wild-type gDNA) at a particular expected variant frequency (e.g., approximately 50%);
- optionally, testing the “variant sequence” alone (e.g., providing an expected variant frequency of 100%);
- performing variant detection using NGS.

In certain embodiment, individual cassettes can be synthesized for all genes of interest and combined with wild type. In certain embodiments, a cassette can be designed with a plurality of variants, which do not interfere with the detection of variants near or adjacent thereto.

In some embodiments, NGS may be performed using the Ion Personal Genome Machine (PGM) by first constructing libraries following the user manuals for the Ion AMPLISEQ® Library Preparation Manual with AMPLISEQ® Cancer Hotspot Panel v2 reagents; preparing template-positive Ion sphere particles (ISPs) and enriching the same using the Ion OneTouch2 instrument following the Ion PGM Template OT2 200 Kit Manual; sequencing using the Ion PGM Sequencing 200 Kit v2 Manual or Sequencing on the Illumina MISEQ® following the TRUSEQ® Amplicon Cancer Panel user manual or the Illumina MiSeq® user manual; and, performing data analysis for PGM using the Torrent Variant Caller v3.4 and v3.6, and for MISEQ® using the MISEQ® Reporter v2.3).

The reagents and methods described herein may be used in a variety of settings with a variety of samples. For instance, these reagents and methods may be used to analyze biological samples such as serum, whole blood, saliva, tissue, urine, dried blood on filter paper (e.g, for newborn screening), nasal samples, stool samples or the like obtained from a patient and/or preparations thereof (e.g., FFPE preparations). In some embodiments, control preparations comprising the control reagents described herein may be provided.

This disclosure further relates to kits comprising one or more control reagents described herein. The kits may be used to carry out the methods described herein or others available to those of ordinary skill in the art along with, optionally, instructions for use. A kit may include, for instance, control sequence(s) including multiple reference sequences and/or variations thereof in the form of, for instance, one or more plasmids. In some embodiments, the kit may contain a combination of control sequences organized to provide controls for many variations of one or more reference sequences. In some embodiments, the variations may relate to an oncogene that is diagnostic for a particular cancer. In some embodiments, for instance, the kit may comprise control reagents and/or control samples (e.g., tissue samples) known to cover the breadth of mutations known for a particular cancer. In some embodiments, the variations of the marker are variations of a mutation in a gene that are prognostic for the usefulness of treating with a drug. In some embodiments, the marker or markers are for a particular disease and/or a variety of diseases (e.g., cancer, infectious disease). In some embodiments, the control reagent(s) may be included in a test to ascertain the efficacy of a drug in testing for the presence of a disease and/or progression thereof. In some embodiments, the kit may comprise control reagents for testing for a series of diseases that have common characteristics and/or symptoms (e.g., related diseases). In some embodiments, the marker may have unknown significance but may otherwise be of interest to the user (e.g., for basic research purposes). The kit may also include a container (e.g., vial, test tube, flask, bottle, syringe or other packaging system (e.g., include injection or blow-molded plastic containers) into which one or more control reagents may be placed/contained, and in some embodiments, aliquoted). Where more than one component is included in the kit, it will generally include at least one second, third or other additional container into which the additional components can be separately placed. Various combinations of components may also be packaged in a single container. The kits may also include reagent containers in close confinement for commercial sale. When the components of the kit are provided in one and/or more liquid solutions, the liquid solution comprises an aqueous solution that may be a sterile aqueous solution. As mentioned above, the kit may also include instructions for employing the kit components as well as the use of any other reagent not included in the kit. Instructions may include variations that may optionally be implemented. The instructions may be provided as a separate part of the kit (e.g., a paper or plastic insert or attachment) or as an internet-based application. In some embodiments, the kit may control reagents relating to between any number of reference sequences and/or variants thereof which may be detected alone or in combination with one another (e.g., a multiplex assay). In some embodiments, the kit may also comprise at least one other sample containing a defined amount of control reagent and “control” test cell admixed such that the same may provide a reference point for the user. Kits may further comprise one or more of a polymerase and/or one or more oligonucleotide primers. Other variations and arrangements for the kits of this disclosure are contemplated as would be understood by those of ordinary skill in the art.

Thus, in some embodiments, the disclosure provides a nucleic acid molecule or mixture of nucleic acid molecules comprising multiple variants of a reference sequence, each variant sequence may optionally be releasable from the nucleic acid molecule. In certain embodiments, the nucleic acid molecule or mixture of nucleic acid molecules comprises variants releasable from the nucleic acid molecule using a restriction enzyme.

In some embodiments, the nucleic acid molecule or mixture of nucleic acid molecules comprises at least one single nucleotide polymorphism (SNP), multiple nucleotide polymorphisms (MNP), insertion, deletion, copy number variation, gene fusion, duplication, inversion, repeat polymorphism, homopolymer of a reference sequence, and/or a non-human sequence. In some embodiments, the nucleic acid molecule or mixture of nucleic acid molecules comprises at least 5 variants. In certain embodiments, at least 15, 20, 30, 50, 100, 200, 300 400, 700, 1000 variants are present. In yet other embodiments, greater than 1000 variants are present. In some embodiments, each variant is present (e.g., in the sample being tested) at a high or low-frequency. For instance, in certain embodiments, each variant may be present at a frequency of 1%, 5%, 10%, 15%, 20%, 30%, 40% or 50% or more. In other embodiments, each variant may be present at a frequency of less than 50%, less than 40%, less than 20%, less than 15%, less than 10%, less than 5%, less than 3%, less than 1%, less than 0.5%, less than 0.1%, and any integer in between.

An advantage of the disclosed control materials is that the “truth” of a sample is known. There are currently no reference materials for which absolute frequency (i.e, the truth) is known, that is, the actual frequency of a given variant or combination of variants present are not known. In contrast, in the disclosed control materials, the actual frequency of variants is known.

Attendant to the teachings of this disclosure, standardized control materials for next generation sequencing (NGS) assays can be produced. Issues such as variant call differences between sites, variability of reagents across instruments, variation introduced by diverse bioinformatics pipelines and filters, run-to-run and lab-to-lab variability can be identified and resolved and/or obviated utilizing the control materials.

A further advantage is that the control materials disclosed herein can comprise any number and type of variants, including insertions and deletions of differing lengths, large numbers of SNPs, etc. No other control material exists that provide such diversity.

The variants can be any of interest. There is no limit provided herein with respect to the type and number of variants that can be utilized in the current disclosure.

In certain embodiments, modified nucleotides can be utilized as variants. In certain embodiments, methylation can be detected. For example, CpG methylation can be utilized as a biomarker variant.

This disclosure also provides reagents and methods for confirming the validity of a sequencing reaction by including a known number of representative sequences and/or variants thereof in a mixture comprising a test sample potentially comprising a test nucleic acid sequence and sequencing the nucleic acids in the mixture, wherein detection of all of the representative sequences and/or variants in the mixture indicates the sequencing reaction was accurate. The representative sequences and/or variants may be of the type described herein. Compositions comprising the same are also provided. The pre-determined percentage may be, for instance, about 1, 5 or 10%. And each species may be from, for instance, 20-500 nucleotides. Each species may comprise a homopolymer sequence of at least 3 nucleotides. The nucleic acids may be DNA. Each species may possess a nucleic acid barcode that may be unique to each species. The nucleic acid species described herein may be used to calibrate a sequencing instrument, for instance. Kits comprising such species, optionally further comprising one or more polymerases and/or one or more oligonucleotide primers are also provided. Plasmids and/or cells comprising multiple nucleic acid species wherein the nucleic acid sequence of each species differs from its neighbor species by a predetermined percentage are also provided.

It is to be understood that the descriptions of this disclosure are exemplary and explanatory only and are not intended to limit the scope of the current teachings. In this application, the use of the singular includes the plural unless specifically stated otherwise. Also, the use of “comprise”, “contain”, and “include”, or modifications of those root words, for example but not limited to, “comprises”, “contained”, and “including”, are not intended to be limiting. Use of “or” means “and/or” unless stated otherwise. The term “and/or” means that the terms before and after can be taken together or separately. For illustration purposes, but not as a limitation, “X and/or Y” can mean “X” or “Y” or “X and Y”. Whenever a range of values is provided herein, the range is meant to include the starting value and the ending value and any value or value range therebetween unless otherwise specifically stated. For example, “from 0.2 to 0.5” may mean 0.2, 0.3, 0.4, and 0.5; ranges therebetween such as 0.2-0.3, 0.3-0.4, 0.2-0.4; increments there between such as 0.25, 0.35, 0.225, 0.335, 0.49; increment ranges there between such as 0.26-0.39; and the like. The term “about” or “approximately” may refer the ordinary meaning of the term but may also indicate a value or values within about any of 1-10 percent of the listed value.

The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described in any way. All literature and similar materials cited in this application including, but not limited to, patents, patent applications, articles, books, treatises, and internet web pages, regardless of the format of such literature and similar materials, are expressly incorporated by reference in their entirety for any purpose. In the event that one or more of the incorporated literature and similar materials defines or uses a term in such a way that it contradicts that term's definition in this application, this application controls. While the present teachings are described in conjunction with various embodiments, it is not intended that the present teachings be limited to such embodiments. On the contrary, the present teachings encompass various alternatives, modifications, and equivalents, as will be appreciated by those of skill in the art. Certain embodiments are further described in the following examples. These embodiments are provided as examples only and are not intended to limit the scope of the claims in any way.

Aspects of this disclosure may be further understood in light of the following examples, which should not be construed as limiting the scope of the disclosure in any way.

EXAMPLES
Example 1

An exemplary control reagent was prepared and tested as described below:

a) amplicons were designed comprising the fragments shown in Tables 1-3;

b) genomic sequences were selected to encompass each amplicon (the selected genomic sequences being the chromosome and nucleotide positions of the reference genome corresponding to the 5′ nucleotide of the forward and reverse primers for each amplicon and all the sequence between these two nucleotides);

c) a cassette was designed comprising an ˜400 bp EGFR sequence comprising the amplicon surrounded by (e.g., 5′ and 3′) the genomic sequence identified in step b) (the reference sequence is added in roughly equally amounts to each end of the region defined in step b) to comprise a ˜400 bp region);

d) restriction enzyme and other sites were designed to each cassette prepared in step c) (e.g., where one version may additionally include sequences that create a hairpin when the DNA is single-stranded; the restriction enzymes being chosen such that the sequences of interest are not digested but simply released from the control reagent) as shown below:

EGFR V1**

**EGFR_1, etc. represent EGFR variants; restriction enzyme sites for ClaI, HindIII, SmaI, XhoI and Not I enzymes were positioned between variants.

EGFR_1-ClaI-EGFR_2-HindIII-EGFR_3-SmaI-EGFR_4-XhoI-EGFR_5-NotI-EGFR_6/7-EGFR_8
EGFR V2***

***Hairpin 7 (HP(7)): GGGGGGGTTTTCCCCCCC (SEQ ID NO: 11); HindIII=HindIII RE site;

EGFR_4-HP(7)-ClaI-EGFR_5-HP(7)-HindIII-EGFR_6/7-HP(9)-Sma1-EGFR_8

Hairpin 9 (HP(9)): GGGGGGGGGAACCCCCCCCC (SEQ ID NO: 12); SmaI=SmaI RE site

e) the cassette of step d) was incorporated into a common vector (pUC57) (e.g., plasmid V1) by automated synthesis of oligonucleotides on solid-phase synthesizers followed by ligation of overlapping oligonucleotides;

f) a second plasmid (e.g., “plasmid V2”) comprising multiple fragments of the gene of interest (and/or variants thereof) with a hairpin structure and a restriction site between each region (e.g., as in exemplary construct EGFR V2 above and Table 4) was also prepared by automated synthesis of oligonucleotides on solid-phase synthesizers followed by ligation of overlapping oligonucleotides;

g) the variant sequences (Tables 4-6) contained within plasmids V1 and/or V2 were then linearized HindIII;

h) the variants were then mixed with genomic DNA (e.g., wild-type gDNA) at a particular expected variant frequency (e.g., approximately 50%) (plasmid DNA and human embryonic kidney (HEK-293) genomic DNA were quantified using a fluorometer (QUBIT®) to determine the concentration; plasmid and genomic DNA were then mixed together to obtain a 1:1 molecular ratio (50% variant frequency));

i) the “variant sequences” were then tested alone to provide an expected variant frequency of 100%) to confirm sequencing; and,

j) variants of step h) were detected by NGS using the Ion Personal Genome Machine (PGM) and Illumina MiSeq (results are presented in Table 7).

Example 2
FFPE-Embedded Controls

The results of monitoring assays using FFPE-embedded controls are presented in FIGS. 4-7. As shown therein, FFPE-embedded control reagents may be used to monitor variant detection, including low frequency variants (e.g., RB1 as indicated by “C” in the figures). Variants may be tracked by the amplicon per se, GC content, sequence context, and/or variant type as desired by those of ordinary skill in the art.

Each embodiment disclosed herein may be used or otherwise combined with any of the other embodiments disclosed. Any element of any embodiment may be used in any embodiment. Although the invention has been described with reference to specific embodiments, it will be understood by those skilled in the art that various changes may be made and equivalents may be substituted for elements thereof without departing from the true spirit and scope of the invention. In addition, modification may be made without departing from the essential teachings of the invention.

Example 3
555-Variant Control Performance Across Multiple Test Sites

A control sample was constructed that contained 555 variants from 53 different genes and tested with the Ion AMPLISEQ® Cancer Hotspot Panel v2 (CHPv2), TRUSEQ® Amplicon Cancer Panel (TSACP) and the TRUSIGHT® Tumor Panel. For each panel, two lots of the AcroMetrix® Oncology Hotspot Control were tested in duplicate, in at least two sites. Additional sites only tested one of the lots at least twice or both lots once. Sources of variation between sites may include different instruments, operators and general workflows. Also, variation in bioinformatics pipelines may have contributed significantly to variation in performance results.

FIG. 8 shows performance across different sites and panels. The average number of variants of different types detected in the ACROMETRIX® Oncology Hotspot Control are reported by site and grouped by panel. Note: The total number of variants of each type is different for each panel. See FIGS. 8-11.

To assess the detection of specific variants across different panels, twenty-two clinically-relevant variants that were targeted by three panels were selected. FIG. 9 shows detection of 22 selected variants across panels. Analysis was conducted with data from sites that tested two lots of the control at least once or one lot at least twice. Detection is indicated in dark squares and absence indicated in light squares. Site-to-site differences are apparent, even amongst those utilizing the same library preparation method, indicating the likelihood of the bioinformatics pipeline having an impact on performance.

Example 4

Performance of the control material comprising 555 variants is shown in Table 9, wherein SNV (single nucleotide variant), MNV (multiple nucleotide variant), DEL (deletion), INS (insertion), for CHPv2 (AMPLISEQ® Cancer Hotspot Panel v2), TSACP (TRUSEQ® Amplicon cancer panel), and TSTP (TRUSIGHT® tumor panel) are shown. A variant was considered to be covered by the test method if the variant was positioned between the upstream and downstream primers. A variant was considered detected if it was detected in at least one run of the control. Sanger sequencing was performed on the synthetic DNA prior to dilution with genomic DNA. Variants detected in the genomic DNA were confirmed using publicly available whole genome sequencing information for GM24385.

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

TABLE 1A

Exemplary Hotspot (HS) Variants

Gene name
Mutation ID
Mutation CDS
Mutation Description
Chr
Start
End

MPL
27286
c.1514G > A
Substitution - Missense
1
43814979
43814979

MPL
18918
c.1544G > T
Substitution - Missense
1
43815009
43815009

MPL
27290
c.1555G > A
Substitution - Missense
1
43815020
43815020

NRAS
584
c.182A > G
Substitution - Missense
1
115256529
115256529

NRAS
1332933
c.174A > G
Substitution - coding silent
1
115256537
115256537

NRAS
577
c.52G > A
Substitution - Missense
1
115258730
115258730

NRAS
564
c.35G > A
Substitution - Missense
1
115258747
115258747

NRAS
24850
c.29G > A
Substitution - Missense
1
115258753
115258753

ALK
28056
c.3824G > A
Substitution - Missense
2
29432664
29432664

ALK
28055
c.3522C > A
Substitution - Missense
2
29443695
29443695

MSH6
13399
c.3246G > T
Substitution - coding silent
2
48030632
48030632

MSH6
13395
c.3261delC
Deletion - Frameshift
2
48030647
48030647

MSH6
1021299
c.3300G > A
Substitution - coding silent
2
48030686
48030686

IDH1
28746
c.395G > A
Substitution - Missense
2
209113112
209113112

IDH1
1404902
c.388A > G
Substitution - Missense
2
209113119
209113119

IDH1
96922
c.367G > A
Substitution - Missense
2
209113140
209113140

ERBB4
48362
c.2791G > T
Substitution - Missense
2
212288954
212288955

ERBB4
169572
c.2782G > T
Substitution - Nonsense
2
212288963
212288964

ERBB4
232263
c.1835G > A
Substitution - Missense
2
212530083
212530084

ERBB4
573362
c.1828C > A
Substitution - Missense
2
212530090
212530091

ERBB4
1405173
c.1784A > G
Substitution - Missense
2
212530134
212530135

ERBB4
1614287
c.1089T > C
Substitution - coding silent
2
212576809
212576810

ERBB4
110095
c.1022C > T
Substitution - Missense
2
212576876
212576877

ERBB4
573356
c.1003G > T
Substitution - Missense
2
212576895
212576896

ERBB4
1405181
c.909T > C
Substitution - coding silent
2
212578347
212578348

ERBB4
160825
c.885T > G
Substitution - Missense
2
212578371
212578372

ERBB4
1015994
c.829C > A
Substitution - Missense
2
212587171
212587172

ERBB4
1251447
c.804C > A
Substitution - Nonsense
2
212587196
212587197

ERBB4
1405184
c.730A > G
Substitution - Missense
2
212589811
212589812

ERBB4
573353
c.704C > T
Substitution - Missense
2
212589837
212589838

ERBB4
1015997
c.633G > A
Substitution - coding silent
2
212589908
212589909

ERBB4
48369
c.542A > G
Substitution - Missense
2
212652763
212652764

ERBB4
442267
c.515C > G
Substitution - Missense
2
212652790
212652791

VHL
14305
c.266T > A
Substitution - Missense
3
10183797
10183797

VHL
18080
c.277G > C
Substitution - Missense
3
10183808
10183808

VHL
17658
c.286C > T
Substitution - Nonsense
3
10183817
10183817

VHL
17886
c.296delC
Deletion - Frameshift
3
10183827
10183827

VHL
17752
c.343C > A
Substitution - Missense
3
10188200
10188200

VHL
14312
c.353T > C
Substitution - Missense
3
10188210
10188210

VHL
14407
c.388G > C
Substitution - Missense
3
10188245
10188245

VHL
14412
c.431delG
Deletion - Frameshift
3
10188288
10188288

VHL
17657
c.472C > G
Substitution - Missense
3
10191479
10191479

VHL
17612
c.481C > T
Substitution - Nonsense
3
10191488
10191488

VHL
14311
c.499C > T
Substitution - Missense
3
10191506
10191506

VHL
17837
c.506T > C
Substitution - Missense
3
10191513
10191513

MLH1
26085
c.1151T > A
Substitution - Missense
3
37067240
37067240

CTNNB1
5677
c.98C > G
Substitution - Missense
3
41266101
41266101

CTNNB1
5662
c.110C > T
Substitution - Missense
3
41266113
41266113

CTNNB1
5664
c.121A > G
Substitution - Missense
3
41266124
41266124

CTNNB1
5667
c.134C > T
Substitution - Missense
3
41266137
41266137

FOXL2
33661
c.402C > G
Substitution - Missense
3
138665163
138665163

PIK3CA
27495
c.35G > A
Substitution - Missense
3
178916648
178916648

PIK3CA
27376
c.93A > G
Substitution - Missense
3
178916706
178916706

PIK3CA
1420738
c.180A > G
Substitution - coding silent
3
178916793
178916793

PIK3CA
1041454
c.210C > T
Substitution - coding silent
3
178916823
178916823

PIK3CA
27497
c.323G > A
Substitution - Missense
3
178916936
178916936

PIK3CA
13570
c.331A > G
Substitution - Missense
3
178916944
178916944

PIK3CA
125368
c.344G > T
Substitution - Missense
3
178916957
178916957

PIK3CA
1420774
c.536A > G
Substitution - Missense
3
178917661
178917661

PIK3CA
21462
c.971C > T
Substitution - Missense
3
178921489
178921489

PIK3CA
353193
c.1002C > T
Substitution - coding silent
3
178921520
178921520

PIK3CA
754
c.1035T > A
Substitution - Missense
3
178921553
178921553

PIK3CA
1420804
c.1213T > C
Substitution - Missense
3
178927450
178927450

PIK3CA
757
c.1258T > C
Substitution - Missense
3
178927980
178927980

PIK3CA
1420828
c.1370A > G
Substitution - Missense
3
178928092
178928092

PIK3CA
759
c.1616C > G
Substitution - Missense
3
178936074
178936074

PIK3CA
760
c.1624G > A
Substitution - Missense
3
178936082
178936082

PIK3CA
763
c.1633G > A
Substitution - Missense
3
178936091
178936091

PIK3CA
1420865
c.1640A > G
Substitution - Missense
3
178936098
178936098

PIK3CA
778
c.2102A > C
Substitution - Missense
3
178938860
178938860

PIK3CA
769
c.2702G > T
Substitution - Missense
3
178947827
178947827

PIK3CA
770
c.2725T > C
Substitution - Missense
3
178947850
178947850

PIK3CA
328026
c.3110A > G
Substitution - Missense
3
178952055
178952055

PIK3CA
775
c.3140A > G
Substitution - Missense
3
178952085
178952085

PIK3CA
12464
c.3204_-3205insA
Insertion - Frameshift
3
178952149
178952150

FGFR3
715
c.746C > G
Substitution - Missense
4
1803568
1803568

FGFR3
29446
c.753C > T
Substitution - coding silent
4
1803575
1803575

FGFR3
723
c.850delC
Deletion - Frameshift
4
1803672
1803672

FGFR3
716
c.1108G > T
Substitution - Missense
4
1806089
1806089

FGFR3
24842
c.1138G > A
Substitution - Missense
4
1806119
1806119

FGFR3
724
c.1150T > C
Substitution - Missense
4
1806131
1806131

FGFR3
721
c.1172C > A
Substitution - Missense
4
1806153
1806153

FGFR3
1428724
c.1928A > G
Substitution - Missense
4
1807869
1807869

FGFR3
719
c.1948A > G
Substitution - Missense
4
1807889
1807889

FGFR3
24802
c.2089G > T
Substitution - Missense
4
1808331
1808331

PDGFRA
12418
c.1698_-1712del15
Complex - deletion inframe
4
55141052
55141066

PDGFRA
1430085
c.1743T > C
Substitution - coding silent
4
55141097
55141097

PDGFRA
22415
c.1977C > A
Substitution - Missense
4
55144148
55144148

PDGFRA
1430086
c.2001A > G
Substitution - coding silent
4
55144172
55144172

PDGFRA
743
c.2021C > T
Substitution - Missense
4
55144547
55144547

PDGFRA
587613
c.2517G > T
Substitution - coding silent
4
55152085
55152085

PDGFRA
736
c.2525A > T
Substitution - Missense
4
55152093
55152093

PDGFRA
28052
c.2544C > A
Substitution - Missense
4
55152112
55152112

KIT
77973
c.92C > T
Substitution - Missense
4
55561702
55561702

KIT
1146
c.154G > A
Substitution - Missense
4
55561764
55561764

KIT
1430106
c.218A > G
Substitution - Missense
4
55561828
55561828

KIT
24637
c.1405T > C
Substitution - Missense
4
55592081
55592081

KIT
41602
c.1416A > G
Substitution - coding silent
4
55592092
55592092

KIT
1326
c.1509_-1510insG
Insertion - In frame
4
55592185
55592186

CCTAT

KIT
96867
c.1516T > C
Substitution - Missense
4
55592192
55592192

KIT
96885
c.1526A > T
Substitution - Missense
4
55592202
55592202

KIT
1430136
c.1535A > G
Substitution - Missense
4
55592211
55592211

KIT
1155
c.1588G > A
Substitution - Missense
4
55593431
55593431

KIT
1275
c.1698C > T
Substitution - coding silent
4
55593632
55593632

KIT
1290
c.1727T > C
Substitution - Missense
4
55593661
55593661

KIT
1299
c.1755C > T
Substitution - coding silent
4
55593689
55593689

KIT
1304
c.1924A > G
Substitution - Missense
4
55594221
55594221

KIT
12706
c.1961T > C
Substitution - Missense
4
55594258
55594258

KIT
36053
c.2089C > T
Substitution - Missense
4
55595599
55595599

KIT
1430171
c.2148T > C
Substitution - coding silent
4
55597500
55597500

KIT
21303
c.2209G > A
Substitution - Missense
4
55597561
55597561

KIT
20402
c.2410C > T
Substitution - Missense
4
55599284
55599284

KIT
19194
c.2484 + 43T > A
Unknown
4
55599401
55599401

KIT
133767
c.2558G > A
Substitution - Nonsense
4
55602737
55602737

KDR
35855
c.4008C > T
Substitution - coding silent
4
55946171
55946171

KDR
1430203
c.3433G > A
Substitution - Missense
4
55955112
55955112

KDR
48464
c.2917G > T
Substitution - Missense
4
55961023
55961023

KDR
1430212
c.2619A > G
Substitution - coding silent
4
55962505
55962505

KDR
32339
c.824G > T
Substitution - Missense
4
55979623
55979623

FBXW7
1427592
c.2079A > G
Substitution - coding silent
4
153244078
153244078

FBXW7
27083
c.2065C > T
Substitution - Missense
4
153244092
153244092

FBXW7
732399
c.2033C > G
Substitution - Nonsense
4
153244124
153244124

FBXW7
34018
c.2001delG
Deletion - Frameshift
4
153244156
153244156

FBXW7
27913
c.1580A > G
Substitution - Missense
4
153247222
153247222

FBXW7
30599
c.1576T > C
Substitution - Missense
4
153247226
153247226

FBXW7
30598
c.1558G > A
Substitution - Missense
4
153247244
153247244

FBXW7
34016
c.1451G > T
Substitution - Missense
4
153247351
153247351

FBXW7
22974
c.1436G > A
Substitution - Missense
4
153247366
153247366

FBXW7
22965
c.1394G > A
Substitution - Missense
4
153249384
153249384

FBXW7
22986
c.1338G > A
Substitution - Nonsense
4
153249440
153249440

FBXW7
161024
c.1322G > T
Substitution - Missense
4
153249456
153249456

FBXW7
22973
c.1177C > T
Substitution - Nonsense
4
153250883
153250883

FBXW7
22971
c.832C > T
Substitution - Nonsense
4
153258983
153258983

FBXW7
1052125
c.744G > T
Substitution - Missense
4
153259071
153259071

APC
18979
c.2543_-2544insA
Insertion - Frameshift
5
112173834
112173835

APC
18852
c.2626C > T
Substitution - Nonsense
5
112173917
112173917

APC
19230
c.2639T > C
Substitution - Missense
5
112173930
112173930

APC
19330
c.2656C > T
Substitution - Nonsense
5
112173947
112173947

APC
19065
c.2752G > T
Substitution - Nonsense
5
112174043
112174043

APC
13872
c.3286C > T
Substitution - Nonsense
5
112174577
112174577

APC
1432250
c.3305A > G
Substitution - Missense
5
112174596
112174596

APC
1432260
c.3435A > G
Substitution - coding silent
5
112174726
112174726

APC
41617
c.3700delA
Deletion - Frameshift
5
112174991
112174991

APC
1432280
c.3795A > G
Substitution - coding silent
5
112175086
112175086

APC
19072
c.3871C > T
Substitution - Nonsense
5
112175162
112175162

APC
18960
c.3880C > T
Substitution - Nonsense
5
112175171
112175171

APC
18719
c.3923_-3924insA
Insertion - Frameshift
5
112175214
112175215

APC
18702
c.3964G > T
Substitution - Nonsense
5
112175255
112175255

APC
19048
c.4057G > T
Substitution - Nonsense
5
112175348
112175348

APC
19652
c.4063T > C
Substitution - Missense
5
112175354
112175354

APC
18862
c.4132C > T
Substitution - Nonsense
5
112175423
112175423

APC
143913
c.4141C > T
Substitution - Missense
5
112175432
112175432

APC
18993
c.4189_-4190delGA
Deletion - Frameshift
5
112175480
112175481

APC
19087
c.4216C > T
Substitution - Nonsense
5
112175507
112175507

APC
18836
c.4285C > T
Substitution - Nonsense
5
112175576
112175576

APC
13864
c.4393_-4394delAG
Deletion - Frameshift
5
112175684
112175685

APC
1173082
c.4540delC
Deletion - Frameshift
5
112175831
112175831

APC
1183180
c.4561G > T
Substitution - Nonsense
5
112175852
112175852

APC
13879
c.4639G > T
Substitution - Nonsense
5
112175930
112175930

APC
41616
c.4654G > T
Substitution - Nonsense
5
112175945
112175945

APC
18561
c.4666_-4667insA
Insertion - Frameshift
5
112175957
112175958

APC
18875
c.4773_-4774insA
Insertion - Frameshift
5
112176064
112176065

APC
42906
c.4826C > T
Substitution - Missense
5
112176117
112176117

CSF1R
947
c.2906A > G
Substitution - Missense
5
149433644
149433645

CSF1R
310349
c.2878G > A
Substitution - Missense
5
149433672
149433673

NPM1
17559
c.863_-864insTCTG
Insertion - Frameshift
5
170837547
170837548

EGFR
21683
c.323G > A
Substitution - Missense
7
55211080
55211080

EGFR
174732
c.340G > A
Substitution - Missense
7
55211097
55211097

EGFR
1451540
c.408C > T
Substitution - coding silent
7
55211165
55211165

EGFR
21687
c.866C > T
Substitution - Missense
7
55221822
55221822

EGFR
43067
c.874G > T
Substitution - Missense
7
55221830
55221830

EGFR
21690
c.1793G > T
Substitution - Missense
7
55233043
55233043

EGFR
35825
c.1859G > A
Substitution - Missense
7
55233109
55233109

EGFR
13177
c.2063T > C
Substitution - Missense
7
55241615
55241615

EGFR
41905
c.2092G > A
Substitution - Missense
7
55241644
55241644

EGFR
6239
c.2156G > C
Substitution - Missense
7
55241708
55241708

EGFR
13979
c.2170G > A
Substitution - Missense
7
55241722
55241722

EGFR
53194
c.2197C > T
Substitution - Missense
7
55242427
55242427

EGFR
13182
c.2203G > A
Substitution - Missense
7
55242433
55242433

EGFR
17570
c.2222C > T
Substitution - Missense
7
55242452
55242452

EGFR
6223
c.2235_-2249del15
Deletion - In frame
7
55242465
55242479

EGFR
28603
c.2293G > A
Substitution - Missense
7
55248995
55248995

EGFR
13190
c.2375T > C
Substitution - Missense
7
55249077
55249077

EGFR
12986
c.2429G > A
Substitution - Missense
7
55249131
55249131

EGFR
28610
c.2441T > C
Substitution - Missense
7
55249143
55249143

EGFR
53291
c.2485G > A
Substitution - Missense
7
55259427
55259427

EGFR
13424
c.2497T > G
Substitution - Missense
7
55259439
55259439

EGFR
6227
c.2504A > T
Substitution - Missense
7
55259446
55259446

EGFR
13430
c.2515G > A
Substitution - Missense
7
55259457
55259457

EGFR
6224
c.2573T > G
Substitution - Missense
7
55259515
55259515

EGFR
6213
c.2582T > A
Substitution - Missense
7
55259524
55259524

EGFR
14070
c.2588G > A
Substitution - Missense
7
55259530
55259530

EGFR
13008
c.2612C > G
Substitution - Missense
7
55259554
55259554

MET
706
c.504G > T
Substitution - Missense
7
116339642
116339642

MET
710
c.1124A > G
Substitution - Missense
7
116340262
116340262

MET
29633
c.3082 + 1G > A
Unknown
7
116412044
116412044

MET
1447462
c.3336T > C
Substitution - coding silent
7
116417465
116417465

MET
697
c.3370C > G
Substitution - Missense
7
116417499
116417499

MET
43064
c.3534G > C
Substitution - Missense
7
116418969
116418969

MET
1214928
c.3562C > T
Substitution - Nonsense
7
116418997
116418997

MET
1447471
c.3573T > C
Substitution - coding silent
7
116419008
116419008

MET
1330154
c.3668T > G
Substitution - Missense
7
116422133
116422133

MET
700
c.3757T > G
Substitution - Missense
7
116423428
116423428

MET
48565
c.3778G > T
Substitution - Missense
7
116423449
116423449

MET
695
c.3785A > G
Substitution - Missense
7
116423456
116423456

MET
691
c.3803T > C
Substitution - Missense
7
116423474
116423474

SMO
13145
c.595C > T
Substitution - Missense
7
128845101
128845101

SMO
13147
c.970G > A
Substitution - Missense
7
128846040
128846040

SMO
216037
c.1234C > T
Substitution - Missense
7
128846398
128846398

SMO
13146
c.1604G > T
Substitution - Missense
7
128850341
128850341

SMO
13150
c.1918A > G
Substitution - Missense
7
128851593
128851593

BRAF
476
c.1799T > A
Substitution - Missense
7
140453136
140453136

BRAF
471
c.1790T > G
Substitution - Missense
7
140453145
140453145

BRAF
467
c.1781A > G
Substitution - Missense
7
140453154
140453154

BRAF
462
c.1742A > G
Substitution - Missense
7
140453193
140453193

BRAF
450
c.1391G > T
Substitution - Missense
7
140481417
140481417

BRAF
27986
c.1380A > G
Substitution - coding silent
7
140481428
140481428

BRAF
1448625
c.1359T > C
Substitution - coding silent
7
140481449
140481449

BRAF
6262
c.1330C > T
Substitution - Missense
7
140481478
140481478

EZH2
37028
c.1937A > T
Substitution - Missense
7
148508727
148508727

FGFR1
1292693
c.816C > T
Substitution - coding silent
8
38282147
38282147

FGFR1
187237
c.448C > T
Substitution - Missense
8
38285864
38285864

FGFR1
1456955
c.421A > G
Substitution - Missense
8
38285891
38285891

FGFR1
601
c.374C > T
Substitution - Missense
8
38285938
38285938

JAK2
12600
c.1849G > T
Substitution - Missense
9
5073770
5073770

JAK2
27063
c.1860C > A
Substitution - Missense
9
5073781
5073781

CDKN2A
12479
c.358G > T
Substitution - Nonsense
9
21971000
21971000

CDKN2A
12476
c.341C > T
Substitution - Missense
9
21971017
21971017

CDKN2A
12547
c.330G > A
Substitution - Nonsense
9
21971028
21971028

CDKN2A
13489
c.322G > T
Substitution - Missense
9
21971036
21971036

CDKN2A
12504
c.247C > T
Substitution - Missense
9
21971111
21971111

CDKN2A
12475
c.238C > T
Substitution - Nonsense
9
21971120
21971120

CDKN2A
13281
c.205G > T
Substitution - Nonsense
9
21971153
21971153

CDKN2A
12473
c.172C > T
Substitution - Nonsense
9
21971186
21971186

GNAQ
1110323
c.1002C > T
Substitution - coding silent
9
80336317
80336317

GNAQ
52975
c.548G > A
Substitution - Missense
9
80412493
80412493

GNAQ
1463119
c.523A > T
Substitution - Missense
9
80412518
80412518

ABL1
12631
c.742C > G
Substitution - Missense
9
133738342
133738342

ABL1
12577
c.749G > A
Substitution - Missense
9
133738349
133738349

ABL1
12576
c.757T > C
Substitution - Missense
9
133738357
133738357

ABL1
12573
c.763G > A
Substitution - Missense
9
133738363
133738363

ABL1
12602
c.827A > G
Substitution - Missense
9
133747520
133747520

ABL1
235737
c.878_-879insGCC
Complex - insertion inframe
9
133747571
133747572

ABL1
12578
c.1052T > C
Substitution - Missense
9
133748391
133748391

ABL1
12611
c.1064A > G
Substitution - Missense
9
133748403
133748403

ABL1
12605
c.1075T > G
Substitution - Missense
9
133748414
133748414

ABL1
49071
c.1150C > A
Substitution - Missense
9
133750319
133750319

ABL1
12604
c.1187A > G
Substitution - Missense
9
133750356
133750356

NOTCH1
87862
c.7412C > A
Substitution - Nonsense
9
139390779
139390779

NOTCH1
13070
c.7386delC
Deletion - Frameshift
9
139390805
139390805

NOTCH1
12776
c.7375C > T
Substitution - Nonsense
9
139390816
139390816

NOTCH1
13061
c.7318C > T
Substitution - Nonsense
9
139390873
139390873

NOTCH1
13048
c.5033T > C
Substitution - Missense
9
139397768
139397768

NOTCH1
308587
c.5025C > T
Substitution - coding silent
9
139397776
139397776

NOTCH1
12771
c.4799T > C
Substitution - Missense
9
139399344
139399344

NOTCH1
13053
c.4793G > C
Substitution - Missense
9
139399350
139399350

NOTCH1
13042
c.4778T > C
Substitution - Missense
9
139399365
139399365

NOTCH1
12772
c.4721T > C
Substitution - Missense
9
139399422
139399422

RET
29803
c.1852T > C
Substitution - Missense
10
43609096
43609096

RET
29804
c.1858T > C
Substitution - Missense
10
43609102
43609102

RET
1048
c.1894_-1906 > AG
Complex - deletion inframe
10
43609942
43609954

CT

RET
1223553
c.1942G > A
Substitution - Missense
10
43609990
43609990

RET
976
c.1991C > A
Substitution - Missense
10
43610039
43610039

RET
21338
c.2304G > C
Substitution - Missense
10
43613840
43613840

RET
977
c.2647_-2648GC >
Substitution - Missense
10
43615568
43615569

TT

RET
963
c.2701G > A
Substitution - Missense
10
43615622
43615622

RET
965
c.2753T > C
Substitution - Missense
10
43617416
43617416

PTEN
5298
c.19G > T
Substitution - Nonsense
10
89624245
89624245

PTEN
5101
c.40A > G
Substitution - Missense
10
89624266
89624266

PTEN
5153
c.49C > T
Substitution - Nonsense
10
89624275
89624275

PTEN
5107
c.71A > G
Substitution - Missense
10
89624297
89624297

PTEN
5134
c.80A > G
Substitution - Missense
10
89653782
89653782

PTEN
5142
c.112C > T
Substitution - Missense
10
89653814
89653814

PTEN
5050
c.142A > G
Substitution - Missense
10
89653844
89653844

PTEN
1349479
c.156T > C
Substitution - coding silent
10
89653858
89653858

PTEN
5129
c.163A > G
Substitution - Missense
10
89653865
89653865

PTEN
5257
c.166T > G
Substitution - Missense
10
89685271
89685271

PTEN
5036
c.202T > C
Substitution - Missense
10
89685307
89685307

PTEN
5916
c.209 + 5G > A
Unknown
10
89685319
89685319

PTEN
5102
c.212G > A
Substitution - Missense
10
89690805
89690805

PTEN
4956
c.227_-228delAT
Deletion - Frameshift
10
89690820
89690821

PTEN
5205
c.245A > C
Substitution - Missense
10
89690838
89690838

PTEN
5983
c.253 + 1G > A
Unknown
10
89690847
89690847

PTEN
5139
c.263A > G
Substitution - Missense
10
89692779
89692779

PTEN
5109
c.302T > C
Substitution - Missense
10
89692818
89692818

PTEN
5266
c.314G > T
Substitution - Missense
10
89692830
89692830

PTEN
5199
c.334C > G
Substitution - Missense
10
89692850
89692850

PTEN
5123
c.395G > A
Substitution - Missense
10
89692911
89692911

PTEN
5130
c.449A > G
Substitution - Missense
10
89692965
89692965

PTEN
5144
c.464A > G
Substitution - Missense
10
89692980
89692980

PTEN
5287
c.477G > T
Substitution - Missense
10
89692993
89692993

PTEN
5907
c.493-12delT
Unknown
10
89711863
89711863

PTEN
35406
c.578T > C
Substitution - Missense
10
89711960
89711960

PTEN
4978
c.595_-597delATG
Deletion - In frame
10
89711977
89711979

PTEN
5279
c.610C > A
Substitution - Missense
10
89711992
89711992

PTEN
5072
c.615G > A
Substitution - Missense
10
89711997
89711997

PTEN
5154
c.697C > T
Substitution - Nonsense
10
89717672
89717672

PTEN
5292
c.703G > T
Substitution - Nonsense
10
89717678
89717678

PTEN
35849
c.721T > C
Substitution - Missense
10
89717696
89717696

PTEN
43075
c.787A > T
Substitution - Nonsense
10
89717762
89717762

PTEN
5809
c.800delA
Deletion - Frameshift
10
89717775
89717775

PTEN
1349606
c.879A > G
Substitution - coding silent
10
89720728
89720728

PTEN
5312
c.895G > T
Substitution - Nonsense
10
89720744
89720744

PTEN
4958
c.955_-958delACTT
Deletion - Frameshift
10
89720804
89720807

PTEN
1349625
c.1025A > G
Substitution - Missense
10
89720874
89720874

PTEN
5966
c.1027 − 2A > G
Unknown
10
89725042
89725042

PTEN
4936
c.1040_-1041delTC
Deletion - Frameshift
10
89725057
89725058

PTEN
1349633
c.1055A > G
Substitution - Missense
10
89725072
89725072

PTEN
23645
c.1091C > G
Substitution - Missense
10
89725108
89725108

FGFR2
36912
c.1647T > A
Substitution - Missense
10
123258034
123258034

FGFR2
36906
c.1144T > C
Substitution - Missense
10
123274774
123274774

FGFR2
36904
c.1124A > G
Substitution - Missense
10
123274794
123274794

FGFR2
1346272
c.1108A > G
Substitution - Missense
10
123274810
123274810

FGFR2
36901
c.929A > G
Substitution - Missense
10
123279503
123279503

FGFR2
29824
c.913G > A
Substitution - Missense
10
123279519
123279519

FGFR2
36903
c.755C > G
Substitution - Missense
10
123279677
123279677

HRAS
499
c.182A > G
Substitution - Missense
11
533874
533874

HRAS
495
c.175G > A
Substitution - Missense
11
533881
533881

HRAS
249860
c.81T > C
Substitution - coding silent
11
534242
534242

HRAS
483
c.35G > T
Substitution - Missense
11
534288
534288

ATM
21323
c.1009C > T
Substitution - Missense
11
108117798
108117798

ATM
21825
c.1229T > C
Substitution - Missense
11
108119823
108119823

ATM
22499
c.1810C > T
Substitution - Missense
11
108123551
108123551

ATM
1158828
c.1898 + 2T > A
Unknown
11
108123641
108123641

ATM
21826
c.2572T > C
Substitution - Missense
11
108138003
108138003

ATM
22507
c.3925G > A
Substitution - Missense
11
108155132
108155132

ATM
21920
c.5044G > T
Substitution - Missense
11
108170479
108170479

ATM
218294
c.5152C > G
Substitution - Missense
11
108170587
108170587

ATM
49005
c.5178 − 1G > T
Unknown
11
108172374
108172374

ATM
172204
c.5188C > T
Substitution - Nonsense
11
108172385
108172385

ATM
21918
c.5224G > C
Substitution - Missense
11
108172421
108172421

ATM
12792
c.5380C > T
Substitution - coding silent
11
108173640
108173640

ATM
1183962
c.5476T > G
Substitution - Missense
11
108173736
108173736

ATM
21922
c.5821G > C
Substitution - Missense
11
108180945
108180945

ATM
12951
c.7325A > C
Substitution - Missense
11
108200958
108200958

ATM
12791
c.7996A > G
Substitution - Missense
11
108204681
108204681

ATM
21636
c.8084G > C
Substitution - Missense
11
108205769
108205769

ATM
1235404
c.8095C > A
Substitution - Missense
11
108205780
108205780

ATM
22481
c.8174A > T
Substitution - Missense
11
108206594
108206594

ATM
1183939
c.8624A > G
Substitution - Missense
11
108218045
108218045

ATM
22485
c.8668C > G
Substitution - Missense
11
108218089
108218089

ATM
21930
c.8839A > T
Substitution - Missense
11
108225590
108225590

ATM
21626
c.9023G > A
Substitution - Missense
11
108236087
108236087

ATM
1351060
c.9054A > G
Substitution - coding silent
11
108236118
108236118

ATM
21624
c.9139C > T
Substitution - Nonsense
11
108236203
108236203

KRAS
41307
c.491G > A
Substitution - Missense
12
25362805
25362805

KRAS
19940
c.351A > C
Substitution - Missense
12
25378647
25378647

KRAS
554
c.183A > C
Substitution - Missense
12
25380275
25380275

KRAS
546
c.175G > A
Substitution - Missense
12
25380283
25380283

KRAS
1169214
c.101C > T
Substitution - Missense
12
25398207
25398207

KRAS
14208
c.104C > T
Substitution - Missense
12
25398215
25398215

KRAS
521
c.35G > A
Substitution - Missense
12
25398284
25398284

KRAS
507
c.24A > G
Substitution - coding silent
12
25398295
25398295

PTPN11
13011
c.181G > T
Substitution - Missense
12
112888165
112888165

PTPN11
13013
c.205G > A
Substitution - Missense
12
112888189
112888189

PTPN11
13015
c.215C > T
Substitution - Missense
12
112888199
112888199

PTPN11
13000
c.226G > A
Substitution - Missense
12
112888210
112888210

PTPN11
13034
c.1472C > T
Substitution - Missense
12
112926852
112926852

PTPN11
13027
c.1508G > C
Substitution - Missense
12
112926888
112926888

PTPN11
1358900
c.1519A > G
Substitution - Missense
12
112926899
112926899

PTPN11
13031
c.1528C > A
Substitution - Missense
12
112926908
112926908

HNF1A
21471
c.617G > T
Substitution - Missense
12
121431413
121431413

HNF1A
24900
c.632A > C
Substitution - Missense
12
121431428
121431428

HNF1A
24832
c.685C > T
Substitution - Nonsense
12
121431481
121431481

HNF1A
21474
c.710A > G
Substitution - Missense
12
121431506
121431506

HNF1A
24923
c.779C > T
Substitution - Missense
12
121432032
121432032

HNF1A
24692
c.787C > T
Substitution - Missense
12
121432040
121432040

HNF1A
21481
c.872_-873insC
Insertion - Frameshift
12
121432125
121432126

FLT3
1166729
c.2516A > G
Substitution - Missense
13
28592629
28592629

FLT3
783
c.2503G > T
Substitution - Missense
13
28592642
28592642

FLT3
25248
c.2492G > A
Substitution - Missense
13
28592653
28592653

FLT3
786
c.2039C > T
Substitution - Missense
13
28602329
28602329

FLT3
27907
c.1800_-1801ins21
Insertion - In frame
13
28608255
28608256

FLT3
19522
c.1775T > C
Substitution - Missense
13
28608281
28608281

FLT3
28042
c.1352C > T
Substitution - Missense
13
28610138
28610138

RB1
890
c.409G > T
Substitution - Nonsense
13
48919244
48919244

RB1
915
c.596T > A
Substitution - Nonsense
13
48923148
48923148

RB1
28816
c.940 − 2A > T
Unknown
13
48941628
48941628

RB1
891
c.958C > T
Substitution - Nonsense
13
48941648
48941648

RB1
1367204
c.968A > G
Substitution - Missense
13
48941658
48941658

RB1
1367206
c.982A > G
Substitution - Missense
13
48941672
48941672

RB1
879
c.1072C > T
Substitution - Nonsense
13
48942685
48942685

RB1
895
c.1363C > T
Substitution - Nonsense
13
48953760
48953760

RB1
887
c.1654C > T
Substitution - Nonsense
13
48955538
48955538

RB1
888
c.1666C > T
Substitution - Nonsense
13
48955550
48955550

RB1
1367255
c.1687T > C
Substitution - Missense
13
48955571
48955571

RB1
892
c.1735C > T
Substitution - Nonsense
13
49027168
49027168

RB1
35483
c.1814 + 2T > C
Unknown
13
49027249
49027249

RB1
870
c.2028_-2040del13
Deletion - Frameshift
13
49033891
49033903

RB1
13117
c.2053C > T
Substitution - Nonsense
13
49033916
49033916

RB1
942
c.2063T > C
Substitution - Missense
13
49033926
49033926

RB1
1042
c.2107 − 2A > G
Unknown
13
49037865
49037865

RB1
883
c.2117G > T
Substitution - Missense
13
49037877
49037877

RB1
940
c.2143A > T
Substitution - Nonsense
13
49037903
49037903

RB1
1367309
c.2153A > G
Substitution - Missense
13
49037913
49037913

RB1
868
c.2242G > T
Substitution - Nonsense
13
49039164
49039164

RB1
916
c.2261T > G
Substitution - Missense
13
49039183
49039183

RB1
551465
c.2267A > G
Substitution - Missense
13
49039189
49039189

RB1
254910
c.2293A > T
Substitution - Nonsense
13
49039215
49039215

AKT1
33765
c.49G > A
Substitution - Missense
14
105246551
105246551

IDH2
33733
c.515G > A
Substitution - Missense
15
90631838
90631838

IDH2
1375400
c.474A > G
Substitution - coding silent
15
90631879
90631879

IDH2
41590
c.419G > A
Substitution - Missense
15
90631934
90631934

CDH1
1379165
c.1058A > G
Substitution - Missense
16
68846087
68846087

CDH1
19748
c.1108G > C
Substitution - Missense
16
68846137
68846137

CDH1
19750
c.1204G > A
Substitution - Missense
16
68847282
68847282

CDH1
25267
c.1733_-1734insC
Insertion - Frameshift
16
68855925
68855926

CDH1
19746
c.1742T > C
Substitution - Missense
16
68855934
68855934

CDH1
19758
c.1774G > A
Substitution - Missense
16
68855966
68855966

CDH1
19743
c.1849G > A
Substitution - Missense
16
68856041
68856041

CDH1
19822
c.1901C > T
Substitution - Missense
16
68856093
68856093

CDH1
19418
c.1913G > A
Substitution - Nonsense
16
68856105
68856105

TP53
13747
c.1146delA
Deletion - Frameshift
17
7572963
7572963

TP53
307348
c.1123C > T
Substitution - Nonsense
17
7572986
7572986

TP53
1191161
c.1101 − 2A > G
Unknown
17
7573010
7573010

TP53
11073
c.1024C > T
Substitution - Nonsense
17
7574003
7574003

TP53
11286
c.1015G > T
Substitution - Nonsense
17
7574012
7574012

TP53
11071
c.1009C > T
Substitution - Missense
17
7574018
7574018

TP53
11514
c.1001G > T
Substitution - Missense
17
7574026
7574026

TP53
11354
c.991C > T
Substitution - Nonsense
17
7576855
7576855

TP53
44823
c.981T > G
Substitution - Nonsense
17
7576865
7576865

TP53
46088
c.963A > G
Substitution - coding silent
17
7576883
7576883

TP53
10786
c.949C > T
Substitution - Nonsense
17
7576897
7576897

TP53
10663
c.916C > T
Substitution - Nonsense
17
7577022
7577022

TP53
10710
c.892G > T
Substitution - Nonsense
17
7577046
7577046

TP53
10863
c.833C > T
Substitution - Missense
17
7577105
7577105

TP53
10660
c.818G > A
Substitution - Missense
17
7577120
7577120

TP53
10662
c.743G > A
Substitution - Missense
17
7577538
7577538

TP53
6932
c.733G > A
Substitution - Missense
17
7577548
7577548

TP53
10812
c.722C > T
Substitution - Missense
17
7577559
7577559

TP53
10725
c.701A > G
Substitution - Missense
17
7577580
7577580

TP53
10758
c.659A > G
Substitution - Missense
17
7578190
7578190

TP53
44317
c.653T > A
Substitution - Missense
17
7578196
7578196

TP53
10667
c.646G > A
Substitution - Missense
17
7578203
7578203

TP53
43947
c.614A > G
Substitution - Missense
17
7578235
7578235

TP53
10738
c.542G > A
Substitution - Missense
17
7578388
7578388

TP53
10808
c.488A > G
Substitution - Missense
17
7578442
7578442

TP53
10739
c.481G > A
Substitution - Missense
17
7578449
7578449

TP53
10670
c.469G > T
Substitution - Missense
17
7578461
7578461

TP53
10801
c.404G > A
Substitution - Missense
17
7578526
7578526

TP53
11582
c.395A > G
Substitution - Missense
17
7578535
7578535

TP53
11462
c.388C > G
Substitution - Missense
17
7578542
7578542

TP53
44226
c.380C > T
Substitution - Missense
17
7578550
7578550

TP53
44985
c.375 + 17G > A
Unknown
17
7579295
7579295

TP53
43904
c.375G > A
Substitution - coding silent
17
7579312
7579312

TP53
10716
c.329G > T
Substitution - Missense
17
7579358
7579358

TP53
46103
c.319T > G
Substitution - Missense
17
7579368
7579368

TP53
44492
c.273G > A
Substitution - Nonsense
17
7579414
7579414

TP53
43910
c.245C > T
Substitution - Missense
17
7579442
7579442

TP53
12168
c.166G > T
Substitution - Nonsense
17
7579521
7579521

TP53
44907
c.151G > T
Substitution - Nonsense
17
7579536
7579536

TP53
43664
c.134T > C
Substitution - Missense
17
7579553
7579553

TP53
46286
c.112C > T
Substitution - Nonsense
17
7579575
7579575

TP53
85573
c.80delC
Deletion - Frameshift
17
7579716
7579716

ERBB2
14060
c.2264T > C
Substitution - Missense
17
37880220
37880220

ERBB2
1251412
c.2305G > T
Substitution - Missense
17
37880261
37880261

ERBB2
20959
c.2324_-2325ins12
Insertion - In frame
17
37880995
37880996

ERBB2
14065
c.2524G > A
Substitution - Missense
17
37881332
37881332

ERBB2
686
c.2570A > G
Substitution - Missense
17
37881378
37881378

ERBB2
21985
c.2632C > T
Substitution - Missense
17
37881440
37881440

SMAD4
1389031
c.306T > C
Substitution - coding silent
18
48575112
48575112

SMAD4
14229
c.377T > C
Substitution - Missense
18
48575183
48575183

SMAD4
218557
c.389C > T
Substitution - Missense
18
48575195
48575195

SMAD4
14168
c.403C > T
Substitution - Nonsense
18
48575209
48575209

SMAD4
13115
c.431C > G
Substitution - Nonsense
18
48575671
48575671

SMAD4
14118
c.502G > T
Substitution - Nonsense
18
48581198
48581198

SMAD4
1226725
c.533C > A
Substitution - Nonsense
18
48581229
48581229

SMAD4
308153
c.547C > T
Substitution - Nonsense
18
48581243
48581243

SMAD4
14057
c.733C > T
Substitution - Nonsense
18
48584560
48584560

SMAD4
22901
c.766C > T
Substitution - Nonsense
18
48584593
48584593

SMAD4
14217
c.776_-777delCT
Deletion - Frameshift
18
48584603
48584604

SMAD4
14163
c.931C > T
Substitution - Nonsense
18
48586262
48586262

SMAD4
14167
c.955 + 5G > C
Unknown
18
48586291
48586291

SMAD4
1389054
c.1001A > G
Substitution - Missense
18
48591838
48591838

SMAD4
1389057
c.1010A > G
Substitution - Missense
18
48591847
48591847

SMAD4
14109
c.1018A > G
Substitution - Missense
18
48591855
48591855

SMAD4
14111
c.1028C > G
Substitution - Nonsense
18
48591865
48591865

SMAD4
14249
c.1156G > C
Substitution - Missense
18
48593405
48593405

SMAD4
14103
c.1216G > A
Substitution - Missense
18
48593465
48593465

SMAD4
14223
c.1229_-1230insCA
Insertion - Frameshift
18
48593478
48593479

SMAD4
1389077
c.1248A > G
Substitution - coding silent
18
48593497
48593497

SMAD4
14096
c.1333C > T
Substitution - Nonsense
18
48603032
48603032

SMAD4
14114
c.1504A > G
Substitution - Missense
18
48604682
48604682

SMAD4
1389099
c.1519A > G
Substitution - Missense
18
48604697
48604697

SMAD4
14134
c.1576G > T
Substitution - Nonsense
18
48604754
48604754

SMAD4
1389106
c.1591C > A
Substitution - coding silent
18
48604769
48604769

STK11
21212
c.169delG
Deletion - Frameshift
19
1207077
1207077

STK11
21570
c.465 − 1G > T
Unknown
19
1220371
1220371

STK11
27316
c.475C > T
Substitution - Nonsense
19
1220382
1220382

STK11
20944
c.580G > T
Substitution - Missense
19
1220487
1220487

STK11
25229
c.595G > T
Substitution - Nonsense
19
1220502
1220502

STK11
29005
c.816C > T
Substitution - coding silent
19
1221293
1221293

STK11
21355
c.842C > T
Substitution - Missense
19
1221319
1221319

STK11
21360
c.1062C > G
Substitution - Missense
19
1223125
1223125

GNA11
21651
c.547C > T
Substitution - Missense
19
3115012
3115012

GNA11
52969
c.626A > T
Substitution - Missense
19
3118942
3118942

JAK3
34213
c.2164G > A
Substitution - Missense
19
17945696
17945696

JAK3
34214
c.1715C > T
Substitution - Missense
19
17948009
17948009

SRC
1227526
c.1460C > T
Substitution - Missense
20
36031630
36031631

GNAS
244725
c.489C > T
Substitution - coding silent
20
57480494
57480494

GNAS
27887
c.601C > T
Substitution - Missense
20
57484420
57484420

GNAS
27888
c.680A > T
Substitution - Missense
20
57484596
57484596

SMARCB1
1002
c.118C > T
Substitution - Nonsense
22
24133967
24133967

SMARCB1
991
c.141C > A
Substitution - Nonsense
22
24133990
24133990

SMARCB1
24595
c.157C > T
Substitution - Nonsense
22
24134006
24134006

SMARCB1
992
c.472C > T
Substitution - Nonsense
22
24143240
24143240

SMARCB1
51386
c.566_-567ins19
Insertion - Frameshift
22
24145547
24145548

SMARCB1
993
c.601C > T
Substitution - Nonsense
22
24145582
24145582

SMARCB1
999
c.607G > A
Substitution - Missense
22
24145588
24145588

SMARCB1
1057
c.1148delC
Deletion - Frameshift
22
24176357
24176357

TABLE 1B

Exemplary Copy Number Variants (CNV)

Gene Name
Chromosome
Start
End

ERBB2
chr17
37845134
37845207

ERBB2
chr17
37852282
37852381

ERBB2
chr17
37860184
37860303

ERBB2
chr17
37871503
37871582

ERBB2
chr17
37876682
37876784

ERBB2
chr17
37884464
37884584

ERBB2
chr17
37854903
37855025

ERBB2
chr17
37884065
37884183

ERBB2
chr17
37866483
37866606

ERBB2
chr17
37880963
37881086

KRAS
chr12
25378600
25378682

PDGFRA
chr4
55140973
55141093

TABLE 2

Control Reagent*

Sequence
A
B
C
D
E
F
G
H

1
CSF1R
APC
APC
APC
APC
CSF1R
APC
APC

2
EGFR
EGFR
CSF1R
CSF1R
CSF1R
EGFR
EGFR
CSF1R

3
FBXW7
FBXW7
EGFR
FGFR3
EGFR
FGFR1
FGFR3
EGFR

4
FGFR3
FGFR3
ERBB4
FLT3
FBXW7
FGFR3
FLT3
FGFR3

5
FLT3
FLT3
FGFR3
KDR
FGFR3
FLT3
HRAS
FLT3

6
GNA11
KDR
FLT3
KRAS
FLT3
HRAS
IDH1
HRAS

7
HNF1A
KRAS
HRAS
PDGFRA
HRAS
KDR
KDR
IDH1

8
HRAS
PDGFRA
KDR
RET
KRAS
KIT
KRAS
KRAS

9
PDGFRA
PIK3CA
KIT
STK11
PDGFRA
KRAS
PDGFRA
PDGFRA

10
PIK3CA
RET
KRAS
TP53
RET
MET
RET
PIK3CA

11
RET
TP53
PDGFRA
—
SMAD4
NOTCH1
TP53
RET

12
STK11
—
RET
—
TP53
PDGFRA
—
STK11

13
TP53
—
SMAD4
—
—
PIK3CA
—
TP53

14
VHL
—
TP53
—
—
SMARCB1
—
—

15
—
—
—
—
—
SMO
—
—

16
—
—
—
—
—
TP53
—
—

*APC (Adenomatous polyposis coli, deleted in polyposis 2.5 (DP2.5); Chr. 5: 112.04-112.18 Mb; Ref. Seq. NM_000038 and NP_000029), CSF1R (Colony stimulating factor 1 receptor, macrophage colony-stimulating factor receptor (M-CSFR), CD115; Chr. 5, 149.43-149.49 Mb; Ref. Seq. NM_005211 and NM_005202), EGFR (epidermal growth factor receptor; Chr. 7: 55.09-55.32 Mb; RefSeq Nos. NM_005228 and NP_0052219), FBXW7 (F-box/WD repeat-containing protein 7; Chr. 4: 153.24-153.46 Mb; RefSeq. Nos. NM_001013415 and NP_001013433), FGFR1 (Fibroblast growth factor receptor 1, basic fibroblast growth factor receptor 1, fms-related tyrosine kinase-2/Pfeiffer syndrome, CD331; Chr. 8: 38.27-38.33 Mb; RefSeq. Nos. NM_001174063 and NP_001167534), FGFR3 (Fibroblast growth factor receptor 3, CD333; chr. 4: 1.8-1.81 Mb; RefSeq Nos. NM_000142 and NP_000133), FLT3 (Fms-like tyrosine kinase 3, CD135, fetal liver kinase-2 (Flk2); Chr. 13: 28.58-28.67 Mb; RefSeq Nos. NM_004119 and NP_004110), GNA11 (Guanine nucleotide-binding protein subunit alpha-11; Chr. 19: 3.09-3.12 Mb; RefSeq Nos. NM_002067 and NP_002058), HNF1A (hepatocyte nuclear factor 1 homeobox A; Chr. 12: 121.42-121.44 Mb; RefSeq Nos. NM_000545 and NP_000536), HRAS (GTPase HRas, transforming protein p21; Chr. 11: 0.53-0.54 Mb; RefSeq Nos. NM_001130442 and NP_001123914), IDH1 (Isocitrate dehydrogenase 1 (NADP+), soluble; Chr. 2: 209.1-209.13 Mb; RefSeq Nos. NM_005896 and NP_005887), KDR (Kinase insert domain receptor, vascular endothelial growth factor receptor 2, CD309; Chr. 4: 55.94-55.99 Mb; RefSeq Nos. NM_002253 and NP_002244), KIT (Mast/stem cell growth factor receptor (SCFR), proto-oncogene c-Kit, tyrosine-protein kinase Kit, CD117; Chr. 4: 55.52-55.61 Mb; RefSeq Nos. NM_000222 and NP_000213), KRAS (GTPase KRas, V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog; Chr. 12: 25.36-25.4 Mb; RefSeq Nos. NM_004985-NP_004976), MET (c-Met, MNNG HOS Transforming gene, hepatocyte growth factor receptor; Chr. 7: 116.31-116.44 Mb; RefSeq Nos. NM_000245 and NP_000236), NOTCH1 (Notch homolog 1, translocation-associated (Drosophila); Chr. 9: 139.39-139.44; RefSeq Nos. NM_017617 and NP_060087), PDGFRA (Alpha-type platelet-derived growth factor receptor; Chr. 4: 55.1-55.16 Mb; RefSeq Nos. NM_006206 and NP_006197), PIK3CA (p110α protein; Chr. 3: 178.87-178.96 Mb; RefSeq Nos. NM_006218 and NP_006209), RET (receptor tyrosine kinase; Chr. 10: 43.57-43.64; RefSeq Nos. NM_000323 and NP_065681), SMAD4 (Chr. 18: 48.49-48.61 Mb; RefSeq Nos. NM_005359 and NP_005350), SMARCB1 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1; Chr. 22: 24.13-24.18 Mb; RefSeq Nos. NM_001007468 and NP_001007469), SMO (Smoothened; Chr. 7: 128.83-128.85 Mb; RefSeq Nos. NM_005631 and NP_005622), STK11 (Serine/threonine kinase 11, liver kinase B1 (LKB1), renal carcinoma antigen NY-REN-19; Chr. 19: 1.19-1.23 Mb; RefSeq Nos. NM_000455 and NP_000446), TP53 (protein 53, tumor protein 53; Chr. 17: 7.57-7.59 Mb; RefSeq Nos. NM_000546 and NP_000537), VHL (Von Hippel-Lindau tumor suppressor; Chr. 3: 10.18-10.19 Mb; RefSeq Nos. NM_000551 and NP_000542).

One or more variants of each of these reference sequences may also be represented in each control sequence and/or control reagent. In some embodiments, for instance, multiple variants may be included for each reference sequence. Panels of reference sequences may also be designed to represent particular metabolic, genetic information processing, environmental information processing, cellular process, organismal system, disease, drug development, or other pathways (e.g., KEGG pathways (http://www.genome.jp/kegg/pathway.html, Nov. 8, 2013)). Control reagents such as these may be assayed separately or combined into a single assay. The control reagents may also be designed to include various amounts of each reference sequences and/or variants thereof.

TABLE 3

Number of Variants
Number of Variants

Run ID
Detected
Expected
Detection Rate

Bad Run
8
15
53%

Bad Run
12
15
80%

Good Run
15
15
100%

Good Run
15
15
100%

Good Run
15
15
100%

Good Run
15
15
100%

Good Run
15
15
100%

Good Run
15
15
100%

TABLE 4

Included in Plasmid
Included in Plasmid

Fragment ID
# of Variants
V1
V2

EGFR_1
1
Yes
No

EGFR_2
2
Yes
No

EGFR_3
2
Yes
No

EGFR_4
13
Yes
Yes

EGFR_5
7
Yes
Yes

EGFR_6/7
10
Yes
Yes

EGFR_8
8
Yes
Yes

TABLE 5

Included variants for each EGFR fragment

EGFR_1
EGFR_2
EGFR_3
EGFR_4
EGFR_5
EGFR_6_7
EGFR_8

COSM21683
COSM21686
COSM21689
COSM41905
COSM13180
COSM28603
COSM6224

COSM21687
COSM21690
COSM28508
COSM53194
COSM26445
COSM12675

COSM28511
COSM18419
COSM6241
COSM6213

COSM12988
COSM13182
COSM12376
COSM14070

COSM13427
COSM17570
COSM12381
COSM28607

COSM41603
COSM6223
COSM13007
COSM33725

COSM28601
COSM21984
COSM6240
COSM13008

COSM6252

COSM13192
COSM26438

COSM6239

COSM28610

COSM12373

COSM41663

COSM22992

COSM28510

COSM13979

TABLE 6

Mutation Detail

Muta-
Gene
Mutation

Mutation

GRCh37

tion ID
name
ID
Mutation CDS
Mutation AA
Description
Chr
Start
End
strand

21683
EGFR
21683
c.323G > A
p.R108K
Substitution -
7
55211080
55211080
+

Missense

21686
EGFR
21686
c.865G > A
p.A289T
Substitution -
7
55221821
55221821
+

Missense

21687
EGFR
21687
c.866C > T
p.A289V
Substitution -
7
55221822
55221822
+

Missense

21689
EGFR
21689
c.1787C > T
p.P596L
Substitution -
7
55233037
55233037
+

Missense

21690
EGFR
21690
c.1793G > T
p.G598V
Substitution -
7
55233043
55233043
+

Missense

41905
EGFR
41905
c.2092G > A
p.A698T
Substitution -
7
55241644
55241644
+

Missense

28508
EGFR
28508
c.2104G > T
p.A702S
Substitution -
7
55241656
55241656
+

Missense

28511
EGFR
28511
c.2108T > C
p.L703P
Substitution -
7
55241660
55241660
+

Missense

12988
EGFR
12988
c.2125G > A
p.E709K
Substitution -
7
55241677
55241677
+

Missense

13427
EGFR
13427
c.2126A > C
p.E709A
Substitution -
7
55241678
55241678
+

Missense

41603
EGFR
41603
c.2134T > C
p.F712L
Substitution -
7
55241686
55241686
+

Missense

28601
EGFR
28601
c.2135T > C
p.F712S
Substitution -
7
55241687
55241687
+

Missense

6252
EGFR
6252
c.2155G > A
p.G719S
Substitution -
7
55241707
55241707
+

Missense

6239
EGFR
6239
c.2156G > C
p.G719A
Substitution -
7
55241708
55241708
+

Missense

12373
EGFR
12373
c.2159C > T
p.S720F
Substitution -
7
55241711
55241711
+

Missense

22992
EGFR
22992
c.2161G > A
p.G721S
Substitution -
7
55241713
55241713
+

Missense

28510
EGFR
28510
c.2162G > C
p.G721A
Substitution -
7
55241714
55241714
+

Missense

13979
EGFR
13979
c.2170G > A
p.G724S
Substitution -
7
55241722
55241722
+

Missense

13180
EGFR
13180
c.2188C > T
p.L730F
Substitution -
7
55242418
55242418
+

Missense

53194
EGFR
53194
c.2197C > T
p.P733S
Substitution -
7
55242427
55242427
+

Missense

18419
EGFR
18419
c.2200G > A
p.E734K
Substitution -
7
55242430
55242430
+

Missense

13182
EGFR
13182
c.2203G > A
p.G735S
Substitution -
7
55242433
55242433
+

Missense

17570
EGFR
17570
c.2222C > T
p.P741L
Substitution -
7
55242452
55242452
+

Missense

6223
EGFR
6223
c.2235_2249del15
p.E746_A750delELREA
Deletion -
7
55242465
55242479
+

In frame

21984
EGFR
21984
c.2281G > T
p.D761Y
Substitution -
7
55242511
55242511
+

Missense

28603
EGFR
28603
c.2293G > A
p.V765M
Substitution -
7
55248995
55248995
+

Missense

26445
EGFR
26445
c.2300C > T
p.A767V
Substitution -
7
55249002
55249002
+

Missense

6241
EGFR
6241
c.2303G > T
p.S768I
Substitution -
7
55249005
55249005
+

Missense

12376
EGFR
12376
c.2307_2308insGCCAGCGTG
p.V769_D770insASV
Insertion -
7
55249009
55249010
+

In frame

12381
EGFR
12381
c.2319_2320insAACCCCCAC
p.H773_V774insNPH
Insertion -
7
55249021
55249022
+

In frame

13007
EGFR
13007
c.2335_2336GG > TT
p.G779F
Substitution -
7
55249037
55249038
+

Missense

6240
EGFR
6240
c.2369C > T
p.T790M
Substitution -
7
55249071
55249071
+

Missense

13192
EGFR
13192
c.2428G > A
p.G810S
Substitution -
7
55249130
55249130
+

Missense

28610
EGFR
28610
c.2441T > C
p.L814P
Substitution -
7
55249143
55249143
+

Missense

41663
EGFR
41663
c.2462T > C
p.I821T
Substitution -
7
55249164
55249164
+

Missense

6224
EGFR
6224
c.2573T > G
p.L858R
Substitution -
7
55259515
55259515
+

Missense

12675
EGFR
12675
c.2575G > A
p.A859T
Substitution -
7
55259517
55259517
+

Missense

6213
EGFR
6213
c.2582T > A
p.L861Q
Substitution -
7
55259524
55259524
+

Missense

14070
EGFR
14070
c.2588G > A
p.G863D
Substitution -
7
55259530
55259530
+

Missense

28607
EGFR
28607
c.2603A > G
p.E868G
Substitution -
7
55259545
55259545
+

Missense

33725
EGFR
33725
c.2609A > G
p.H870R
Substitution -
7
55259551
55259551
+

Missense

13008
EGFR
13008
c.2612C > G
p.A871G
Substitution -
7
55259554
55259554
+

Missense

26438
EGFR
26438
c.2620G > A
p.G874S
Substitution -
7
55259562
55259562
+

Missense

TABLE 7

Results of EGFR plasmid

EGFR Plasmid V1
EGFR Plasmid V2

Mutation
Ion AmpliSeq
Illumina
Ion AmpliSeq
Illumina

ID
CHP2
TruSeq
CHP2
TruSeq

21683
Called
Called
Not Included
Not Included

21686
Called
Called
Not Included
Not Included

21687
Called
Called
Not Included
Not Included

21689
Called
Not Targeted
Not Included
Not Included

21690
Called
Called
Not Included
Not Included

41905
Called
Not Called**
Called
Not Called**

28508
Called
Not Called**
Called
Not Called**

28511
Called
Not Called**
Called
Not Called**

12988
Not Called
Not Called**
Not Called
Not Called**

13427
Called
Not Called**
Called
Not Called**

41603
Called
Not Called**
Called
Not Called**

28601
Called
Not Called**
Called
Not Called**

6252
Called
Not Called**
Called
Not Called**

6239
Called
Not Called**
Called
Not Called**

12373
Not Called
Not Called**
Not Called
Not Called**

22992
Called
Not Called**
Called
Not Called**

28510
Called
Not Called**
Called
Not Called**

13979
Called
Not Called**
Called
Not Called**

13180
Called
Called
Called
Called

53194
Called
Called
Called
Called

18419
Called
Called
Called
Called

13182
Called
Called
Called
Called

17570
Called
Called
Called
Called

6223
Not Called*
Called
Not Called*
Called

21984
Called
Called
Called
Called

28603
Called
Called
Called
Called

26445
Called
Not Called
Called
Not Called

6241
Called
Not Called
Called
Not Called

12376
Called
Not Called
Called
Not Called

12381
Called
Not Called
Called
Not Called

13007
Called
Called
Called
Called

6240
Called
Called
Called
Called

13192
Called
Called
Called
Called

28610
Called
Called
Called
Called

41663
Called
Not Called
Called
Not Called

6224
Called
Not Called
Called
Not Called

12675
Called
Not Called
Called
Not Called

6213
Called
Not Called
Called
Not Called

14070
Called
Not Called
Called
Not Called

28607
Called
Not Called
Called
Not Called

33725
Called
Not Called
Called
Not Called

13008
Called
Not Called
Called
Not Called

26438
Called
Not Called
Called
Not Called

*Mutation not called by software, but manual inspection revealed that the sequence corresponded to the correct mutation

**Variant introduced in primer region of test method

Called: sequence variant noted by analysis software

Not Targeted: sequence variant not included in sequence analyzed by the test method

TABLE 8

Gene
Mutation CDS
Mutation AA
Mutation
2.8
2.8
5.4
5.4
11.0
11.0
18.4
18.4
29.5
29.5
47.9
47.9

BRAF
c. 1359T > C
p. P453P
SNP

4.7
8.8
7
14.3
15.5
24.3
27.4
39.4
39.3
59.8
58.3

EGFR
c.340G > A
p.E114K
SNP

4.7
7.5
7.8
14.5
15.4
25.3
23.9
38.6
39.3
59
58.8

EGFR
c.323G > A
p.R108K
SNP

5.1
7.8
7.9
15
14.8
26.7
25.3
40.4
39.3
59
59.2

BRAF
c. 1380A > G
p.G460G
SNP

4.8
8.7
7
14.9
15.5
24.2
27.4
39.3
39.2
59.5
57.8

EGFR
c.874G > T
p.V292L
SNP

4.1
8.7
5.5
12.9
14.4
27.9
27.1
41.5
41.4
62.9
58.9

EGFR
c.2235_2249del15
p.E746_A750delELREA
DEL

18.3
16.8
26.2
27.7
41.4
43.6
61.2
59.5

KRAS
c.111 + 1C > T
p.?
SNP
4.5

8
6.3
15.4
13.4
24.3
24.7
38.2
37.4
58.5
59.7

EGFR
c.2429G > A
p.G810D
SNP
3.1
5.6
8.3
6.7
12.1
14.4
25.3
25.4
36.8
40
55.1
55.7

EGFR
c.2612C > G
p.A871G
SNP
3.1
5.8
8
7.2
13.7
17.4
24.9
27.5
39.6
40.4
61.2
60.8

EGFR
c.2208G > A
p.G735S
SNP
3.4
4.7
7.8
8.5
15.9
16.2
24.8
29.6
39.8
43.5
57.9
60.7

EGRF
c.2375T > C
p.L792P
SNP
3.9
4.2
8.6
5.7
14.6
14.5
22.1
27.2
39.2
41.1
59
59.5

EGFR
c.2170G > A
p.G724S
SNP
3.8
5
8.8
8.6
16.7
16.9
27.9
28.6
43.1
39.1
62
57.6

EGFR
c.2588G > A
p.G863D
SNP
3.3
5.2
8
7.1
13.9
17.4
23.8
26.9
40.4
40.3
61.6
60.5

KRAS
c.104C > T
p.T35I
SNP
3.9
3.7
7.8
6.9
15.4
13.6
24.4
25.8
38.5
37.4
57.7
59.8

EGFR
c.2222C > T
p.P741L
SNP
3.2
4.6
7.8
7.9
16.2
16.5
25.8
28.1
41.4
43.5
59.1
60.2

KRAS
c.351A > C
p.K117N
SNP
5.2
4.2
7.6
7.1
14.7
15.3
23
24.4
38.3
46.5
55.4
61.2

EGFR
c.866C > T
p.A289V
SNP
3
4.2
9.3
5.6
12.8
14.6
27.9
27
44.2
41.4
62.9
57.6

EGFR
c.1793G > T
p.G598V
SNP
4.2
5.5
7
6.6
14.3
16.1
23.6
24.7
38
41.8
54.8
58.3

EGFR
c.2293G > A
p.V765M
SNP
3.9
4.3
8.8
5.5
14.6
14.3
223
27.6
39.3
40.8
58.9
59.9

EGFR
c.2441T > C
p.L814P
SNP
3.1
6.6
9.3
6.8
12
16.2
26.1
25.8
37.5
41.5
55.6
58.7

EGFR
c.2092G > A
p.A698T
SNP
3.7
5.2
9.1
8.9
16.6
17.1
28.2
28.8
41
38.5
62.5
58.5

BRAF
c.1391G > T
p.G464V
SNP
2.7
4.6
8.7
7
14.5
15.4
24.1
27
39.4
39.2
59.4
57.8

BRAF
c.1742A > G
p.N581S
SNP
3.7
4.9
8.9
8.2
12.4

25.1
28.6
39.3
43.9
59.4
57.2

BRAF
c.1781A < G
p.D594G
SNP
4
4.8
8.3
8.4
12.3

25.7
28.4
39.7
43.8
58.2
57.2

BRAF
c.1790T > G
p.L597T
SNP
3.6
4.7
8.1
8.3
12.3

25.9
28.6
38.6
44
57.1
57.4

BRAF
c.1799T > A
p.V600E
SNP
4
4.7
8.6
8.3
12.2

26.4
28.6
39
43.9
58
57.4

KRAS
c.24A > G
p.V8V
SNP
4.7
3
8.3
6.7
14.8
13.2
25
24.3
37
36.7
56.2
59.1

KRAS
c.35G > A
p.G12D
SNP
4.6
3.4
8.1
6.8
15.2
12.8
24.5
24.5
36
36.7
57.4
60

EGFR
c.2197C > T
p.P733S
SNP
3.5
5.2
8
7.5
16
16.8
24.8
28.1
40.9
43.6
59
60.1

KRAS
c.175G > A
p.A59T
SNP
4.5
4.4
8.3
6.5
15.6
14.2
24
26.4
38.1
40.9
58.6
60.7

KRAS
c.183A > C
p.Q61H
SNP
4.5
4.5
7.5
7
15.5
14.3
23.2
26.9
40.3
40.8
60.5
61

EGFR
c.2582T > A
p.L861Q
SNP
2.7
5.7
8.2
6.7
13.8
17.2
23.8
27.1
39.9
40.2
60.6
60.4

EGFR
c.2573T > G
p.L858R
SNP
2.7
5.3
8.4
7.1
13.8
17.1
22.9
26
39.8
40.1
60.7
60.6

EGFR
c.2156G > C
p.G719A
SNP
3.6
5.4
9.3
8.4
16.6
16.5
27.9
29.3
42.5
38.7
62.4
57.8

BRAF
c.1330C > T
p.R444W
SNP
2.9
4.5
8.6
6.7
14.5
15.6
24.4
27.9
38
39.2
60.2
59.3

TABLE 9

Chromosome
Position
Reference

1
43814979
G

1
43815009
G

1
43815020
G

1
115256529
T

1
115256537
T

1
115256669
G

1
115258730
C

1
115258747
C

1
115258753
C

2
29432664
C

2
29443695
G

2
48030632
G

2
48030639
AC

2
48030686
G

2
48030838
A

2
209113112
C

2
209113119
T

2
209113140
C

2
212288955
C

2
212288964
C

2
212530084
C

2
212530091
G

2
212530135
T

2
212576810
A

2
212576877
G

2
212576896
C

2
212578348
A

2
212578372
A

2
212587172
G

2
212587197
G

2
212589812
T

2
212589838
G

2
212589909
C

Chromosome
Position
Alternate

1
43814979
A

1
43815009
T

1
43815020
A

1
115256529
C

1
115256537
C

1
115256669
A

1
115258730
T

1
115258747
T

1
115258753
T

2
29432664
T

2
29443695
T

2
48030632
T

2
48030639
A

2
48030686
A

2
48030838
T

2
209113112
T

2
209113119
C

2
209113140
T

2
212288955
A

2
212288964
A

2
212530084
T

2
212530091
T

2
212530135
C

2
212576810
G

2
212576877
A

2
212576896
A

2
212578348
G

2
212578372
C

2
212587172
T

2
212587197
T

2
212589812
C

2
212589838
A

2
212589909
T

Chromosome
Position
Length
Mutation ID
Gene

1
43814979
1
COSM27286
MPL

1
43815009
1
COSM18918
MPL

1
43815020
1
COSM27290
MPL

1
115256529
1
COSM584
NRAS

1
115256537
1
COSM1332933
NRAS

1
115256669
1
gDNA31
NRAS

1
115258730
1
COSM577
NRAS

1
115258747
1
COSM564
NRAS

1
115258753
1
COSM24850
NRAS

2
29432664
1
COSM28056
ALK

2
29443695
1
COSM28055
ALK

2
48030632
1
COSM13399
MSH6

2
48030639
1
COSM13395
MSH6

2
48030686
1
COSM1021299
MSH6

2
48030838
1
gDNA32
MSH6

2
209113112
1
COSM28746
IDH1

2
209113119
1
COSM1404902
IDH1

2
209113140
1
COSM96922
IDH1

2
212288955
1
COSM48362
ERBB4

2
212288964
1
COSM169572
ERBB4

2
212530084
1
COSM232263
ERBB4

2
212530091
1
COSM573362
ERBB4

2
212530135
1
COSM1405173
ERBB4

2
212576810
1
COSM1614287
ERBB4

2
212576877
1
COSM110095
ERBB4

2
212576896
1
COSM573356
ERBB4

2
212578348
1
COSM1405181
ERBB4

2
212578372
1
COSM160825
ERBB4

2
212587172
1
COSM1015994
ERBB4

2
212587197
1
COSM1251447
ERBB4

2
212589812
1
COSM1405184
ERBB4

2
212589838
1
COSM573353
ERBB4

2
212589909
1
COSM1015997
ERBB4

Chromosome
Position
Mutation CDS

1
43814979
c.1514G > A

1
43815009
c.1544G > T

1
43815020
c.1555G > A

1
115256529
c.182A > G

1
115256537
c.174A > G

1
115256669
c.112 − 70C > T

1
115258730
c.52G > A

1
115258747
c.35G > A

1
115258753
c.29G > A

2
29432664
c.3824G > A

2
29443695
c.3522C > A

2
48030632
c.3246G > T

2
48030639
c.3261delC

2
48030686
c.3300G > A

2
48030838
c.3438 + 14A > T

2
209113112
c.395G > A

2
209113119
c.388A > G

2
209113140
c.367G > A

2
212288955
c.2791G > T

2
212288964
c.2782G > T

2
212530084
c.1835G > A

2
212530091
c.1828C > A

2
212530135
c.1784A > G

2
212576810
c.1089T > C

2
212576877
c.1022C > T

2
212576896
c.1003G > T

2
212578348
c.909T > C

2
212578372
c.885T > G

2
212587172
c.829C > A

2
212587197
c.804C > A

2
212589812
c.730A > G

2
212589838
c.704C > T

2
212589909
c.633G > A

Mutation

Target
Sanger
CHPv2

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*
Detection

1
43814979
p.S505N
SNV
+
5-15%
Detected
Detected

1
43815009
p.W515L
SNV
+
5-15%
Detected
Detected

1
43815020
p.A519T
SNV
+
5-15%
Detected
Detected

1
115256529
p.Q61R
SNV
−
5-15%
Detected
Detected

1
115256537
p.T58T
SNV
−
5-15%
Detected
Detected

1
115256669
p.(=)
SNV
−
genomic
Not Covered
Not

Covered

1
115258730
p.A18T
SNV
−
5-15%
Detected
Detected

1
115258747
p.G12D
SNV
−
5-15%
Detected
Detected

1
115258753
p.G10E
SNV
−
5-15%
Detected
Detected

2
29432664
p.R1275Q
SNV
−
5-15%
Detected
Detected

2
29443695
p.F1174L
SNV
−
5-15%
Detected
Detected

2
48030632
p.P1082P
SNV
+
5-15%
Detected
Not

Covered

2
48030639
p.F1088fs*2
DEL
+
5-15%
Detected
Not

Covered

2
48030686
p.T1100T
SNV
+
5-15%
Detected
Not

Covered

2
48030838
p.(=)
SNV
+
genomic
Not Covered
Not

Covered

2
209113112
p.R132H
SNV
−
5-15%
Detected
Detected

2
209113119
p.I130V
SNV
−
5-15%
Detected
Detected

2
209113140
p.G123R
SNV
−
5-15%
Detected
Detected

2
212288955
p.D931Y
SNV
−
5-15%
Detected
Detected

2
212288964
p.E928*
SNV
−
5-15%
Detected
Detected

2
212530084
p.R612Q
SNV
−
5-15%
Detected
Detected

2
212530091
p.P610T
SNV
−
5-15%
Detected
Detected

2
212530135
p.D595G
SNV
−
5-15%
Detected
Detected

2
212576810
p.N363N
SNV
−
5-15%
Detected
Detected

2
212576877
p.S341L
SNV
−
5-15%
Detected
Detected

2
212576896
p.D335Y
SNV
−
5-15%
Detected
Detected

2
212578348
p.S303S
SNV
−
5-15%
Detected
Detected

2
212578372
p.H295Q
SNV
−
5-15%
Detected
Detected

2
212587172
p.H277N
SNV
−
5-15%
Detected
Detected

2
212587197
p.Y268*
SNV
−
5-15%
Detected
Detected

2
212589812
p.T244A
SNV
−
5-15%
Detected
Detected

2
212589838
p.A235V
SNV
−
5-15%
Detected
Detected

2
212589909
p.T211T
SNV
−
5-15%
Detected
Not

Covered

TSACP
TSTP

Chromosome
Position
Detection
Detection

1
43814979
Not Covered
Not Covered

1
43815009
Detected
Not Covered

1
43815020
Detected
Not Covered

1
115256529
Detected
Detected

1
115256537
Detected
Detected

1
115256669
Not Covered
Detected

1
115258730
Detected
Detected

1
115258747
Detected
Detected

1
115258753
Detected
Detected

2
29432664
Detected
Not Covered

2
29443695
Detected
Detected

2
48030632
Not Covered
Detected

2
48030639
Not Covered
Detected

2
48030686
Not Covered
Detected

2
48030838
Not Covered
Detected

2
209113112
Detected
Not Covered

2
209113119
Detected
Not Covered

2
209113140
Detected
Not Covered

2
212288955
Detected
Not Covered

2
212288964
Detected
Not Covered

2
212530084
Detected
Not Covered

2
212530091
Detected
Not Covered

2
212530135
Detected
Not Covered

2
212576810
Not Covered
Not Covered

2
212576877
Detected
Not Covered

2
212576896
Detected
Not Covered

2
212578348
Detected
Not Covered

2
212578372
Detected
Not Covered

2
212587172
Detected
Not Covered

2
212587197
Detected
Not Covered

2
212589812
Detected
Not Covered

2
212589838
Detected
Not Covered

2
212589909
Detected
Not Covered

Chromosome
Position
Reference

2
212652764
T

2
212652791
G

3
10183797
T

3
10183808
G

3
10183817
C

3
10183824
AC

3
10188200
C

3
10188210
T

3
10188245
G

3
10188286
CG

3
10191479
C

3
10191488
C

3
10191506
C

3
10191513
T

3
37067240
T

3
41266101
C

3
41266113
C

3
41266124
A

3
41266137
C

3
138665163
G

3
178916648
G

3
178916706
A

3
178916793
A

3
178916823
C

3
178916936
G

3
178916944
A

3
178916957
G

3
178917661
A

3
178921489
C

3
178921520
C

3
178921553
T

3
178927450
T

3
178927980
T

Chromosome
Position
Alternate

2
212652764
C

2
212652791
C

3
10183797
A

3
10183808
C

3
10183817
T

3
10183824
A

3
10188200
A

3
10188210
C

3
10188245
C

3
10188286
C

3
10191479
G

3
10191488
T

3
10191506
T

3
10191513
C

3
37067240
A

3
41266101
G

3
41266113
T

3
41266124
G

3
41266137
T

3
138665163
C

3
178916648
A

3
178916706
G

3
178916793
G

3
178916823
T

3
178916936
A

3
178916944
G

3
178916957
T

3
178917661
G

3
178921489
T

3
178921520
T

3
178921553
A

3
178927450
C

3
178927980
C

Chromosome
Position
Length
Mutation ID
Gene

2
212652764
1
COSM48369
ERBB4

2
212652791
1
COSM442267
ERBB4

3
10183797
1
COSM14305
VHL

3
10183808
1
COSM18080
VHL

3
10183817
1
COSM17658
VHL

3
10183824
1
COSM17886
VHL

3
10188200
1
COSM17752
VHL

3
10188210
1
COSM14312
VHL

3
10188245
1
COSM14407
VHL

3
10188286
1
COSM14412
VHL

3
10191479
1
COSM17657
VHL

3
10191488
1
COSM17612
VHL

3
10191506
1
COSM14311
VHL

3
10191513
1
COSM17837
VHL

3
37067240
1
COSM26085
MLH1

3
41266101
1
COSM5677
CTNNB1

3
41266113
1
COSM5662
CTNNB1

3
41266124
1
COSM5664
CTNNB1

3
41266137
1
COSM5667
CTNNB1

3
138665163
1
COSM33661
FOXL2

3
178916648
1
COSM27495
PIK3CA

3
178916706
1
COSM27376
PIK3CA

3
178916793
1
COSM1420738
PIK3CA

3
178916823
1
COSM1041454
PIK3CA

3
178916936
1
COSM27497
PIK3CA

3
178916944
1
COSM13570
PIK3CA

3
178916957
1
COSM125368
PIK3CA

3
178917661
1
COSM1420774
PIK3CA

3
178921489
1
COSM21462
PIK3CA

3
178921520
1
COSM353193
PIK3CA

3
178921553
1
COSM754
PIK3CA

3
178927450
1
COSM1420804
PIK3CA

3
178927980
1
COSM757
PIK3CA

Chromosome
Position
Mutation CDS

2
212652764
c.542A > G

2
212652791
c.515C > G

3
10183797
c.266T > A

3
10183808
c.277G > C

3
10183817
c.286C > T

3
10183824
c.296delC

3
10188200
c.343C > A

3
10188210
c.353T > C

3
10188245
c.388G > C

3
10188286
c.431delG

3
10191479
c.472C > G

3
10191488
c.481C > T

3
10191506
c.499C > T

3
10191513
c.506T > C

3
37067240
c.1151T > A

3
41266101
c.98C > G

3
41266113
c.110C > T

3
41266124
c.121A > G

3
41266137
c.134C > T

3
138665163
c.402C > G

3
178916648
c.35G > A

3
178916706
c.93A > G

3
178916793
c.180A > G

3
178916823
c.210C > T

3
178916936
c.323G > A

3
178916944
c.331A > G

3
178916957
c.344G > T

3
178917661
c.536A > G

3
178921489
c.971C > T

3
178921520
c.1002C > T

3
178921553
c.1035T > A

3
178927450
c.1213T > C

3
178927980
c.1258T > C

Mutation

Target
Sanger
CHPv2

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*
Detection

2
212652764
p.N181S
SNV
−
5-15%
Detected
Detected

2
212652791
p.P172R
SNV
−
5-15%
Detected
Detected

3
10183797
p.L89H
SNV
+
5-15%
Detected
Detected

3
10183808
p.G93R
SNV
+
5-15%
Detected
Detected

3
10183817
p.Q96*
SNV
+
5-15%
Detected
Detected

3
10183824
p.P99fs*60
DEL
+
5-15%
Detected
Detected

3
10188200
p.H115N
SNV
+
5-15%
Detected
Detected

3
10188210
p.L118P
SNV
+
5-15%
Detected
Detected

3
10188245
p.V130L
SNV
+
5-15%
Detected
Detected

3
10188286
p.G144fs*15
DEL
+
5-15%
Detected
Detected

3
10191479
p.L158V
SNV
+
5-15%
Detected
Detected

3
10191488
p.R161*
SNV
+
5-15%
Detected
Detected

3
10191506
p.R167W
SNV
+
5-15%
Detected
Detected

3
10191513
p.L169P
SNV
+
5-15%
Detected
Detected

3
37067240
p.V384D
SNV
+
5-15%
Detected
Detected

3
41266101
p.S33C
SNV
+
5-15%
Detected
Detected

3
41266113
p.S37F
SNV
+
5-15%
Detected
Detected

3
41266124
p.T41A
SNV
+
5-15%
Detected
Detected

3
41266137
p.S45F
SNV
+
5-15%
Detected
Detected

3
138665163
p.C134W
SNV
−
5-15%
Detected
Not

Covered

3
178916648
p.G12D
SNV
+
5-15%
Detected
Not

Covered

3
178916706
p.131M
SNV
+
5-15%
Detected
Not

Covered

3
178916793
p.Q60Q
SNV
+
5-15%
Detected
Detected

3
178916823
p.F70F
SNV
+
5-15%
Detected
Detected

3
178916936
p.R108H
SNV
+
5-15%
Detected
Detected

3
178916944
p.K111E
SNV
+
5-15%
Detected
Detected

3
178916957
p.R115L
SNV
+
5-15%
Detected
Detected

3
178917661
p.K179R
SNV
+
5-15%
Detected
Not

Covered

3
178921489
p.T3241
SNV
+
5-15%
Detected
Detected

3
178921520
p.L334L
SNV
+
5-15%
Detected
Detected

3
178921553
p.N345K
SNV
+
5-15%
Detected
Detected

3
178927450
p.S405P
SNV
+
5-15%
Detected
Detected

3
178927980
p.C420R
SNV
+
5-15%
Detected
Detected

TSACP
TSTP

Chromosome
Position
Detection
Detection

2
212652764
Detected
Not Covered

2
212652791
Detected
Not Covered

3
10183797
Detected
Not Covered

3
10183808
Detected
Not Covered

3
10183817
Detected
Not Covered

3
10183824
Detected
Not Covered

3
10188200
Not Covered
Not Covered

3
10188210
Not Covered
Not Covered

3
10188245
Detected
Not Covered

3
10188286
Detected
Not Covered

3
10191479
Not Detected
Not Covered

3
10191488
Detected
Not Covered

3
10191506
Detected
Not Covered

3
10191513
Not Detected
Not Covered

3
37067240
Detected
Not Covered

3
41266101
Detected
Detected

3
41266113
Detected
Detected

3
41266124
Detected
Detected

3
41266137
Detected
Detected

3
138665163
Not Covered
Detected

3
178916648
Not Covered
Detected

3
178916706
Not Covered
Detected

3
178916793
Not Covered
Detected

3
178916823
Not Covered
Detected

3
178916936
Detected
Detected

3
178916944
Detected
Detected

3
178916957
Detected
Detected

3
178917661
Not Covered
Detected

3
178921489
Not Covered
Not Covered

3
178921520
Not Covered
Not Covered

3
178921553
Detected
Not Covered

3
178927450
Not Covered
Not Covered

3
178927980
Detected
Detected

Chromosome
Position
Reference

3
178928092
A

3
178936074
C

3
178936082
G

3
178936091
G

3
178936098
A

3
178938860
A

3
178947827
G

3
178947850
T

3
178952055
A

3
178952085
A

3
178952149
C

4
1803568
C

4
1803575
C

4
1803668
GC

4
1806089
G

4
1806119
G

4
1806131
T

4
1806153
C

4
1807869
A

4
1807889
A

4
1807894
G

4
1808331
G

4
1808962
A

4
55141051
GCCCAGATGGACATGA (SEQ ID NO: 19)

4
55141055
A

4
55141097
T

4
55144148
C

4
55144172
A

4
55144547
C

4
55151958
T

4
55152085
G

4
55152093
A

4
55152112
C

Chromosome
Position
Alternate

3
178928092
G

3
178936074
G

3
178936082
A

3
178936091
A

3
178936098
G

3
178938860
C

3
178947827
T

3
178947850
C

3
178952055
G

3
178952085
G

3
178952149
CA

4
1803568
G

4
1803575
T

4
1803668
G

4
1806089
T

4
1806119
A

4
1806131
C

4
1806153
A

4
1807869
G

4
1807889
G

4
1807894
A

4
1808331
T

4
1808962
C

4
55141051
G

4
55141055
G

4
55141097
C

4
55144148
A

4
55144172
G

4
55144547
T

4
55151958
TA

4
55152085
T

4
55152093
T

4
55152112
A

Chromosome
Position
Length
Mutation ID
Gene

3
178928092
1
COSM1420828
PIK3CA

3
178936074
1
COSM759
PIK3CA

3
178936082
1
COSM760
PIK3CA

3
178936091
1
COSM763
PIK3CA

3
178936098
1
COSM1420865
PIK3CA

3
178938860
1
COSM778
PIK3CA

3
178947827
1
COSM769
PIK3CA

3
178947850
1
COSM770
PIK3CA

3
178952055
1
COSM328026
PIK3CA

3
178952085
1
COSM775
PIK3CA

3
178952149
1
COSM12464
PIK3CA

4
1803568
1
COSM715
FGFR3

4
1803575
1
COSM29446
FGFR3

4
1803668
1
COSM723
FGFR3

4
1806089
1
COSM716
FGFR3

4
1806119
1
COSM24842
FGFR3

4
1806131
1
COSM724
FGFR3

4
1806153
1
COSM721
FGFR3

4
1807869
1
COSM1428724
FGFR3

4
1807889
1
COSM719
FGFR3

4
1807894
1
gDNA1
FGFR3

4
1808331
1
COSM24802
FGFR3

4
1808962
1
AMXsyntl
FGFR3

4
55141051
15
COSM12418
PDGFRA

4
55141055
1
gDNA2, COSM1430082
PDGFRA

4
55141097
1
COSM1430085
PDGFRA

4
55144148
1
COSM22415
PDGFRA

4
55144172
1
COSM1430086
PDGFRA

4
55144547
1
COSM743
PDGFRA

4
55151958
1
gDNA33
PDGFRA

4
55152085
1
COSM587613
PDGFRA

4
55152093
1
COSM736
PDGFRA

4
55152112
1
COSM28052
PDGFRA

Chromosome
Position
Mutation CDS

3
178928092
c.1370A > G

3
178936074
c.1616C > G

3
178936082
c.1624G > A

3
178936091
c.1633G > A

3
178936098
c.1640A > G

3
178938860
c.2102A > C

3
178947827
c.2702G > T

3
178947850
c.2725T > C

3
178952055
c.3110A > G

3
178952085
c.3140A > G

3
178952149
c.3204_3205insA

4
1803568
c.746C > G

4
1803575
c.753C > T

4
1803668
c.850delC

4
1806089
c.1108G > T

4
1806119
c.1138G > A

4
1806131
c.1150T > C

4
1806153
c.1172C > A

4
1807869
c.1928A > G

4
1807889
c.1948A > G

4
1807894
c.1959A > G

4
1808331
c.2089G > T

4
1808962
c.2401A > C

4
55141051
c.1698_1712del15

4
55141055
c.1701A > G

4
55141097
c.1743T > C

4
55144148
c.1977C > A

4
55144172
c.2001A > G

4
55144547
c.2021C > T

4
55151958
c.2440 − 50 c.2440 − 49insA

4
55152085
c.2517G > T

4
55152093
c.2525A > T

4
55152112
c.2544C > A

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

3
178928092
p.N457S
SNV
+
5-15%
Detected

3
178936074
p.P539R
SNV
+
5-15%
Detected

3
178936082
p.E542K
SNV
+
5-15%
Detected

3
178936091
p.E545K
SNV
+
5-15%
Detected

3
178936098
p.E547G
SNV
+
5-15%
Detected

3
178938860
p.H701P
SNV
+
5-15%
Detected

3
178947827
p.C901F
SNV
+
5-15%
Detected

3
178947850
p.F909L
SNV
+
5-15%
Detected

3
178952055
p.E1037G
SNV
+
5-15%
Detected

3
178952085
p.H1047R
SNV
+
5-15%
Detected

3
178952149
p.N1068fs*4
INS
+
5-15%
Detected

4
1803568
p.S249C
SNV
+
5-15%
Detected

4
1803575
p.H251H
SNV
+
5-15%
Detected

4
1803668
p.H284fs*10
DEL
+
5-15%
Detected

4
1806089
p.G370C
SNV
+
5-15%
Detected

4
1806119
p.G380R
SNV
+
5-15%
Detected

4
1806131
p.F384L
SNV
+
5-15%
Detected

4
1806153
p.A391E
SNV
+
5-15%
Detected

4
1807869
p.H643R
SNV
+
5-15%
Detected

4
1807889
p.K650E
SNV
+
5-15%
Detected

4
1807894
p.T651T
SNV
+
genomic
Not Covered

4
1808331
p.G697C
SNV
+
5-15%
Detected

4
1808962
p.P800P
SNV
+
5-15%
Detected

4
55141051
p.S566 E571 > R
DEL
+
5-15%
Detected

4
55141055
p.P567P
SNV
+
genomic
Not Covered

4
55141097
p.P581P
SNV
+
5-15%
Detected

4
55144148
p.N659K
SNV
+
5-15%
Detected

4
55144172
p.S667S
SNV
+
5-15%
Detected

4
55144547
p.T674I
SNV
+
5-15%
Detected

4
55151958
p.(=)
INS
+
genomic
Not Covered

4
55152085
p.L839L
SNV
+
5-15%
Detected

4
55152093
p.D842V
SNV
+
5-15%
Detected

4
55152112
p.N848K
SNV
+
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

3
178928092
Detected
Not Covered
Detected

3
178936074
Detected
Detected
Detected

3
178936082
Detected
Detected
Detected

3
178936091
Detected
Detected
Detected

3
178936098
Detected
Detected
Detected

3
178938860
Detected
Detected
Not Covered

3
178947827
Detected
Not Covered
Not Covered

3
178947850
Detected
Not Covered
Not Covered

3
178952055
Detected
Not Detected
Detected

3
178952085
Detected
Not Detected
Detected

3
178952149
Detected
Detected
Not Detected

4
1803568
Detected
Detected
Not Covered

4
1803575
Detected
Detected
Not Covered

4
1803668
Not Covered
Detected
Not Covered

4
1806089
Detected
Not Covered
Not Covered

4
1806119
Detected
Detected
Not Covered

4
1806131
Detected
Detected
Not Covered

4
1806153
Detected
Detected
Not Covered

4
1807869
Detected
Detected
Not Covered

4
1807889
Detected
Detected
Not Covered

4
1807894
Detected
Detected
Not Covered

4
1808331
Detected
Not Detected
Not Covered

4
1808962
Detected
Detected
Not Covered

4
55141051
Detected
Detected
Detected

4
55141055
Detected
Detected
Detected

4
55141097
Detected
Detected
Detected

4
55144148
Detected
Detected
Detected

4
55144172
Detected
Detected
Detected

4
55144547
Detected
Detected
Not Covered

4
55151958
Not Covered
Not Covered
Detected

4
55152085
Detected
Detected
Detected

4
55152093
Detected
Detected
Detected

4
55152112
Detected
Detected
Detected

Chromosome
Position
Reference

4
55561702
C

4
55561764
G

4
55561828
A

4
55592081
T

4
55592092
A

4
55592178
C

4
55592192
T

4
55592202
A

4
55592211
A

4
55593431
G

4
55593464
A

4
55593632
C

4
55593661
T

4
55593689
C

4
55594221
A

4
55594258
T

4
55595599
C

4
55597500
T

4
55597561
G

4
55599284
C

4
55599401
T

4
55599436
T

4
55602737
G

4
55602765
G

4
55946081
A

4
55946171
G

4
55953816
ACTTCCTCCTCCTCCATACAGGAAAC (SEQ ID NO: 20)

4
55955112
C

4
55961023
C

4
55962505
T

4
55962545
T

4
55972974
T

4
55972978
CTATAAGAAAGAGATAACAGCGCATATTATGATTTAATTTTT

(SEQ ID NO: 21)

Chromosome
Position
Alternate

4
55561702
T

4
55561764
A

4
55561828
G

4
55592081
C

4
55592092
G

4
55592178
CTGCCTA

4
55592192
C

4
55592202
T

4
55592211
G

4
55593431
A

4
55593464
C

4
55593632
T

4
55593661
C

4
55593689
T

4
55594221
G

4
55594258
C

4
55595599
T

4
55597500
C

4
55597561
A

4
55599284
T

4
55599401
A

4
55599436
C

4
55602737
A

4
55602765
C

4
55946081
G

4
55946171
A

4
55953816
A

4
55955112
T

4
55961023
A

4
55962505
C

4
55962545
TG

4
55972974
A

4
55972978
C

Chromosome
Position
Length
Mutation ID
Gene

4
55561702
1
COSM77973
KIT

4
55561764
1
COSM1146
KIT

4
55561828
1
COSM1430106
KIT

4
55592081
1
COSM24637
KIT

4
55592092
1
COSM41602
KIT

4
55592178
6
COSM1326
KIT

4
55592192
1
COSM96867
KIT

4
55592202
1
COSM96885
KIT

4
55592211
1
COSM1430136
KIT

4
55593431
1
COSM1155
KIT

4
55593464
1
gDNA3, COSM28026
KIT

4
55593632
1
COSM1275
KIT

4
55593661
1
COSM1290
KIT

4
55593689
1
COSM1299
KIT

4
55594221
1
COSM1304
KIT

4
55594258
1
COSM12706
KIT

4
55595599
1
COSM36053
KIT

4
55597500
1
COSM1430171
KIT

4
55597561
1
COSM21303
KIT

4
55599284
1
COSM20402
KIT

4
55599401
1
COSM19194
KIT

4
55599436
1
gDNA4
KIT

4
55602737
1
COSM133767
KIT

4
55602765
1
gDNA5, COSM1325
KIT

4
55946081
1
gDNA6
KDR

4
55946171
1
COSM35855
KDR

4
55953816
25
AMXsynt2
KDR

4
55955112
1
COSM1430203
KDR

4
55961023
1
COSM48464
KDR

4
55962505
1
COSM1430212
KDR

4
55962545
1
gDNA7
KDR

4
55972974
1
gDNA8, COSM149673
KDR

4
55972978
41
AMXsynt3
KDR

Chromosome
Position
Mutation CDS

4
55561702
c.92C > T

4
55561764
c.154G > A

4
55561828
c.218A > G

4
55592081
c.1405T > C

4
55592092
c.1416A > G

4
55592178
c.1509_1510insGCCTAT

4
55592192
c.1516T > C

4
55592202
c.1526A > T

4
55592211
c.1535A > G

4
55593431
c.1588G > A

4
55593464
c.1621A > C

4
55593632
c.1698C > T

4
55593661
c.1727T > C

4
55593689
c.1755C > T

4
55594221
c.1924A > G

4
55594258
c.1961T > C

4
55595599
c.2089C > T

4
55597500
c.2148T > C

4
55597561
c.2209G > A

4
55599284
c.2410C > T

4
55599401
c.2484 + 43T > A

4
55599436
c.2484 + 78T > C

4
55602737
c.2558G > A

4
55602765
c.2586G > C

4
55946081
c.*27T > C

4
55946171
c.4008C > T

4
55953816
c.3594del25

4
55955112
c.3433G > A

4
55961023
c.2917G > T

4
55962505
c.2619A > G

4
55962545
c.2615 − 37_2615 − 36insC

4
55972974
c.1416A > T

4
55972978
c.1413 − 42del41

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

4
55561702
p.P31L
SNV
+
5-15%
Detected

4
55561764
p.D52N
SNV
+
5-15%
Detected

4
55561828
p.E73G
SNV
+
5-15%
Detected

4
55592081
p.F469L
SNV
+
5-15%
Detected

4
55592092
p.L472L
SNV
+
5-15%
Detected

4
55592178
p.Y503_F504insAY
INS
+
5-15%
Detected

4
55592192
p.F506L
SNV
+
5-15%
Detected

4
55592202
p.K509I
SNV
+
5-15%
Detected

4
55592211
p.N512S
SNV
+
5-15%
Detected

4
55593431
p.V530I
SNV
+
5-15%
Detected

4
55593464
p.M541L
SNV
+
genomic
Not Covered

4
55593632
p.N566N
SNV
+
5-15%
Detected

4
55593661
p.L576P
SNV
+
5-15%
Detected

4
55593689
p.P585P
SNV
+
5-15%
Detected

4
55594221
p.K642E
SNV
+
5-15%
Detected

4
55594258
p.V654A
SNV
+
5-15%
Detected

4
55595599
p.H697Y
SNV
+
5-15%
Detected

4
55597500
p.D716D
SNV
+
5-15%
Detected

4
55597561
p.D737N
SNV
+
5-15%
Detected

4
55599284
p.R804W
SNV
+
5-15%
Detected

4
55599401
p.?
SNV
+
5-15%
Detected

4
55599436
p.(=)
SNV
+
genomic
Not Covered

4
55602737
p.W853*
SNV
+
5-15%
Detected

4
55602765
p.L862L
SNV
+
genomic
Not Covered

4
55946081
p.(=)
SNV
−
genomic
Not Covered

4
55946171
p.T1336T
SNV
−
5-15%
Detected

4
55953816
p.V1199fs*27
DEL
−
5-15%
Detected

4
55955112
p.G1145R
SNV
−
5-15%
Detected

4
55961023
p.A973S
SNV
−
5-15%
Detected

4
55962505
p.G873G
SNV
−
5-15%
Detected

4
55962545
p.(=)
INS
−
genomic
Not Covered

4
55972974
p.Q472H
SNV
−
genomic
Not Covered

4
55972978
p.?
DEL
−
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

4
55561702
Detected
Not Covered
Not Covered

4
55561764
Detected
Detected
Not Covered

4
55561828
Not Covered
Detected
Not Covered

4
55592081
Not Covered
Not Covered
Detected

4
55592092
Not Covered
Not Covered
Detected

4
55592178
Detected
Not Covered
Detected

4
55592192
Detected
Detected
Detected

4
55592202
Detected
Detected
Detected

4
55592211
Detected
Detected
Detected

4
55593431
Detected
Detected
Not Covered

4
55593464
Detected
Detected
Not Covered

4
55593632
Detected
Detected
Detected

4
55593661
Detected
Detected
Detected

4
55593689
Detected
Detected
Detected

4
55594221
Detected
Detected
Detected

4
55594258
Detected
Detected
Detected

4
55595599
Not Covered
Detected
Not Covered

4
55597500
Detected
Detected
Not Covered

4
55597561
Not Covered
Detected
Not Covered

4
55599284
Detected
Not Covered
Detected

4
55599401
Not Covered
Detected
Detected

4
55599436
Not Covered
Detected
Not Detected

4
55602737
Detected
Detected
Detected

4
55602765
Not Covered
Detected
Detected

4
55946081
Not Covered
Detected
Not Covered

4
55946171
Detected
Detected
Not Covered

4
55953816
Detected
Detected
Not Covered

4
55955112
Detected
Detected
Not Covered

4
55961023
Detected
Detected
Not Covered

4
55962505
Detected
Detected
Not Covered

4
55962545
Detected
Detected
Not Covered

4
55972974
Detected
Detected
Not Covered

4
55972978
Detected
Not Detected
Not Covered

Chromosome
Position
Reference

4
55979623
C

4
55980239
C

4
153244078
T

4
153244092
G

4
153244124
G

4
153244155
TC

4
153245477
T

4
153247222
T

4
153247226
A

4
153247244
C

4
153247351
C

4
153247366
C

4
153249384
C

4
153249440
C

4
153249456
C

4
153250883
G

4
153258983
G

4
153259071
C

5
112173830
G

5
112173917
C

5
112173930
T

5
112173947
C

5
112174043
G

5
112174577
C

5
112174596
A

5
112174726
A

5
112174989
CA

5
112175086
A

5
112175162
C

5
112175171
C

5
112175211
T

5
112175255
G

5
112175348
G

Chromosome
Position
Alternate

4
55979623
A

4
55980239
T

4
153244078
C

4
153244092
A

4
153244124
C

4
153244155
T

4
153245477
TGATCATATTCATATTCTCTGAAATCAACGAG (SEQ ID NO:

22)

4
153247222
C

4
153247226
G

4
153247244
T

4
153247351
A

4
153247366
T

4
153249384
T

4
153249440
T

4
153249456
A

4
153250883
A

4
153258983
A

4
153259071
A

5
112173830
GA

5
112173917
T

5
112173930
C

5
112173947
T

5
112174043
T

5
112174577
T

5
112174596
G

5
112174726
G

5
112174989
C

5
112175086
G

5
112175162
T

5
112175171
T

5
112175211
TA

5
112175255
T

5
112175348
T

Chromosome
Position
Length
Mutation ID
Gene

4
55979623
1
COSM32339
KDR

4
55980239
1
gDNA9
KDR

4
153244078
1
COSM1427592
FBXW7

4
153244092
1
COSM27083
FBXW7

4
153244124
1
COSM732399
FBXW7

4
153244155
1
COSM34018
FBXW7

4
153245477
31
AMXsynt4
FBXW7

4
153247222
1
COSM27913
FBXW7

4
153247226
1
COSM30599
FBXW7

4
153247244
1
COSM30598
FBXW7

4
153247351
1
COSM34016
FBXW7

4
153247366
1
COSM22974
FBXW7

4
153249384
1
COSM22965
FBXW7

4
153249440
1
COSM22986
FBXW7

4
153249456
1
COSM161024
FBXW7

4
153250883
1
COSM22973
FBXW7

4
153258983
1
COSM22971
FBXW7

4
153259071
1
COSM1052125
FBXW7

5
112173830
1
COSM18979
APC

5
112173917
1
COSM18852
APC

5
112173930
1
COSM19230
APC

5
112173947
1
COSM19330
APC

5
112174043
1
COSM19065
APC

5
112174577
1
COSM13872
APC

5
112174596
1
COSM1432250
APC

5
112174726
1
COSM1432260
APC

5
112174989
1
COSM41617
APC

5
112175086
1
COSM1432280
APC

5
112175162
1
COSM19072
APC

5
112175171
1
COSM18960
APC

5
112175211
1
COSM18719
APC

5
112175255
1
COSM18702
APC

5
112175348
1
COSM19048
APC

Chromosome
Position
Mutation CDS

4
55979623
c.824G > T

4
55980239
c.798 + 54G > A

4
153244078
c.2079A > G

4
153244092
c.2065C > T

4
153244124
c.2033C > G

4
153244155
c.2001delG

4
153245477
c.1473_1474insCTCGTTGATTTCAGAGAATATGAATATGATC

(SEQ ID NO: 23)

4
153247222
c.1580A > G

4
153247226
c.1576T > C

4
153247244
c.1558G > A

4
153247351
c.1451G > T

4
153247366
c.1436G > A

4
153249384
c.1394G > A

4
153249440
c.1338G > A

4
153249456
c.1322G > T

4
153250883
c.1177C > T

4
153258983
c.832C > T

4
153259071
c.744G > T

5
112173830
c.2543_2544insA

5
112173917
c.2626C > T

5
112173930
c.2639T > C

5
112173947
c.2656C > T

5
112174043
c.2752G > T

5
112174577
c.3286C > T

5
112174596
c.3305A > G

5
112174726
c.3435A > G

5
112174989
c.3700delA

5
112175086
c.3795A > G

5
112175162
c.3871C > T

5
112175171
c.3880C > T

5
112175211
c.3923_3924insA

5
112175255
c.3964G > T

5
112175348
c.4057G > T

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

4
55979623
p.R275L
SNV
−
5-15%
Detected

4
55980239
p.(=)
SNV
−
genomic
Not Covered

4
153244078
p.E693E
SNV
−
5-15%
Detected

4
153244092
p.R689W
SNV
−
5-15%
Detected

4
153244124
p.S678*
SNV
−
5-15%
Detected

4
153244155
p.S668fs*39
DEL
−
5-15%
Detected

4
153245477
p.N492fs*42
INS
−
5-15%
Detected

4
153247222
p.D527G
SNV
−
5-15%
Detected

4
153247226
p.W526R
SNV
−
5-15%
Detected

4
153247244
p.D520N
SNV
−
5-15%
Detected

4
153247351
p.R484M
SNV
−
5-15%
Detected

4
153247366
p.R479Q
SNV
−
5-15%
Detected

4
153249384
p.R465H
SNV
−
5-15%
Detected

4
153249440
p.W446*
SNV
−
5-15%
Detected

4
153249456
p.R441L
SNV
−
5-15%
Detected

4
153250883
p.R393*
SNV
−
5-15%
Detected

4
153258983
p.R278*
SNV
−
5-15%
Detected

4
153259071
p.E248D
SNV
−
5-15%
Detected

5
112173830
p.D849fs*2
INS
+
15-35%
Detected

5
112173917
p.R876*
SNV
+
15-35%
Detected

5
112173930
p.1880T
SNV
+
15-35%
Detected

5
112173947
p.Q886*
SNV
+
15-35%
Detected

5
112174043
p.E918*
SNV
+
15-35%
Detected

5
112174577
p.Q1096*
SNV
+
15-35%
Detected

5
112174596
p.Y1102C
SNV
+
15-35%
Detected

5
112174726
p.E1145E
SNV
+
15-35%
Detected

5
112174989
p.S1234fs*31
DEL
+
15-35%
Detected

5
112175086
p.E1265E
SNV
+
15-35%
Detected

5
112175162
p.Q1291*
SNV
+
15-35%
Detected

5
112175171
p.Q1294*
SNV
+
15-35%
Detected

5
112175211
p.E1309fs*6
INS
+
15-35%
Detected

5
112175255
p.E1322*
SNV
+
15-35%
Detected

5
112175348
p.E1353*
SNV
+
15-35%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

4
55979623
Detected
Detected
Not Covered

4
55980239
Detected
Not Covered
Not Covered

4
153244078
Not Covered
Not Covered
Detected

4
153244092
Not Covered
Not Covered
Detected

4
153244124
Not Covered
Not Covered
Detected

4
153244155
Not Covered
Not Covered
Detected

4
153245477
Not Detected
Detected
Detected

4
153247222
Not Covered
Not Covered
Detected

4
153247226
Not Covered
Not Covered
Detected

4
153247244
Not Covered
Not Covered
Detected

4
153247351
Detected
Detected
Detected

4
153247366
Detected
Detected
Detected

4
153249384
Detected
Detected
Detected

4
153249440
Detected
Detected
Detected

4
153249456
Detected
Detected
Detected

4
153250883
Detected
Detected
Detected

4
153258983
Detected
Detected
Not Covered

4
153259071
Not Covered
Detected
Not Covered

5
112173830
Not Covered
Not Covered
Detected

5
112173917
Detected
Detected
Detected

5
112173930
Detected
Detected
Detected

5
112173947
Detected
Detected
Detected

5
112174043
Not Covered
Detected
Not Covered

5
112174577
Detected
Not Covered
Detected

5
112174596
Detected
Not Covered
Detected

5
112174726
Not Covered
Detected
Detected

5
112174989
Not Covered
Not Covered
Detected

5
112175086
Not Covered
Detected
Detected

5
112175162
Detected
Detected
Detected

5
112175171
Detected
Detected
Detected

5
112175211
Detected
Detected
Detected

5
112175255
Detected
Detected
Detected

5
112175348
Detected
Detected
Detected

Chromosome
Position
Reference

5
112175354
T

5
112175423
C

5
112175432
C

5
112175479
TGA

5
112175507
C

5
112175576
C

5
112175675
AAG

5
112175830
GC

5
112175852
G

5
112175930
G

5
112175945
G

5
112175951
G

5
112176063
C

5
112176117
C

5
149433596
T

5
149433597
G

5
149433645
T

5
149433673
C

5
149453057
C

5
170837543
C

7
55211080
G

7
55211097
G

7
55211165
C

7
55221822
C

7
55221830
G

7
55233043
G

7
55233109
G

7
55241615
T

7
55241644
G

7
55241708
G

7
55241722
G

7
55241755
G

7
55242427
C

Chromosome
Position
Alternate

5
112175354
C

5
112175423
T

5
112175432
T

5
112175479
T

5
112175507
T

5
112175576
T

5
112175675
A

5
112175830
G

5
112175852
T

5
112175930
T

5
112175945
T

5
112175951
GA

5
112176063
CA

5
112176117
T

5
149433596
G

5
149433597
A

5
149433645
C

5
149433673
T

5
149453057
CACTGCTTGA (SEQ ID NO: 24)

5
170837543
CTCTG

7
55211080
A

7
55211097
A

7
55211165
T

7
55221822
T

7
55221830
T

7
55233043
T

7
55233109
A

7
55241615
C

7
55241644
A

7
55241708
C

7
55241722
A

7
55241755
A

7
55242427
T

Chromosome
Position
Length
Mutation ID
Gene

5
112175354
1
COSM19652
APC

5
112175423
1
COSM18862
APC

5
112175432
1
COSM143913
APC

5
112175479
2
COSM18993
APC

5
112175507
1
COSM19087
APC

5
112175576
1
COSM18836
APC

5
112175675
2
COSM13864
APC

5
112175830
1
COSM1173082
APC

5
112175852
1
COSM1183180
APC

5
112175930
1
COSM13879
APC

5
112175945
1
COSM41616
APC

5
112175951
1
COSM18561
APC

5
112176063
1
COSM18875
APC

5
112176117
1
COSM42906
APC

5
149433596
1
gDNA10
CSF1R

5
149433597
1
gDNAll
CSF1R

5
149433645
1
COSM947
CSF1R

5
149433673
1
COSM310349
CSF1R

5
149453057
9
AMXsynt5
CSF1R

5
170837543
4
COSM17559
NPM1

7
55211080
1
COSM21683
EGFR

7
55211097
1
COSM174732
EGFR

7
55211165
1
COSM1451540
EGFR

7
55221822
1
COSM21687
EGFR

7
55221830
1
COSM43067
EGFR

7
55233043
1
COSM21690
EGFR

7
55233109
1
COSM35825
EGFR

7
55241615
1
COSM13177
EGFR

7
55241644
1
COSM41905
EGFR

7
55241708
1
COSM6239
EGFR

7
55241722
1
COSM13979
EGFR

7
55241755
1
gDNA15
EGFR

7
55242427
1
COSM53194
EGFR

Chromosome
Position
Mutation CDS

5
112175354
c.4063T > C

5
112175423
c.4132C > T

5
112175432
c.4141C > T

5
112175479
c.4189_4190delGA

5
112175507
c.4216C > T

5
112175576
c.4285C > T

5
112175675
c.4393_4394delAG

5
112175830
c.4540delC

5
112175852
c.4561G > T

5
112175930
c.4639G > T

5
112175945
c.4654G > T

5
112175951
c.4666_4667insA

5
112176063
c.4773_4774insA

5
112176117
c.4826C > T

5
149433596
c.*36A > C

5
149433597
c.*35C > T

5
149433645
c.2906A > G

5
149433673
c.2878G > A

5
149453057
c.890 − 2_c.890 − 1insTCAAGCAGT

5
170837543
c.863_864insTCTG

7
55211080
c.323G > A

7
55211097
c.340G > A

7
55211165
c.408C > T

7
55221822
c.866C > T

7
55221830
c.874G > T

7
55233043
c.1793G > T

7
55233109
c.1859G > A

7
55241615
c.2063T > C

7
55241644
c.2092G > A

7
55241708
c.2156G > C

7
55241722
c.2170G > A

7
55241755
c.2184 + 19G > A

7
55242427
c.2197C > T

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

5
112175354
p.S1355P
SNV
+
15-35%
Detected

5
112175423
p.Q1378*
SNV
+
15-35%
Detected

5
112175432
p.P1381S
SNV
+
15-35%
Detected

5
112175479
p.R1399fs*9
DEL
+
15-35%
Detected

5
112175507
p.Q1406*
SNV
+
15-35%
Detected

5
112175576
p.Q1429*
SNV
+
15-35%
Detected

5
112175675
p.S1465fs*3
DEL
+
15-35%
Detected

5
112175830
p.P1514fs*9
DEL
+
15-35%
Detected

5
112175852
p.E1521*
SNV
+
15-35%
Detected

5
112175930
p.E1547*
SNV
+
15-35%
Detected

5
112175945
p.E1552*
SNV
+
15-35%
Detected

5
112175951
p.T1556fs*3
INS
+
15-35%
Detected

5
112176063
p.P1594fs*38
INS
+
15-35%
Detected

5
112176117
p.P1609L
SNV
+
15-35%
Detected

5
149433596
p.(=)
SNV
−
genomic
Not Covered

5
149433597
p.(=)
SNV
−
genomic
Not Covered

5
149433645
p.Y969C
SNV
−
15-35%
Detected

5
149433673
p.A960T
SNV
−
15-35%
Detected

5
149453057
p.?
INS
−
15-35%
Detected

5
170837543
p.W288fs*12
INS
+
15-35%
Detected

7
55211080
p.R108K
SNV
+
15-35%
Detected

7
55211097
p.E114K
SNV
+
15-35%
Detected

7
55211165
p.P136P
SNV
+
15-35%
Detected

7
55221822
p.A289V
SNV
+
15-35%
Detected

7
55221830
p.V292L
SNV
+
15-35%
Detected

7
55233043
p.G598V
SNV
+
15-35%
Detected

7
55233109
p.C620Y
SNV
+
15-35%
Detected

7
55241615
p.L688P
SNV
+
15-35%
Detected

7
55241644
p.A698T
SNV
+
15-35%
Detected

7
55241708
p.G719A
SNV
+
15-35%
Detected

7
55241722
p.G724S
SNV
+
15-35%
Detected

7
55241755
p.(=)
SNV
+
genomic
Not Covered

7
55242427
p.P733S
SNV
+
15-35%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

5
112175354
Detected
Detected
Detected

5
112175423
Detected
Detected
Detected

5
112175432
Detected
Detected
Detected

5
112175479
Not Covered
Detected
Detected

5
112175507
Not Covered
Detected
Detected

5
112175576
Detected
Detected
Detected

5
112175675
Detected
Detected
Detected

5
112175830
Detected
Detected
Detected

5
112175852
Detected
Detected
Detected

5
112175930
Detected
Detected
Detected

5
112175945
Detected
Detected
Detected

5
112175951
Detected
Detected
Detected

5
112176063
Not Covered
Not Covered
Detected

5
112176117
Not Covered
Not Covered
Detected

5
149433596
Detected
Not Covered
Not Covered

5
149433597
Detected
Detected
Not Covered

5
149433645
Detected
Detected
Not Covered

5
149433673
Detected
Detected
Not Covered

5
149453057
Detected
Detected
Not Covered

5
170837543
Detected
Detected
Not Covered

7
55211080
Detected
Detected
Not Covered

7
55211097
Detected
Detected
Not Covered

7
55211165
Not Covered
Detected
Not Covered

7
55221822
Detected
Detected
Not Covered

7
55221830
Detected
Detected
Not Covered

7
55233043
Detected
Detected
Not Covered

7
55233109
Not Covered
Detected
Not Covered

7
55241615
Not Covered
Not Covered
Detected

7
55241644
Detected
Not Covered
Detected

7
55241708
Detected
Detected
Detected

7
55241722
Detected
Detected
Detected

7
55241755
Not Covered
Detected
Not Detected

7
55242427
Detected
Detected
Detected

Chromosome
Position
Reference

7
55242433
G

7
55242452
C

7
55242464
AGGAATTAAGAGAAGC (SEQ ID NO: 25)

7
55248995
G

7
55249063
G

7
55249077
T

7
55249131
G

7
55249143
T

7
55259427
G

7
55259439
T

7
55259446
A

7
55259457
G

7
55259515
T

7
55259524
T

7
55259530
G

7
55259554
C

7
116339642
G

7
116340262
A

7
116412044
G

7
116417465
T

7
116417499
C

7
116418969
G

7
116418997
C

7
116419008
T

7
116422133
T

7
116423428
T

7
116423449
G

7
116423456
A

7
116423474
T

7
116436022
G

7
116436097
G

7
128845101
C

7
128846040
G

Chromosome
Position
Alternate

7
55242433
A

7
55242452
T

7
55242464
A

7
55248995
A

7
55249063
A

7
55249077
C

7
55249131
A

7
55249143
C

7
55259427
A

7
55259439
G

7
55259446
T

7
55259457
A

7
55259515
G

7
55259524
A

7
55259530
A

7
55259554
G

7
116339642
T

7
116340262
G

7
116412044
A

7
116417465
C

7
116417499
G

7
116418969
C

7
116418997
T

7
116419008
C

7
116422133
G

7
116423428
G

7
116423449
T

7
116423456
G

7
116423474
C

7
116436022
A

7
116436097
A

7
128845101
T

7
128846040
A

Chromosome
Position
Length
Mutation ID
Gene

7
55242433
1
COSM13182
EGFR

7
55242452
1
COSM17570
EGFR

7
55242464
15
COSM6223
EGFR

7
55248995
1
COSM28603
EGFR

7
55249063
1
gDNA16, COSM1451600
EGFR

7
55249077
1
COSM13190
EGFR

7
55249131
1
COSM12986
EGFR

7
55249143
1
COSM28610
EGFR

7
55259427
1
COSM53291
EGFR

7
55259439
1
COSM13424
EGFR

7
55259446
1
COSM6227
EGFR

7
55259457
1
COSM13430
EGFR

7
55259515
1
COSM6224
EGFR

7
55259524
1
COSM6213
EGFR

7
55259530
1
COSM14070
EGFR

7
55259554
1
COSM13008
EGFR

7
116339642
1
COSM706
MET

7
116340262
1
COSM710
MET

7
116412044
1
COSM29633
MET

7
116417465
1
COSM1447462
MET

7
116417499
1
COSM697
MET

7
116418969
1
COSM43064
MET

7
116418997
1
COSM1214928
MET

7
116419008
1
COSM1447471
MET

7
116422133
1
COSM1330154
MET

7
116423428
1
COSM700
MET

7
116423449
1
COSM48565
MET

7
116423456
1
COSM695
MET

7
116423474
1
COSM691
MET

7
116436022
1
gDNA12, COSM150378
MET

7
116436097
1
gDNA13, COSM150379
MET

7
128845101
1
COSM13145
SMO

7
128846040
1
COSM13147
SMO

Chromosome
Position
Mutation CDS

7
55242433
c.2203G > A

7
55242452
c.2222C > T

7
55242464
c.2235_2249del15

7
55248995
c.2293G > A

7
55249063
c.2361G > A

7
55249077
c.2375T > C

7
55249131
c.2429G > A

7
55249143
c.2441T > C

7
55259427
c.2485G > A

7
55259439
c.2497T > G

7
55259446
c.2504A > T

7
55259457
c.2515G > A

7
55259515
c.2573T > G

7
55259524
c.2582T > A

7
55259530
c.2588G > A

7
55259554
c.2612C > G

7
116339642
c.504G > T

7
116340262
c.1124A > G

7
116412044
c.3082 + 1G > A

7
116417465
c.3336T > C

7
116417499
c.3370C > G

7
116418969
c.3534G > C

7
116418997
c.3562C > T

7
116419008
c.3573T > C

7
116422133
c.3668T > G

7
116423428
c.3757T > G

7
116423449
c.3778G > T

7
116423456
c.3785A > G

7
116423474
c.3803T > C

7
116436022
c.4071G > A

7
116436097
c.4146G > A

7
128845101
c.595C > T

7
128846040
c.970G > A

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

7
55242433
p.G735S
SNV
+
15-35%
Detected

7
55242452
p.P741L
SNV
+
15-35%
Detected

7
55242464
p.E746_A750delELREA
DEL
+
15-35%
Detected

7
55248995
p.V765M
SNV
+
15-35%
Detected

7
55249063
p.Q787Q
SNV
+
genomic
Not Covered

7
55249077
p.L792P
SNV
+
15-35%
Detected

7
55249131
p.G810D
SNV
+
15-35%
Detected

7
55249143
p.L814P
SNV
+
15-35%
Detected

7
55259427
p.E829K
SNV
+
15-35%
Detected

7
55259439
p.L833V
SNV
+
15-35%
Detected

7
55259446
p.H835L
SNV
+
15-35%
Detected

7
55259457
p.A839T
SNV
+
15-35%
Detected

7
55259515
p.L858R
SNV
+
15-35%
Detected

7
55259524
p.L861Q
SNV
+
15-35%
Detected

7
55259530
p.G863D
SNV
+
15-35%
Detected

7
55259554
p.A871G
SNV
+
15-35%
Detected

7
116339642
p.E168D
SNV
+
15-35%
Detected

7
116340262
p.N375S
SNV
+
15-35%
Detected

7
116412044
p.?
SNV
+
15-35%
Detected

7
116417465
p.H1112H
SNV
+
15-35%
Detected

7
116417499
p.H1124D
SNV
+
15-35%
Detected

7
116418969
p.M11781
SNV
+
15-35%
Detected

7
116418997
p.R1188*
SNV
+
15-35%
Detected

7
116419008
p.T1191T
SNV
+
15-35%
Detected

7
116422133
p.L1223W
SNV
+
15-35%
Detected

7
116423428
p.Y1253D
SNV
+
15-35%
Detected

7
116423449
p.G1260C
SNV
+
15-35%
Detected

7
116423456
p.K1262R
SNV
+
15-35%
Detected

7
116423474
p.M1268T
SNV
+
15-35%
Detected

7
116436022
p.A1357A
SNV
+
genomic
Not Covered

7
116436097
p.P1382P
SNV
+
genomic
Not Covered

7
128845101
p.R199W
SNV
+
15-35%
Detected

7
128846040
p.A324T
SNV
+
15-35%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

7
55242433
Detected
Detected
Detected

7
55242452
Detected
Detected
Detected

7
55242464
Detected
Detected
Detected

7
55248995
Detected
Detected
Detected

7
55249063
Detected
Detected
Detected

7
55249077
Detected
Detected
Detected

7
55249131
Detected
Detected
Detected

7
55249143
Detected
Detected
Detected

7
55259427
Not Covered
Not Covered
Detected

7
55259439
Not Covered
Not Covered
Detected

7
55259446
Not Covered
Not Covered
Detected

7
55259457
Not Covered
Not Covered
Detected

7
55259515
Detected
Detected
Detected

7
55259524
Detected
Detected
Detected

7
55259530
Detected
Detected
Detected

7
55259554
Detected
Detected
Detected

7
116339642
Detected
Detected
Detected

7
116340262
Detected
Detected
Detected

7
116412044
Not Covered
Detected
Detected

7
116417465
Detected
Detected
Detected

7
116417499
Detected
Detected
Detected

7
116418969
Not Covered
Not Covered
Detected

7
116418997
Not Covered
Not Covered
Detected

7
116419008
Not Covered
Not Covered
Detected

7
116422133
Not Covered
Not Covered
Detected

7
116423428
Detected
Detected
Detected

7
116423449
Detected
Detected
Detected

7
116423456
Detected
Detected
Detected

7
116423474
Detected
Detected
Detected

7
116436022
Not Covered
Not Covered
Detected

7
116436097
Not Covered
Not Covered
Detected

7
128845101
Detected
Detected
Not Covered

7
128846040
Detected
Detected
Not Covered

Chromosome
Position
Reference

7
128846398
C

7
128846469
A

7
128850341
G

7
128851593
A

7
140453136
A

7
140453145
A

7
140453154
T

7
140453193
T

7
140481417
C

7
140481428
T

7
140481449
A

7
140481478
G

7
148508727
T

8
38282147
G

8
38285864
G

8
38285891
T

8
38285938
G

9
5073770
G

9
5073781
C

9
21971000
C

9
21971017
G

9
21971028
C

9
21971036
C

9
21971111
G

9
21971120
G

9
21971153
C

9
21971186
G

9
80336317
G

9
80343489
T

9
80343605
GAAAAAACAAGGA (SEQ ID NO: 26)

9
80409345
A

9
80409432
ACA

9
80409533
TAATAACATATAAAGTAAAACTAAAAAGTCAACATAAATATA

(SEQ ID NO: 27)

Chromosome
Position
Alternate

7
128846398
T

7
128846469
G

7
128850341
T

7
128851593
G

7
140453136
T

7
140453145
C

7
140453154
C

7
140453193
C

7
140481417
A

7
140481428
C

7
140481449
G

7
140481478
A

7
148508727
A

8
38282147
A

8
38285864
A

8
38285891
C

8
38285938
A

9
5073770
T

9
5073781
A

9
21971000
A

9
21971017
A

9
21971028
T

9
21971036
A

9
21971111
A

9
21971120
A

9
21971153
A

9
21971186
A

9
80336317
A

9
80343489
TGTAC

9
80343605
G

9
80409345
G

9
80409432
TGC

9
80409533
T

Chromosome
Position
Length
Mutation ID
Gene

7
128846398
1
COSM216037
SMO

7
128846469
1
gDNA14
SMO

7
128850341
1
COSM13146
SMO

7
128851593
1
COSM13150
SMO

7
140453136
1
COSM476
BRAF

7
140453145
1
COSM471
BRAF

7
140453154
1
COSM467
BRAF

7
140453193
1
COSM462
BRAF

7
140481417
1
COSM450
BRAF

7
140481428
1
COSM27986
BRAF

7
140481449
1
COSM1448625
BRAF

7
140481478
1
COSM6262
BRAF

7
148508727
1
COSM37028
EZH2

8
38282147
1
COSM1292693
FGFR1

8
38285864
1
COSM187237
FGFR1

8
38285891
1
COSM1456955
FGFR1

8
38285938
1
COSM601
FGFR1

9
5073770
1
COSM12600
JAK2

9
5073781
1
COSM27063
JAK2

9
21971000
1
COSM12479
CDKN2A

9
21971017
1
COSM12476
CDKN2A

9
21971028
1
COSM12547
CDKN2A

9
21971036
1
COSM13489
CDKN2A

9
21971111
1
COSM12504
CDKN2A

9
21971120
1
COSM12475
CDKN2A

9
21971153
1
COSM13281
CDKN2A

9
21971186
1
COSM12473
CDKN2A

9
80336317
1
COSM1110323
GNAQ

9
80343489
4
AMXsynt6
GNAQ

9
80343605
12
AMXsynt7
GNAQ

9
80409345
1
gDNA17
GNAQ

9
80409432
3
AMXsynt8
GNAQ

9
80409533
41
AMXsynt9
GNAQ

Chromosome
Position
Mutation CDS

7
128846398
c.1234C > T

7
128846469
c.1264 + 41A > G

7
128850341
c.1604G > T

7
128851593
c.1918A > G

7
140453136
c.1799T > A

7
140453145
c.1790T > G

7
140453154
c.1781A > G

7
140453193
c.1742A > G

7
140481417
c.1391G > T

7
140481428
c.1380A > G

7
140481449
c.1359T > C

7
140481478
c.1330C > T

7
148508727
c.1937A > T

8
38282147
c.816C > T

8
38285864
c.448C > T

8
38285891
c.421A > G

8
38285938
c.374C > T

9
5073770
c.1849G > T

9
5073781
c.1860C > A

9
21971000
c.358G > T

9
21971017
c.341C > T

9
21971028
c.330G > A

9
21971036
c.322G > T

9
21971111
c.247C > T

9
21971120
c.238C > T

9
21971153
c.205G > T

9
21971186
c.172C > T

9
80336317
c.1002C > T

9
80343489
c.829_830insGTAC

9
80343605
c.736 − 34del12

9
80409345
c.735 + 34T > C

9
80409432
c.679_681TGT > GCA

9
80409533
c.606 − 66del41

Chromosome
Position
Mutation AA
Mutation Type
Strand
Target Frequency

7
128846398
p.L412F
SNV
+
15-35%

7
128846469
p.(=)
SNV
+
genomic

7
128850341
p.W535L
SNV
+
15-35%

7
128851593
p.T640A
SNV
+
15-35%

7
140453136
p.V600E
SNV
−
15-35%

7
140453145
p.L597R
SNV
−
15-35%

7
140453154
p.D594G
SNV
−
15-35%

7
140453193
p.N581S
SNV
−
15-35%

7
140481417
p.G464V
SNV
−
15-35%

7
140481428
p.G460G
SNV
−
15-35%

7
140481449
p.P453P
SNV
−
15-35%

7
140481478
p.R444W
SNV
−
15-35%

7
148508727
p.Y646F
SNV
−
15-35%

8
38282147
p.N272N
SNV
−
15-35%

8
38285864
p.P150S
SNV
−
15-35%

8
38285891
p.T141A
SNV
−
15-35%

8
38285938
p.S125L
SNV
−
15-35%

9
5073770
p.V617F
SNV
+
15-35%

9
5073781
p.D620E
SNV
+
15-35%

9
21971000
p.E120*
SNV
−
15-35%

9
21971017
p.P114L
SNV
−
15-35%

9
21971028
p.W110*
SNV
−
15-35%

9
21971036
p.D108Y
SNV
−
15-35%

9
21971111
p.H83Y
SNV
−
15-35%

9
21971120
p.R80*
SNV
−
15-35%

9
21971153
p.E69*
SNV
−
15-35%

9
21971186
p.R58*
SNV
−
15-35%

9
80336317
p.T334T
SNV
−
15-35%

9
80343489
p.D277fs*20
INS
−
15-35%

9
80343605
p.?
DEL
−
15-35%

9
80409345
p.(=)
SNV
−
genomic

9
80409432
p.M227_F228 > SI
MNV
−
15-35%

9
80409533
p.?
DEL
−
15-35%

Sanger
CHPv2
TSACP
TSTP

Chromosome
Position
Detection*
Detection
Detection
Detection

7
128846398
Detected
Detected
Detected
Not Covered

7
128846469
Not Covered
Not Covered
Detected
Not Covered

7
128850341
Detected
Detected
Detected
Not Covered

7
128851593
Detected
Detected
Detected
Not Covered

7
140453136
Detected
Detected
Detected
Detected

7
140453145
Detected
Detected
Detected
Detected

7
140453154
Detected
Detected
Detected
Detected

7
140453193
Detected
Detected
Detected
Detected

7
140481417
Detected
Detected
Detected
Detected

7
140481428
Detected
Detected
Detected
Detected

7
140481449
Detected
Detected
Detected
Detected

7
140481478
Detected
Detected
Detected
Detected

7
148508727
Detected
Detected
Not Covered
Not Covered

8
38282147
Detected
Detected
Not Covered
Not Covered

8
38285864
Detected
Detected
Not Covered
Not Covered

8
38285891
Detected
Detected
Not Covered
Not Covered

8
38285938
Detected
Detected
Detected
Not Covered

9
5073770
Detected
Detected
Detected
Not Covered

9
5073781
Detected
Detected
Detected
Not Covered

9
21971000
Detected
Detected
Not Covered
Not Covered

9
21971017
Detected
Detected
Not Covered
Not Covered

9
21971028
Detected
Detected
Not Covered
Not Covered

9
21971036
Detected
Detected
Not Covered
Not Covered

9
21971111
Detected
Detected
Not Covered
Not Covered

9
21971120
Detected
Detected
Not Covered
Not Covered

9
21971153
Detected
Detected
Not Detected
Not Covered

9
21971186
Detected
Detected
Detected
Not Covered

9
80336317
Detected
Not Covered
Detected
Not Covered

9
80343489
Detected
Not Covered
Detected
Detected

9
80343605
Detected
Not Covered
Detected
Not Detected

9
80409345
Not Covered
Not Covered
Detected
Not Covered

9
80409432
Detected
Detected
Detected
Detected

9
80409533
Detected
Not Covered
Not Detected
Not Detected

Chromosome
Position
Reference

9
80412493
C

9
80412518
T

9
133738342
C

9
133738349
G

9
133738357
T

9
133738363
G

9
133747520
A

9
133747571
T

9
133748391
T

9
133748403
A

9
133748414
T

9
133750319
C

9
133750356
A

9
139390779
G

9
139390804
CG

9
139390816
G

9
139390873
G

9
139397768
A

9
139397776
G

9
139399344
A

9
139399350
C

9
139399365
A

9
139399422
A

10
43609096
T

10
43609102
T

10
43609942
GAGCTGTGCCGCA (SEQ ID NO: 28)

10
43609990
G

10
43610039
C

10
43613840
G

10
43613843
G

10
43615568
GC

10
43615622
G

10
43617416
T

Chromosome
Position
Alternate

9
80412493
T

9
80412518
A

9
133738342
G

9
133738349
A

9
133738357
C

9
133738363
A

9
133747520
G

9
133747571
TGCC

9
133748391
C

9
133748403
G

9
133748414
G

9
133750319
A

9
133750356
G

9
139390779
T

9
139390804
C

9
139390816
A

9
139390873
A

9
139397768
G

9
139397776
A

9
139399344
G

9
139399350
G

9
139399365
G

9
139399422
G

10
43609096
C

10
43609102
C

10
43609942
AGCT

10
43609990
A

10
43610039
A

10
43613840
C

10
43613843
T

10
43615568
TT

10
43615622
A

10
43617416
C

Chromosome
Position
Length
Mutation ID
Gene

9
80412493
1
COSM52975
GNAQ

9
80412518
1
COSM1463119
GNAQ

9
133738342
1
COSM12631
ABL1

9
133738349
1
COSM12577
ABL1

9
133738357
1
COSM12576
ABL1

9
133738363
1
COSM12573
ABL1

9
133747520
1
COSM12602
ABL1

9
133747571
3
COSM235737
ABL1

9
133748391
1
COSM12578
ABL1

9
133748403
1
COSM12611
ABL1

9
133748414
1
COSM12605
ABL1

9
133750319
1
COSM49071
ABL1

9
133750356
1
COSM12604
ABL1

9
139390779
1
COSM87862
NOTCH1

9
139390804
1
COSM13070
NOTCH1

9
139390816
1
COSM12776
NOTCH1

9
139390873
1
COSM13061
NOTCH1

9
139397768
1
COSM13048
NOTCH1

9
139397776
1
COSM308587
NOTCH1

9
139399344
1
COSM12771
NOTCH1

9
139399350
1
COSM13053
NOTCH1

9
139399365
1
COSM13042
NOTCH1

9
139399422
1
COSM12772
NOTCH1

10
43609096
1
COSM29803
RET

10
43609102
1
COSM29804
RET

10
43609942
13
COSM1048
RET

10
43609990
1
COSM1223553
RET

10
43610039
1
COSM976
RET

10
43613840
1
COSM21338
RET

10
43613843
1
gDNA18
RET

10
43615568
3
COSM977
RET

10
43615622
1
COSM963
RET

10
43617416
1
COSM965
RET

Chromosome
Position
Mutation CDS

9
80412493
c.548G > A

9
80412518
c.523A > T

9
133738342
c.742C > G

9
133738349
c.749G > A

9
133738357
c.757T > C

9
133738363
c.763G > A

9
133747520
c.827A > G

9
133747571
c.878_879insGCC

9
133748391
c.1052T > C

9
133748403
c.1064A > G

9
133748414
c.1075T > G

9
133750319
c.1150C > A

9
133750356
c.1187A > G

9
139390779
c.7412C > A

9
139390804
c.7386delC

9
139390816
c.7375C > T

9
139390873
c.7318C > T

9
139397768
c.5033T > C

9
139397776
c.5025C > T

9
139399344
c.4799T > C

9
139399350
c.4793G > C

9
139399365
c.4778T > C

9
139399422
c.4721T > C

10
43609096
c.1852T > C

10
43609102
c.1858T > C

10
43609942
c.1894_1906 > AGCT

10
43609990
c.1942G > A

10
43610039
c.1991C > A

10
43613840
c.2304G > C

10
43613843
c.2307T > A

10
43615568
c.2647_2648GC > TT

10
43615622
c.2701G > A

10
43617416
c.2753T > C

Chromosome
Position
Mutation AA
Mutation Type
Strand
Target Frequency

9
80412493
p.R183Q
SNV
−
15-35%

9
80412518
p.T175S
SNV
−
15-35%

9
133738342
p.L248V
SNV
+
15-35%

9
133738349
p.G250E
SNV
+
15-35%

9
133738357
p.Y253H
SNV
+
15-35%

9
133738363
p.E255K
SNV
+
15-35%

9
133747520
p.D276G
SNV
+
15-35%

9
133747571
p.I293 > MP
INS
+
15-35%

9
133748391
p.M351T
SNV
+
15-35%

9
133748403
p.E355G
SNV
+
15-35%

9
133748414
p.F359V
SNV
+
15-35%

9
133750319
p.L384M
SNV
+
15-35%

9
133750356
p.H396R
SNV
+
15-35%

9
139390779
p.S2471*
SNV
−
15-35%

9
139390804
p.A2463fs*14
DEL
−
15-35%

9
139390816
p.Q2459*
SNV
−
15-35%

9
139390873
p.Q2440*
SNV
−
15-35%

9
139397768
p.L1678P
SNV
−
15-35%

9
139397776
p.11675I
SNV
−
15-35%

9
139399344
p.L1600P
SNV
−
15-35%

9
139399350
p.R1598P
SNV
−
15-35%

9
139399365
p.L1593P
SNV
−
15-35%

9
139399422
p.L1574P
SNV
−
15-35%

10
43609096
p.C618R
SNV
+
15-35%

10
43609102
p.C620R
SNV
+
15-35%

10
43609942
p.E632_T636 > SS
Complex
+
15-35%

10
43609990
p.V648I
SNV
+
15-35%

10
43610039
p.A664D
SNV
+
15-35%

10
43613840
p.E768D
SNV
+
15-35%

10
43613843
p.L769L
SNV
+
genomic

10
43615568
p.A883F
MNV
+
15-35%

10
43615622
p.E901K
SNV
+
15-35%

10
43617416
p.M918T
SNV
+
15-35%

Sanger
CHPv2

Chromosome
Position
Detection*
Detection
TSACP Detection
TSTP Detection

9
80412493
Detected
Not Covered
Detected
Detected

9
80412518
Detected
Not Covered
Detected
Detected

9
133738342
Detected
Detected
Detected
Not Covered

9
133738349
Detected
Detected
Detected
Not Covered

9
133738357
Detected
Detected
Detected
Not Covered

9
133738363
Detected
Detected
Detected
Not Covered

9
133747520
Detected
Detected
Detected
Not Covered

9
133747571
Detected
Not Covered
Detected
Not Covered

9
133748391
Detected
Detected
Detected
Not Covered

9
133748403
Detected
Detected
Detected
Not Covered

9
133748414
Detected
Detected
Detected
Not Covered

9
133750319
Detected
Detected
Not Covered
Not Covered

9
133750356
Detected
Detected
Detected
Not Covered

9
139390779
Detected
Detected
Not Covered
Not Covered

9
139390804
Detected
Not Detected
Not Covered
Not Covered

9
139390816
Detected
Detected
Not Covered
Not Covered

9
139390873
Detected
Detected
Not Covered
Not Covered

9
139397768
Detected
Detected
Detected
Not Covered

9
139397776
Detected
Detected
Detected
Not Covered

9
139399344
Detected
Detected
Detected
Not Covered

9
139399350
Detected
Detected
Detected
Not Covered

9
139399365
Detected
Detected
Detected
Not Covered

9
139399422
Detected
Detected
Detected
Not Covered

10
43609096
Detected
Detected
Detected
Not Covered

10
43609102
Detected
Detected
Detected
Not Covered

10
43609942
Detected
Detected
Detected
Not Covered

10
43609990
Detected
Detected
Detected
Not Covered

10
43610039
Detected
Not Covered
Detected
Not Covered

10
43613840
Detected
Detected
Detected
Not Covered

10
43613843
Not Covered
Detected
Detected
Not Covered

10
43615568
Detected
Detected
Detected
Not Covered

10
43615622
Detected
Detected
Detected
Not Covered

10
43617416
Detected
Detected
Detected
Not Covered

Chromosome
Position
Reference

10
89624245
G

10
89624266
A

10
89624275
C

10
89624297
A

10
89653686
A

10
89653782
A

10
89653814
C

10
89653844
A

10
89653858
T

10
89653865
A

10
89685271
T

10
89685307
T

10
89685319
G

10
89690805
G

10
89690818
TTA

10
89690838
A

10
89690847
G

10
89692779
A

10
89692818
T

10
89692830
G

10
89692850
C

10
89692911
G

10
89692965
A

10
89692980
A

10
89692993
G

10
89711855
CT

10
89711960
T

10
89711972
AGAT

10
89711992
C

10
89711997
G

10
89717672
C

10
89717678
G

10
89717696
T

Chromosome
Position
Alternate

10
89624245
T

10
89624266
G

10
89624275
T

10
89624297
G

10
89653686
G

10
89653782
G

10
89653814
T

10
89653844
G

10
89653858
C

10
89653865
G

10
89685271
G

10
89685307
C

10
89685319
A

10
89690805
A

10
89690818
T

10
89690838
C

10
89690847
A

10
89692779
G

10
89692818
C

10
89692830
T

10
89692850
G

10
89692911
A

10
89692965
G

10
89692980
G

10
89692993
T

10
89711855
C

10
89711960
C

10
89711972
A

10
89711992
A

10
89711997
A

10
89717672
T

10
89717678
T

10
89717696
C

Chromosome
Position
Length
Mutation ID
Gene

10
89624245
1
COSM5298
PTEN

10
89624266
1
COSM5101
PTEN

10
89624275
1
COSM5153
PTEN

10
89624297
1
COSM5107
PTEN

10
89653686
1
gDNA34
PTEN

10
89653782
1
COSM5134
PTEN

10
89653814
1
COSM5142
PTEN

10
89653844
1
COSM5050
PTEN

10
89653858
1
COSM1349479
PTEN

10
89653865
1
COSM5129
PTEN

10
89685271
1
COSM5257
PTEN

10
89685307
1
COSM5036
PTEN

10
89685319
1
COSM5916
PTEN

10
89690805
1
COSM5102
PTEN

10
89690818
2
COSM4956
PTEN

10
89690838
1
COSM5205
PTEN

10
89690847
1
COSM5983
PTEN

10
89692779
1
COSM5139
PTEN

10
89692818
1
COSM5109
PTEN

10
89692830
1
COSM5266
PTEN

10
89692850
1
COSM5199
PTEN

10
89692911
1
COSM5123
PTEN

10
89692965
1
COSM5130
PTEN

10
89692980
1
COSM5144
PTEN

10
89692993
1
COSM5287
PTEN

10
89711855
1
COSM5907
PTEN

10
89711960
1
COSM35406
PTEN

10
89711972
3
COSM4978
PTEN

10
89711992
1
COSM5279
PTEN

10
89711997
1
COSM5072
PTEN

10
89717672
1
COSM5154
PTEN

10
89717678
1
COSM5292
PTEN

10
89717696
1
COSM35849
PTEN

Chromosome
Position
Mutation CDS

10
89624245
c.19G > T

10
89624266
c.40A > G

10
89624275
c.49C > T

10
89624297
c.71A > G

10
89653686
c.80 − 96A > G

10
89653782
c.80A > G

10
89653814
c.112C > T

10
89653844
c.142A > G

10
89653858
c.156T > C

10
89653865
c.163A > G

10
89685271
c.166T > G

10
89685307
c.202T > C

10
89685319
c.209 + 5G > A

10
89690805
c.212G > A

10
89690818
c.227_228delAT

10
89690838
c.245A > C

10
89690847
c.253 + 1G > A

10
89692779
c.263A > G

10
89692818
c.302T > C

10
89692830
c.314G > T

10
89692850
c.334C > G

10
89692911
c.395G > A

10
89692965
c.449A > G

10
89692980
c.464A > G

10
89692993
c.477G > T

10
89711855
c.493 − 12delT

10
89711960
c.578T > C

10
89711972
c.595_597delATG

10
89711992
c.610C > A

10
89711997
c.615G > A

10
89717672
c.697C > T

10
89717678
c.703G > T

10
89717696
c.721T > C

Mutation

Target

Chromosome
Position
Mutation AA
Type
Strand
Frequency

10
89624245
p.E7*
SNV
+
15-35%

10
89624266
p.R14G
SNV
+
15-35%

10
89624275
p.Q17*
SNV
+
15-35%

10
89624297
p.D24G
SNV
+
15-35%

10
89653686
p.(=)
SNV
+
genomic

10
89653782
p.Y27C
SNV
+
15-35%

10
89653814
p.P38S
SNV
+
15-35%

10
89653844
p.N48D
SNV
+
15-35%

10
89653858
p.D52D
SNV
+
15-35%

10
89653865
p.R55G
SNV
+
15-35%

10
89685271
p.F56V
SNV
+
15-35%

10
89685307
p.Y68H
SNV
+
15-35%

10
89685319
p.?
SNV
+
15-35%

10
89690805
p.C71Y
SNV
+
15-35%

10
89690818
p.Y76fs*1
DEL
+
15-35%

10
89690838
p.N82T
SNV
+
15-35%

10
89690847
p.?
SNV
+
15-35%

10
89692779
p.Y88C
SNV
+
15-35%

10
89692818
p.I101T
SNV
+
15-35%

10
89692830
p.C105F
SNV
+
15-35%

10
89692850
p.L112V
SNV
+
15-35%

10
89692911
p.G132D
SNV
+
15-35%

10
89692965
p.E150G
SNV
+
15-35%

10
89692980
p.Y155C
SNV
+
15-35%

10
89692993
p.R159S
SNV
+
15-35%

10
89711855
p.?
DEL
+
15-35%

10
89711960
p.L193P
SNV
+
15-35%

10
89711972
p.M199del
DEL
+
15-35%

10
89711992
p.P204T
SNV
+
15-35%

10
89711997
p.M2051
SNV
+
15-35%

10
89717672
p.R233*
SNV
+
15-35%

10
89717678
p.E235*
SNV
+
15-35%

10
89717696
p.F241L
SNV
+
15-35%

Sanger
CHPv2
TSACP
TSTP

Chromosome
Position
Detection*
Detection
Detection
Detection

10
89624245
Detected
Detected
Detected
Detected

10
89624266
Detected
Detected
Detected
Detected

10
89624275
Detected
Detected
Detected
Detected

10
89624297
Detected
Detected
Detected
Detected

10
89653686
Not Covered
Not Covered
Not Covered
Detected

10
89653782
Detected
Not Covered
Not Covered
Detected

10
89653814
Detected
Not Covered
Not Covered
Detected

10
89653844
Detected
Not Covered
Not Covered
Detected

10
89653858
Detected
Not Covered
Not Covered
Detected

10
89653865
Detected
Not Covered
Not Covered
Detected

10
89685271
Detected
Detected
Not Covered
Detected

10
89685307
Detected
Detected
Detected
Detected

10
89685319
Detected
Detected
Detected
Detected

10
89690805
Detected
Not Covered
Not Covered
Detected

10
89690818
Detected
Not Covered
Not Covered
Detected

10
89690838
Detected
Not Covered
Not Covered
Detected

10
89690847
Detected
Not Covered
Not Covered
Detected

10
89692779
Detected
Not Covered
Not Covered
Detected

10
89692818
Detected
Detected
Not Covered
Detected

10
89692830
Detected
Detected
Not Covered
Detected

10
89692850
Detected
Detected
Not Covered
Detected

10
89692911
Detected
Detected
Not Covered
Detected

10
89692965
Detected
Not Covered
Not Covered
Detected

10
89692980
Detected
Not Covered
Not Covered
Detected

10
89692993
Detected
Not Covered
Not Covered
Detected

10
89711855
Detected
Detected
Not Covered
Not Detected

10
89711960
Detected
Not Covered
Detected
Detected

10
89711972
Detected
Not Covered
Detected
Detected

10
89711992
Detected
Not Covered
Detected
Detected

10
89711997
Detected
Not Covered
Detected
Detected

10
89717672
Detected
Detected
Detected
Detected

10
89717678
Detected
Detected
Detected
Detected

10
89717696
Detected
Detected
Detected
Detected

Chromosome
Position
Reference

10
89717762
A

10
89717769
TA

10
89720728
A

10
89720744
G

10
89720798
GTACT

10
89720874
A

10
89720907
T

10
89725042
A

10
89725056
TTC

10
89725072
A

10
89725108
C

10
123258034
A

10
123274774
A

10
123274794
T

10
123274810
T

10
123279503
T

10
123279519
C

10
123279677
G

11
533874
T

11
533881
C

11
534242
A

11
534288
C

11
108117798
C

11
108119823
T

11
108123551
C

11
108123641
T

11
108138003
T

11
108155132
G

11
108170479
G

11
108170587
C

11
108172374
G

11
108172385
C

11
108172421
G

Chromosome
Position
Alternate

10
89717762
T

10
89717769
T

10
89720728
G

10
89720744
T

10
89720798
G

10
89720874
G

10
89720907
G

10
89725042
G

10
89725056
T

10
89725072
G

10
89725108
G

10
123258034
T

10
123274774
G

10
123274794
C

10
123274810
C

10
123279503
C

10
123279519
T

10
123279677
C

11
533874
C

11
533881
T

11
534242
G

11
534288
A

11
108117798
T

11
108119823
C

11
108123551
T

11
108123641
A

11
108138003
C

11
108155132
A

11
108170479
T

11
108170587
G

11
108172374
T

11
108172385
T

11
108172421
C

Chromosome
Position
Length
Mutation ID
Gene

10
89717762
1
COSM43075
PTEN

10
89717769
1
COSM5809
PTEN

10
89720728
1
COSM1349606
PTEN

10
89720744
1
COSM5312
PTEN

10
89720798
4
COSM4958
PTEN

10
89720874
1
COSM1349625
PTEN

10
89720907
1
gDNA19
PTEN

10
89725042
1
COSM5966
PTEN

10
89725056
2
COSM4936
PTEN

10
89725072
1
COSM1349633
PTEN

10
89725108
1
COSM23645
PTEN

10
123258034
1
COSM36912
FGFR2

10
123274774
1
COSM36906
FGFR2

10
123274794
1
COSM36904
FGFR2

10
123274810
1
COSM1346272
FGFR2

10
123279503
1
COSM36901
FGFR2

10
123279519
1
COSM29824
FGFR2

10
123279677
1
COSM36903
FGFR2

11
533874
1
COSM499
HRAS

11
533881
1
COSM495
HRAS

11
534242
1
gDNA20, COSM249860
HRAS

11
534288
1
COSM483
HRAS

11
108117798
1
COSM21323
ATM

11
108119823
1
COSM21825
ATM

11
108123551
1
COSM22499
ATM

11
108123641
1
COSM1158828
ATM

11
108138003
1
COSM21826
ATM

11
108155132
1
COSM22507
ATM

11
108170479
1
COSM21920
ATM

11
108170587
1
COSM218294
ATM

11
108172374
1
COSM49005
ATM

11
108172385
1
COSM172204
ATM

11
108172421
1
COSM21918
ATM

Chromosome
Position
Mutation CDS

10
89717762
c.787A > T

10
89717769
c.800delA

10
89720728
c.879A > G

10
89720744
c.895G > T

10
89720798
c.955_958delACTT

10
89720874
c.1025A > G

10
89720907
c.1026 + 32T > G

10
89725042
c.1027 − 2A > G

10
89725056
c.1040_1041delTC

10
89725072
c.1055A > G

10
89725108
c.1091C > G

10
123258034
c.1647T > A

10
123274774
c.1144T > C

10
123274794
c.1124A > G

10
123274810
c.1108A > G

10
123279503
c.929A > G

10
123279519
c.913G > A

10
123279677
c.755C > G

11
533874
c.182A > G

11
533881
c.175G > A

11
534242
c.81T > C

11
534288
c.35G > T

11
108117798
c.1009C > T

11
108119823
c.1229T > C

11
108123551
c.1810C > T

11
108123641
c.1898 + 2T > A

11
108138003
c.2572T > C

11
108155132
c.3925G > A

11
108170479
c.5044G > T

11
108170587
c.5152C > G

11
108172374
c.5178 − 1G > T

11
108172385
c.5188C > T

11
108172421
c.5224G > C

Mutation

Target

Chromosome
Position
Mutation AA
Type
Strand
Frequency

10
89717762
p.K263*
SNV
+
15-35%

10
89717769
p.K267fs*9
DEL
+
15-35%

10
89720728
p.G293G
SNV
+
15-35%

10
89720744
p.E299*
SNV
+
15-35%

10
89720798
p.T319fs*1
DEL
+
15-35%

10
89720874
p.K342R
SNV
+
15-35%

10
89720907
p.(=)
SNV
+
genomic

10
89725042
p.?
SNV
+
15-35%

10
89725056
p.F347fs*13
DEL
+
15-35%

10
89725072
p.E352G
SNV
+
15-35%

10
89725108
p.S364C
SNV
+
15-35%

10
123258034
p.N549K
SNV
−
5-15%

10
123274774
p.C382R
SNV
−
5-15%

10
123274794
p.Y375C
SNV
−
5-15%

10
123274810
p.T370A
SNV
−
5-15%

10
123279503
p.K310R
SNV
−
5-15%

10
123279519
p.G305R
SNV
−
5-15%

10
123279677
p.S252W
SNV
−
5-15%

11
533874
p.Q61R
SNV
−
5-15%

11
533881
p.A59T
SNV
−
5-15%

11
534242
p.H27H
SNV
−
genomic

11
534288
p.G12V
SNV
−
5-15%

11
108117798
p.R337C
SNV
+
5-15%

11
108119823
p.V410A
SNV
+
5-15%

11
108123551
p.P604S
SNV
+
5-15%

11
108123641
p.?
SNV
+
5-15%

11
108138003
p.F858L
SNV
+
5-15%

11
108155132
p.A1309T
SNV
+
5-15%

11
108170479
p.D1682Y
SNV
+
5-15%

11
108170587
p.L1718V
SNV
+
5-15%

11
108172374
p.?
SNV
+
5-15%

11
108172385
p.R1730*
SNV
+
5-15%

11
108172421
p.A1742P
SNV
+
5-15%

Sanger
CHPv2
TSACP
TSTP

Chromosome
Position
Detection*
Detection
Detection
Detection

10
89717762
Detected
Detected
Detected
Detected

10
89717769
Detected
Detected
Detected
Detected

10
89720728
Detected
Detected
Detected
Not Covered

10
89720744
Detected
Detected
Detected
Not Covered

10
89720798
Detected
Detected
Detected
Not Covered

10
89720874
Detected
Detected
Detected
Not Covered

10
89720907
Not Covered
Not Covered
Detected
Not Covered

10
89725042
Detected
Not Covered
Not Covered
Detected

10
89725056
Detected
Not Covered
Not Covered
Detected

10
89725072
Detected
Not Covered
Not Covered
Detected

10
89725108
Detected
Not Covered
Not Covered
Detected

10
123258034
Detected
Detected
Detected
Not Covered

10
123274774
Detected
Detected
Detected
Not Covered

10
123274794
Detected
Detected
Detected
Not Covered

10
123274810
Detected
Detected
Detected
Not Covered

10
123279503
Detected
Detected
Detected
Detected

10
123279519
Detected
Detected
Detected
Detected

10
123279677
Detected
Detected
Detected
Detected

11
533874
Detected
Detected
Detected
Not Covered

11
533881
Detected
Detected
Detected
Not Covered

11
534242
Not Covered
Detected
Not Covered
Not Covered

11
534288
Detected
Detected
Detected
Not Covered

11
108117798
Detected
Detected
Not Covered
Not Covered

11
108119823
Detected
Detected
Detected
Not Covered

11
108123551
Detected
Detected
Detected
Not Covered

11
108123641
Detected
Not Covered
Detected
Not Covered

11
108138003
Detected
Detected
Detected
Not Covered

11
108155132
Detected
Detected
Not Detected
Not Covered

11
108170479
Detected
Detected
Detected
Not Covered

11
108170587
Detected
Not Covered
Detected
Not Covered

11
108172374
Detected
Detected
Not Covered
Not Covered

11
108172385
Detected
Detected
Not Covered
Not Covered

11
108172421
Detected
Detected
Detected
Not Covered

Chromosome
Position
Reference

11
108173640
C

11
108173736
T

11
108180945
G

11
108200958
A

11
108204681
A

11
108205769
G

11
108205780
C

11
108206594
A

11
108218045
A

11
108218089
C

11
108218196
T

11
108225590
A

11
108225661
A

11
108236087
G

11
108236118
A

11
108236203
C

12
25362805
C

12
25378647
T

12
25380275
T

12
25380283
C

12
25398207
C

12
25398215
G

12
25398284
C

12
25398295
T

12
112888165
G

12
112888189
G

12
112888199
C

12
112888210
G

12
112926852
C

12
112926888
G

12
112926899
A

12
112926908
C

12
121431413
G

Chromosome
Position
Alternate

11
108173640
T

11
108173736
G

11
108180945
C

11
108200958
C

11
108204681
G

11
108205769
C

11
108205780
A

11
108206594
T

11
108218045
G

11
108218089
G

11
108218196
C

11
108225590
T

11
108225661
G

11
108236087
A

11
108236118
G

11
108236203
T

12
25362805
T

12
25378647
G

12
25380275
G

12
25380283
T

12
25398207
A

12
25398215
A

12
25398284
T

12
25398295
C

12
112888165
T

12
112888189
A

12
112888199
T

12
112888210
A

12
112926852
T

12
112926888
C

12
112926899
G

12
112926908
A

12
121431413
T

Chromosome
Position
Length
Mutation ID
Gene

11
108173640
1
COSM12792
ATM

11
108173736
1
COSM1183962
ATM

11
108180945
1
COSM21922
ATM

11
108200958
1
COSM12951
ATM

11
108204681
1
COSM12791
ATM

11
108205769
1
COSM21636
ATM

11
108205780
1
COSM1235404
ATM

11
108206594
1
COSM22481
ATM

11
108218045
1
COSM1183939
ATM

11
108218089
1
COSM22485
ATM

11
108218196
1
gDNA21
ATM

11
108225590
1
COSM21930
ATM

11
108225661
1
gDNA22
ATM

11
108236087
1
COSM21626
ATM

11
108236118
1
COSM1351060
ATM

11
108236203
1
COSM21624
ATM

12
25362805
1
COSM41307
KRAS

12
25378647
1
COSM19940
KRAS

12
25380275
1
COSM554
KRAS

12
25380283
1
COSM546
KRAS

12
25398207
1
AMXsynt11
KRAS

12
25398215
1
COSM14208
KRAS

12
25398284
1
COSM521
KRAS

12
25398295
1
COSM507
KRAS

12
112888165
1
COSM13011
PTPN11

12
112888189
1
COSM13013
PTPN11

12
112888199
1
COSM13015
PTPN11

12
112888210
1
COSM13000
PTPN11

12
112926852
1
COSM13034
PTPN11

12
112926888
1
COSM13027
PTPN11

12
112926899
1
COSM1358900
PTPN11

12
112926908
1
COSM13031
PTPN11

12
121431413
1
COSM21471
HNF1A

Chromosome
Position
Mutation CDS

11
108173640
c.5380C > T

11
108173736
c.5476T > G

11
108180945
c.5821G > C

11
108200958
c.7325A > C

11
108204681
c.7996A > G

11
108205769
c.8084G > C

11
108205780
c.8095C > A

11
108206594
c.8174A > T

11
108218045
c.8624A > G

11
108218089
c.8668C > G

11
108218196
c.8671 + 104T > C

11
108225590
c.8839A > T

11
108225661
c.8850 + 60A > G

11
108236087
c.9023G > A

11
108236118
c.9054A > G

11
108236203
c.9139C > T

12
25362805
c.491G > A

12
25378647
c.351A > C

12
25380275
c.183A > C

12
25380283
c.175G > A

12
25398207
c.111 + 1C > T

12
25398215
c.104C > T

12
25398284
c.35G > A

12
25398295
c.24A > G

12
112888165
c.181G > T

12
112888189
c.205G > A

12
112888199
c.215C > T

12
112888210
c.226G > A

12
112926852
c.1472C > T

12
112926888
c.1508G > C

12
112926899
c.1519A > G

12
112926908
c.1528C > A

12
121431413
c.617G > T

Mutation

Target

Chromosome
Position
Mutation AA
Type
Strand
Frequency

11
108173640
p.L1794L
SNV
+
5-15%

11
108173736
p.L1826V
SNV
+
5-15%

11
108180945
p.V1941L
SNV
+
5-15%

11
108200958
p.Q2442P
SNV
+
5-15%

11
108204681
p.T2666A
SNV
+
5-15%

11
108205769
p.G2695A
SNV
+
5-15%

11
108205780
p.P2699T
SNV
+
5-15%

11
108206594
p.D2725V
SNV
+
5-15%

11
108218045
p.N2875S
SNV
+
5-15%

11
108218089
p.L2890V
SNV
+
5-15%

11
108218196
p.(=)
SNV
+
genomic

11
108225590
p.T2947S
SNV
+
5-15%

11
108225661
p.(=)
SNV
+
genomic

11
108236087
p.R3008H
SNV
+
5-15%

11
108236118
p.K3018K
SNV
+
5-15%

11
108236203
p.R3047*
SNV
+
5-15%

12
25362805
p.R164Q
SNV
−
5-15%

12
25378647
p.K117N
SNV
−
5-15%

12
25380275
p.Q61H
SNV
−
5-15%

12
25380283
p.A59T
SNV
−
5-15%

12
25398207
p.?
SNV
−
5-15%

12
25398215
p.T35I
SNV
−
5-15%

12
25398284
p.G12D
SNV
−
5-15%

12
25398295
p.V8V
SNV
−
5-15%

12
112888165
p.D61Y
SNV
+
5-15%

12
112888189
p.E69K
SNV
+
5-15%

12
112888199
p.A72V
SNV
+
5-15%

12
112888210
p.E76K
SNV
+
5-15%

12
112926852
p.P491L
SNV
+
5-15%

12
112926888
p.G503A
SNV
+
5-15%

12
112926899
p.T507A
SNV
+
5-15%

12
112926908
p.Q510K
SNV
+
5-15%

12
121431413
p.W206L
SNV
+
5-15%

Sanger
CHPv2
TSACP
TSTP

Chromosome
Position
Detection*
Detection
Detection
Detection

11
108173640
Detected
Detected
Detected
Not Covered

11
108173736
Detected
Not Covered
Detected
Not Covered

11
108180945
Detected
Detected
Detected
Not Covered

11
108200958
Detected
Detected
Detected
Not Covered

11
108204681
Detected
Detected
Detected
Not Covered

11
108205769
Detected
Detected
Detected
Not Covered

11
108205780
Detected
Detected
Detected
Not Covered

11
108206594
Detected
Detected
Detected
Not Covered

11
108218045
Detected
Detected
Not Covered
Not Covered

11
108218089
Detected
Detected
Detected
Not Covered

11
108218196
Not Covered
Not Covered
Detected
Not Covered

11
108225590
Detected
Detected
Detected
Not Covered

11
108225661
Not Covered
Not Covered
Detected
Not Covered

11
108236087
Detected
Detected
Detected
Not Covered

11
108236118
Detected
Detected
Detected
Not Covered

11
108236203
Detected
Detected
Detected
Not Covered

12
25362805
Detected
Not Covered
Not Covered
Detected

12
25378647
Detected
Detected
Detected
Detected

12
25380275
Detected
Detected
Detected
Detected

12
25380283
Detected
Detected
Detected
Detected

12
25398207
Detected
Detected
Not Covered
Detected

12
25398215
Detected
Detected
Not Covered
Detected

12
25398284
Detected
Detected
Detected
Detected

12
25398295
Detected
Detected
Detected
Detected

12
112888165
Detected
Detected
Detected
Not Covered

12
112888189
Detected
Detected
Detected
Not Covered

12
112888199
Detected
Detected
Detected
Not Covered

12
112888210
Detected
Detected
Detected
Not Covered

12
112926852
Detected
Detected
Not Covered
Not Covered

12
112926888
Detected
Detected
Detected
Not Covered

12
112926899
Detected
Detected
Detected
Not Covered

12
112926908
Detected
Detected
Detected
Not Covered

12
121431413
Detected
Detected
Detected
Not Covered

Chromosome
Position
Reference

12
121431428
A

12
121431481
C

12
121431506
A

12
121432032
C

12
121432040
C

12
121432117
G

12
121432117
G

13
28592629
T

13
28592642
C

13
28592653
C

13
28602329
G

13
28608255
G

13
28608281
A

13
28610138
G

13
28610183
A

13
48919244
G

13
48923148
T

13
48941628
A

13
48941648
C

13
48941658
A

13
48941672
A

13
48942685
C

13
48953760
C

13
48955538
C

13
48955550
C

13
48955571
T

13
49027168
C

13
49027249
T

13
49033890
TAGAACATATCATC (SEQ ID NO: 29)

13
49033916
C

13
49033926
T

13
49037865
A

13
49037877
G

Chromosome
Position
Alternate

12
121431428
C

12
121431481
T

12
121431506
G

12
121432032
T

12
121432040
T

12
121432117
GC

12
121432117
C

13
28592629
C

13
28592642
A

13
28592653
T

13
28602329
A

13
28608255
GATCATATTCATATTCTCTGAA (SEQ ID NO: 30)

13
28608281
G

13
28610138
A

13
28610183
G

13
48919244
T

13
48923148
A

13
48941628
T

13
48941648
T

13
48941658
G

13
48941672
G

13
48942685
T

13
48953760
T

13
48955538
T

13
48955550
T

13
48955571
C

13
49027168
T

13
49027249
C

13
49033890
T

13
49033916
T

13
49033926
C

13
49037865
G

13
49037877
T

Chromosome
Position
Length
Mutation ID
Gene

12
121431428
1
COSM24900
HNF1A

12
121431481
1
COSM24832
HNF1A

12
121431506
1
COSM21474
HNF1A

12
121432032
1
COSM24923
HNF1A

12
121432040
1
COSM24692
HNF1A

12
121432117
1
COSM21481
HNF1A

12
121432117
1
gDNA23
HNF1A

13
28592629
1
COSM1166729
FLT3

13
28592642
1
COSM783
FLT3

13
28592653
1
COSM25248
FLT3

13
28602329
1
COSM786
FLT3

13
28608255
21
COSM27907
FLT3

13
28608281
1
COSM19522
FLT3

13
28610138
1
COSM28042
FLT3

13
28610183
1
gDNA24
FLT3

13
48919244
1
COSM890
RB1

13
48923148
1
COSM915
RB1

13
48941628
1
COSM28816
RB1

13
48941648
1
COSM891
RB1

13
48941658
1
COSM1367204
RB1

13
48941672
1
COSM1367206
RB1

13
48942685
1
COSM879
RB1

13
48953760
1
COSM895
RB1

13
48955538
1
COSM887
RB1

13
48955550
1
COSM888
RB1

13
48955571
1
COSM1367255
RB1

13
49027168
1
COSM892
RB1

13
49027249
1
COSM35483
RB1

13
49033890
13
COSM870
RB1

13
49033916
1
COSM13117
RB1

13
49033926
1
COSM942
RB1

13
49037865
1
COSM1042
RB1

13
49037877
1
COSM883
RB1

Chromosome
Position
Mutation CDS

12
121431428
c.632A > C

12
121431481
c.685C > T

12
121431506
c.710A > G

12
121432032
c.779C > T

12
121432040
c.787C > T

12
121432117
c.872_873insC

12
121432117
c.864G > C

13
28592629
c.2516A > G

13
28592642
c.2503G > T

13
28592653
c.2492G > A

13
28602329
c.2039C > T

13
28608255
c.1800_1801insTTCAGAGAATATGAATATGAT (SEQ ID

NO: 31)

13
28608281
c.1775T > C

13
28610138
c.1352C > T

13
28610183
c.1310 − 3T > C

13
48919244
c.409G > T

13
48923148
c.596T > A

13
48941628
c.940 − 2A > T

13
48941648
c.958C > T

13
48941658
c.968A > G

13
48941672
c.982A > G

13
48942685
c.1072C > T

13
48953760
c.1363C > T

13
48955538
c.1654C > T

13
48955550
c.1666C > T

13
48955571
c.1687T > C

13
49027168
c.1735C > T

13
49027249
c.1814 + 2T > C

13
49033890
c.2028_2040del13

13
49033916
c.2053C > T

13
49033926
c.2063T > C

13
49037865
c.2107 − 2A > G

13
49037877
c.2117G > T

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

12
121431428
p.Q211P
SNV
+
5-15%
Detected

12
121431481
p.R229*
SNV
+
5-15%
Detected

12
121431506
p.N237S
SNV
+
5-15%
Detected

12
121432032
p.T260M
SNV
+
5-15%
Detected

12
121432040
p.R263C
SNV
+
5-15%
Detected

12
121432117
p.G292fs*25
INS
+
5-15%
Detected

12
121432117
p.G288G
SNV
+
genomic
Not Covered

13
28592629
p.D839G
SNV
−
5-15%
Detected

13
28592642
p.D835Y
SNV
−
5-15%
Detected

13
28592653
p.G831E
SNV
−
5-15%
Detected

13
28602329
p.A680V
SNV
−
5-15%
Detected

13
28608255
p.D600_L60linsFREYEYD
INS
−
5-15%
Detected

13
28608281
p.V592A
SNV
−
5-15%
Detected

13
28610138
p.S451F
SNV
−
5-15%
Detected

13
28610183
p.?
SNV
−
genomic
Not Covered

13
48919244
p.E137*
SNV
+
5-15%
Detected

13
48923148
p.L199*
SNV
+
5-15%
Detected

13
48941628
p.?
SNV
+
5-15%
Detected

13
48941648
p.R320*
SNV
+
5-15%
Detected

13
48941658
p.E323G
SNV
+
5-15%
Detected

13
48941672
p.N328D
SNV
+
5-15%
Detected

13
48942685
p.R358*
SNV
+
5-15%
Detected

13
48953760
p.R455*
SNV
+
5-15%
Detected

13
48955538
p.R552*
SNV
+
5-15%
Detected

13
48955550
p.R556*
SNV
+
5-15%
Detected

13
48955571
p.W563R
SNV
+
5-15%
Detected

13
49027168
p.R579*
SNV
+
5-15%
Detected

13
49027249
p.?
SNV
+
5-15%
Detected

13
49033890
p.L676fs*16
DEL
+
5-15%
Detected

13
49033916
p.Q685*
SNV
+
5-15%
Detected

13
49033926
p.L688P
SNV
+
5-15%
Detected

13
49037865
p.?
SNV
+
5-15%
Detected

13
49037877
p.C706F
SNV
+
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

12
121431428
Detected
Detected
Not Covered

12
121431481
Not Covered
Detected
Not Covered

12
121431506
Not Covered
Detected
Not Covered

12
121432032
Detected
Not Covered
Not Covered

12
121432040
Detected
Not Covered
Not Covered

12
121432117
Not Covered
Detected
Not Covered

12
121432117
Not Covered
Detected
Not Covered

13
28592629
Detected
Detected
Not Covered

13
28592642
Detected
Detected
Not Covered

13
28592653
Detected
Detected
Not Covered

13
28602329
Detected
Detected
Not Covered

13
28608255
Not Detected
Not Detected
Not Covered

13
28608281
Detected
Detected
Not Covered

13
28610138
Detected
Detected
Not Covered

13
28610183
Detected
Detected
Not Covered

13
48919244
Detected
Detected
Not Covered

13
48923148
Detected
Detected
Not Covered

13
48941628
Detected
Not Covered
Not Covered

13
48941648
Detected
Not Covered
Not Covered

13
48941658
Detected
Not Covered
Not Covered

13
48941672
Detected
Not Covered
Not Covered

13
48942685
Detected
Detected
Not Covered

13
48953760
Detected
Not Covered
Not Covered

13
48955538
Detected
Detected
Not Covered

13
48955550
Detected
Detected
Not Covered

13
48955571
Detected
Detected
Not Covered

13
49027168
Detected
Detected
Not Covered

13
49027249
Not Covered
Detected
Not Covered

13
49033890
Detected
Detected
Not Covered

13
49033916
Detected
Detected
Not Covered

13
49033926
Detected
Detected
Not Covered

13
49037865
Detected
Detected
Not Covered

13
49037877
Detected
Detected
Not Covered

Chromosome
Position
Reference

13
49037903
A

13
49037913
A

13
49039164
G

13
49039183
T

13
49039189
A

13
49039215
A

14
105246551
C

15
66727455
G

15
66727483
G

15
90631838
C

15
90631879
T

15
90631934
C

16
68835650
GGTGTGATTACAGTCAAAAGGCCTCTACGGT (SEQ ID NO: 32)

16
68846087
A

16
68846137
G

16
68847282
G

16
68855924
A

16
68855934
T

16
68855966
G

16
68856041
G

16
68856093
C

16
68856105
G

17
7572962
GT

17
7572986
G

17
7573010
T

17
7574003
G

17
7574012
C

17
7574018
G

17
7574026
C

17
7576855
G

17
7576865
A

17
7576883
T

17
7576897
G

Chromosome
Position
Alternate

13
49037903
T

13
49037913
G

13
49039164
T

13
49039183
G

13
49039189
G

13
49039215
T

14
105246551
T

15
66727455
T

15
66727483
A

15
90631838
T

15
90631879
C

15
90631934
T

16
68835650
G

16
68846087
G

16
68846137
C

16
68847282
A

16
68855924
AC

16
68855934
C

16
68855966
A

16
68856041
A

16
68856093
T

16
68856105
A

17
7572962
G

17
7572986
A

17
7573010
C

17
7574003
A

17
7574012
A

17
7574018
A

17
7574026
A

17
7576855
A

17
7576865
C

17
7576883
C

17
7576897
A

Chromosome
Position
Length
Mutation ID
Gene

13
49037903
1
COSM940
RB1

13
49037913
1
COSM1367309
RB1

13
49039164
1
COSM868
RB1

13
49039183
1
COSM916
RB1

13
49039189
1
COSM551465
RB1

13
49039215
1
COSM254910
RB1

14
105246551
1
COSM33765
AKT1

15
66727455
1
COSM1235478
MAP2K1

15
66727483
1
COSM1235479
MAP2K1

15
90631838
1
COSM33733
IDH2

15
90631879
1
COSM1375400
IDH2

15
90631934
1
COSM41590
IDH2

16
68835650
30
AMXsynt10
CDH1

16
68846087
1
COSM1379165
CDH1

16
68846137
1
COSM19748
CDH1

16
68847282
1
COSM19750
CDH1

16
68855924
1
COSM25267
CDH1

16
68855934
1
COSM19746
CDH1

16
68855966
1
COSM19758
CDH1

16
68856041
1
COSM19743
CDH1

16
68856093
1
COSM19822
CDH1

16
68856105
1
COSM19418
CDH1

17
7572962
1
COSM13747
TP53

17
7572986
1
COSM307348
TP53

17
7573010
1
COSM1191161
TP53

17
7574003
1
COSM11073
TP53

17
7574012
1
COSM11286
TP53

17
7574018
1
COSM11071
TP53

17
7574026
1
COSM11514
TP53

17
7576855
1
COSM11354
TP53

17
7576865
1
COSM44823
TP53

17
7576883
1
COSM46088
TP53

17
7576897
1
COSM10786
TP53

Chromosome
Position
Mutation CDS

13
49037903
c.2143A > T

13
49037913
c.2153A > G

13
49039164
c.2242G > T

13
49039183
c.2261T > G

13
49039189
c.2267A > G

13
49039215
c.2293A > T

14
105246551
c.49G > A

15
66727455
c.171G > T

15
66727483
c.199G > A

15
90631838
c.515G > A

15
90631879
c.474A > G

15
90631934
c.419G > A

16
68835650
c.241del30

16
68846087
c.1058A > G

16
68846137
c.1108G > C

16
68847282
c.1204G > A

16
68855924
c.1733_1734insC

16
68855934
c.1742T > C

16
68855966
c.1774G > A

16
68856041
c.1849G > A

16
68856093
c.1901C > T

16
68856105
c.1913G > A

17
7572962
c.1146delA

17
7572986
c.1123C > T

17
7573010
c.1101 − 2A > G

17
7574003
c.1024C > T

17
7574012
c.1015G > T

17
7574018
c.1009C > T

17
7574026
c.1001G > T

17
7576855
c.991C > T

17
7576865
c.981T > G

17
7576883
c.963A > G

17
7576897
c.949C > T

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

13
49037903
p.K715*
SNV
+
5-15%
Detected

13
49037913
p.D718G
SNV
+
5-15%
Detected

13
49039164
p.E748*
SNV
+
5-15%
Detected

13
49039183
p.V754G
SNV
+
5-15%
Detected

13
49039189
p.Y756C
SNV
+
5-15%
Detected

13
49039215
p.K765*
SNV
+
5-15%
Detected

14
105246551
p.E17K
SNV
−
5-15%
Detected

15
66727455
p.K57N
SNV
+
5-15%
Detected

15
66727483
p.D67N
SNV
+
5-15%
Detected

15
90631838
p.R172K
SNV
−
5-15%
Detected

15
90631879
p.P158P
SNV
−
5-15%
Detected

15
90631934
p.R140Q
SNV
−
5-15%
Detected

16
68835650
p.G81_F91del
DEL
+
5-15%
Detected

16
68846087
p.E353G
SNV
+
5-15%
Detected

16
68846137
p.D370H
SNV
+
5-15%
Detected

16
68847282
p.D402N
SNV
+
5-15%
Detected

16
68855924
p.G579fs*9
INS
+
5-15%
Detected

16
68855934
p.L581P
SNV
+
5-15%
Detected

16
68855966
p.A592T
SNV
+
5-15%
Detected

16
68856041
p.A617T
SNV
+
5-15%
Detected

16
68856093
p.A634V
SNV
+
5-15%
Detected

16
68856105
p.W638*
SNV
+
5-15%
Detected

17
7572962
p.K382fs* > 12
DEL
−
5-15%
Detected

17
7572986
p.Q375*
SNV
−
5-15%
Detected

17
7573010
p.?
SNV
−
5-15%
Detected

17
7574003
p.R342*
SNV
−
5-15%
Detected

17
7574012
p.E339*
SNV
−
5-15%
Detected

17
7574018
p.R337C
SNV
−
5-15%
Detected

17
7574026
p.G334V
SNV
−
5-15%
Detected

17
7576855
p.Q331*
SNV
−
5-15%
Detected

17
7576865
p.Y327*
SNV
−
5-15%
Detected

17
7576883
p.K321K
SNV
−
5-15%
Detected

17
7576897
p.Q317*
SNV
−
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

13
49037903
Detected
Detected
Not Covered

13
49037913
Detected
Detected
Not Covered

13
49039164
Detected
Detected
Not Covered

13
49039183
Detected
Detected
Not Covered

13
49039189
Detected
Detected
Not Covered

13
49039215
Detected
Detected
Not Covered

14
105246551
Detected
Detected
Detected

15
66727455
Not Covered
Not Covered
Detected

15
66727483
Not Covered
Not Covered
Detected

15
90631838
Detected
Not Covered
Not Covered

15
90631879
Detected
Not Covered
Not Covered

15
90631934
Detected
Not Covered
Not Covered

16
68835650
Not Detected
Not Detected
Not Covered

16
68846087
Detected
Not Covered
Detected

16
68846137
Detected
Detected
Detected

16
68847282
Detected
Detected
Detected

16
68855924
Not Covered
Not Covered
Detected

16
68855934
Not Covered
Not Covered
Detected

16
68855966
Not Covered
Not Covered
Detected

16
68856041
Not Covered
Not Covered
Detected

16
68856093
Not Covered
Not Covered
Detected

16
68856105
Not Covered
Not Covered
Detected

17
7572962
Not Covered
Not Covered
Detected

17
7572986
Not Covered
Not Covered
Detected

17
7573010
Not Covered
Not Covered
Detected

17
7574003
Detected
Detected
Detected

17
7574012
Detected
Detected
Detected

17
7574018
Detected
Detected
Detected

17
7574026
Detected
Detected
Detected

17
7576855
Not Covered
Not Covered
Detected

17
7576865
Not Covered
Not Covered
Detected

17
7576883
Not Covered
Not Covered
Detected

17
7576897
Not Covered
Not Covered
Detected

Chromosome
Position
Reference

17
7577022
G

17
7577046
C

17
7577105
G

17
7577120
C

17
7577538
C

17
7577548
C

17
7577559
G

17
7577580
T

17
7578115
T

17
7578190
T

17
7578196
A

17
7578203
C

17
7578235
T

17
7578388
C

17
7578442
T

17
7578449
C

17
7578461
C

17
7578526
C

17
7578535
T

17
7578542
G

17
7578550
G

17
7579295
C

17
7579312
C

17
7579358
C

17
7579368
A

17
7579414
C

17
7579442
G

17
7579472
G

17
7579521
C

17
7579536
C

17
7579553
A

17
7579575
G

17
7579715
AG

Chromosome
Position
Alternate

17
7577022
A

17
7577046
A

17
7577105
A

17
7577120
T

17
7577538
T

17
7577548
T

17
7577559
A

17
7577580
C

17
7578115
C

17
7578190
C

17
7578196
T

17
7578203
T

17
7578235
C

17
7578388
T

17
7578442
C

17
7578449
T

17
7578461
A

17
7578526
T

17
7578535
C

17
7578542
C

17
7578550
A

17
7579295
T

17
7579312
T

17
7579358
A

17
7579368
C

17
7579414
T

17
7579442
A

17
7579472
C

17
7579521
A

17
7579536
A

17
7579553
G

17
7579575
A

17
7579715
A

Chromosome
Position
Length
Mutation ID
Gene

17
7577022
1
COSM10663
TP53

17
7577046
1
COSM10710
TP53

17
7577105
1
COSM10863
TP53

17
7577120
1
COSM10660
TP53

17
7577538
1
COSM10662
TP53

17
7577548
1
COSM6932
TP53

17
7577559
1
COSM10812
TP53

17
7577580
1
COSM10725
TP53

17
7578115
1
gDNA25
TP53

17
7578190
1
COSM10758
TP53

17
7578196
1
COSM44317
TP53

17
7578203
1
COSM10667
TP53

17
7578235
1
COSM43947
TP53

17
7578388
1
COSM10738
TP53

17
7578442
1
COSM10808
TP53

17
7578449
1
COSM10739
TP53

17
7578461
1
COSM10670
TP53

17
7578526
1
COSM10801
TP53

17
7578535
1
COSM11582
TP53

17
7578542
1
COSM11462
TP53

17
7578550
1
COSM44226
TP53

17
7579295
1
COSM44985
TP53

17
7579312
1
COSM43904
TP53

17
7579358
1
COSM10716
TP53

17
7579368
1
COSM46103
TP53

17
7579414
1
COSM44492
TP53

17
7579442
1
COSM43910
TP53

17
7579472
1
gDNA26, COSM250061
TP53

17
7579521
1
COSM12168
TP53

17
7579536
1
COSM44907
TP53

17
7579553
1
COSM43664
TP53

17
7579575
1
COSM46286
TP53

17
7579715
1
COSM85573
TP53

Chromosome
Position
Mutation CDS

17
7577022
c.916C > T

17
7577046
c.892G > T

17
7577105
c.833C > T

17
7577120
c.818G > A

17
7577538
c.743G > A

17
7577548
c.733G > A

17
7577559
c.722C > T

17
7577580
c.701A > G

17
7578115
c.672 + 62A > G

17
7578190
c.659A > G

17
7578196
c.653T > A

17
7578203
c.646G > A

17
7578235
c.614A > G

17
7578388
c.542G > A

17
7578442
c.488A > G

17
7578449
c.481G > A

17
7578461
c.469G > T

17
7578526
c.404G > A

17
7578535
c.395A > G

17
7578542
c.388C > G

17
7578550
c.380C > T

17
7579295
c.375 + 17G > A

17
7579312
c.375G > A

17
7579358
c.329G > T

17
7579368
c.319T > G

17
7579414
c.273G > A

17
7579442
c.245C > T

17
7579472
c.215G > C

17
7579521
c.166G > T

17
7579536
c.151G > T

17
7579553
c.134T > C

17
7579575
c.112C > T

17
7579715
c.80delC

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

17
7577022
p.R306*
SNV
−
5-15%
Detected

17
7577046
p.E298*
SNV
−
5-15%
Detected

17
7577105
p.P278L
SNV
−
5-15%
Detected

17
7577120
p.R273H
SNV
−
5-15%
Detected

17
7577538
p.R248Q
SNV
−
5-15%
Detected

17
7577548
p.G245S
SNV
−
5-15%
Detected

17
7577559
p.S241F
SNV
−
5-15%
Detected

17
7577580
p.Y234C
SNV
−
5-15%
Detected

17
7578115
p.(=)
SNV
−
genomic
Not Covered

17
7578190
p.Y220C
SNV
−
5-15%
Detected

17
7578196
p.V218E
SNV
−
5-15%
Detected

17
7578203
p.V216M
SNV
−
5-15%
Detected

17
7578235
p.Y205C
SNV
−
5-15%
Detected

17
7578388
p.R181H
SNV
−
5-15%
Detected

17
7578442
p.Y163C
SNV
−
5-15%
Detected

17
7578449
p.A161T
SNV
−
5-15%
Detected

17
7578461
p.V157F
SNV
−
5-15%
Detected

17
7578526
p.C135Y
SNV
−
5-15%
Detected

17
7578535
p.K132R
SNV
−
5-15%
Detected

17
7578542
p.L130V
SNV
−
5-15%
Detected

17
7578550
p.S127F
SNV
−
5-15%
Detected

17
7579295
p.?
SNV
−
5-15%
Detected

17
7579312
p.T125T
SNV
−
5-15%
Detected

17
7579358
p.R110L
SNV
−
5-15%
Detected

17
7579368
p.Y107D
SNV
−
5-15%
Detected

17
7579414
p.W91*
SNV
−
5-15%
Detected

17
7579442
p.P82L
SNV
−
5-15%
Detected

17
7579472
p.R72P
SNV
−
genomic
Not Covered

17
7579521
p.E56*
SNV
−
5-15%
Detected

17
7579536
p.E51*
SNV
−
5-15%
Detected

17
7579553
p.L45P
SNV
−
5-15%
Detected

17
7579575
p.Q38*
SNV
−
5-15%
Detected

17
7579715
p.P27fs*17
DEL
−
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

17
7577022
Detected
Detected
Detected

17
7577046
Detected
Detected
Detected

17
7577105
Detected
Detected
Detected

17
7577120
Detected
Detected
Detected

17
7577538
Detected
Detected
Detected

17
7577548
Detected
Detected
Detected

17
7577559
Detected
Detected
Detected

17
7577580
Detected
Detected
Detected

17
7578115
Not Covered
Detected
Not Covered

17
7578190
Detected
Detected
Detected

17
7578196
Detected
Detected
Detected

17
7578203
Detected
Detected
Detected

17
7578235
Detected
Detected
Detected

17
7578388
Detected
Detected
Detected

17
7578442
Detected
Detected
Detected

17
7578449
Detected
Detected
Detected

17
7578461
Detected
Detected
Detected

17
7578526
Detected
Detected
Detected

17
7578535
Detected
Detected
Detected

17
7578542
Detected
Detected
Detected

17
7578550
Detected
Detected
Detected

17
7579295
Not Covered
Not Covered
Not Detected

17
7579312
Not Covered
Not Covered
Detected

17
7579358
Detected
Detected
Detected

17
7579368
Detected
Detected
Detected

17
7579414
Detected
Detected
Detected

17
7579442
Detected
Detected
Detected

17
7579472
Detected
Detected
Detected

17
7579521
Not Covered
Not Covered
Detected

17
7579536
Not Covered
Not Covered
Detected

17
7579553
Not Covered
Not Covered
Detected

17
7579575
Not Covered
Not Covered
Detected

17
7579715
Not Covered
Not Covered
Detected

Chromosome
Position
Reference

17
7579801
G

17
37880220
T

17
37880261
G

17
37880981
A

17
37881332
G

17
37881378
A

17
37881440
C

18
48575112
T

18
48575183
T

18
48575195
C

18
48575209
C

18
48575671
C

18
48581198
G

18
48581229
C

18
48581243
C

18
48584560
C

18
48584593
C

18
48584602
ACT

18
48586262
C

18
48586291
G

18
48591838
A

18
48591847
A

18
48591855
A

18
48591865
C

18
48593405
G

18
48593465
G

18
48593475
T

18
48593495
A

18
48603032
C

18
48604682
A

18
48604697
A

18
48604754
G

18
48604769
C

Chromosome
Position
Alternate

17
7579801
C

17
37880220
C

17
37880261
T

17
37880981
AGCATACGTGATG (SEQ ID NO: 33)

17
37881332
A

17
37881378
G

17
37881440
T

18
48575112
C

18
48575183
C

18
48575195
T

18
48575209
T

18
48575671
G

18
48581198
T

18
48581229
A

18
48581243
T

18
48584560
T

18
48584593
T

18
48584602
A

18
48586262
T

18
48586291
C

18
48591838
G

18
48591847
G

18
48591855
G

18
48591865
G

18
48593405
C

18
48593465
A

18
48593475
TAC

18
48593495
G

18
48603032
T

18
48604682
G

18
48604697
G

18
48604754
T

18
48604769
A

Chromosome
Position
Length
Mutation ID
Gene

17
7579801
1
gDNA35
TP53

17
37880220
1
COSM14060
ERBB2

17
37880261
1
COSM1251412
ERBB2

17
37880981
12
COSM20959
ERBB2

17
37881332
1
COSM14065
ERBB2

17
37881378
1
COSM686
ERBB2

17
37881440
1
COSM21985
ERBB2

18
48575112
1
COSM1389031
SMAD4

18
48575183
1
COSM14229
SMAD4

18
48575195
1
COSM218557
SMAD4

18
48575209
1
COSM14168
SMAD4

18
48575671
1
COSM13115
SMAD4

18
48581198
1
COSM14118
SMAD4

18
48581229
1
COSM1226725
SMAD4

18
48581243
1
COSM308153
SMAD4

18
48584560
1
COSM14057
SMAD4

18
48584593
1
COSM22901
SMAD4

18
48584602
2
COSM14217
SMAD4

18
48586262
1
COSM14163
SMAD4

18
48586291
1
COSM14167
SMAD4

18
48591838
1
COSM1389054
SMAD4

18
48591847
1
COSM1389057
SMAD4

18
48591855
1
COSM14109
SMAD4

18
48591865
1
COSM14111
SMAD4

18
48593405
1
COSM14249
SMAD4

18
48593465
1
COSM14103
SMAD4

18
48593475
2
COSM14223
SMAD4

18
48593495
1
AMXsynt12
SMAD4

18
48603032
1
COSM14096
SMAD4

18
48604682
1
COSM14114
SMAD4

18
48604697
1
COSM1389099
SMAD4

18
48604754
1
COSM14134
SMAD4

18
48604769
1
COSM1389106
SMAD4

Chromosome
Position
Mutation CDS

17
7579801
c.74 + 38C > G

17
37880220
c.2264T > C

17
37880261
c.2305G > T

17
37880981
c.2324_2325ins12

17
37881332
c.2524G > A

17
37881378
c.2570A > G

17
37881440
c.2632C > T

18
48575112
c.306T > C

18
48575183
c.377T > C

18
48575195
c.389C > T

18
48575209
c.403C > T

18
48575671
c.431C > G

18
48581198
c.502G > T

18
48581229
c.533C > A

18
48581243
c.547C > T

18
48584560
c.733C > T

18
48584593
c.766C > T

18
48584602
c.776_777delCT

18
48586262
c.931C > T

18
48586291
c.955 + 5G > C

18
48591838
c.1001A > G

18
48591847
c.1010A > G

18
48591855
c.1018A > G

18
48591865
c.1028C > G

18
48593405
c.1156G > C

18
48593465
c.1216G > A

18
48593475
c.1229_1230insCA

18
48593495
c.1246A > G

18
48603032
c.1333C > T

18
48604682
c.1504A > G

18
48604697
c.1519A > G

18
48604754
c.1576G > T

18
48604769
c.1591C > A

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

17
7579801
p.(=)
SNV
−
genomic
Not Covered

17
37880220
p.L755S
SNV
+
5-15%
Detected

17
37880261
p.D769Y
SNV
+
5-15%
Detected

17
37880981
p.A775_G776insYVMA
INS
+
5-15%
Detected

17
37881332
p.V842I
SNV
+
5-15%
Detected

17
37881378
p.N857S
SNV
+
5-15%
Detected

17
37881440
p.H878Y
SNV
+
5-15%
Detected

18
48575112
p.P102P
SNV
+
5-15%
Detected

18
48575183
p.V126A
SNV
+
5-15%
Detected

18
48575195
p.P130L
SNV
+
5-15%
Detected

18
48575209
p.R135*
SNV
+
5-15%
Detected

18
48575671
p.S144*
SNV
+
5-15%
Detected

18
48581198
p.G168*
SNV
+
5-15%
Detected

18
48581229
p.S178*
SNV
+
5-15%
Detected

18
48581243
p.Q183*
SNV
+
5-15%
Detected

18
48584560
p.Q245*
SNV
+
5-15%
Detected

18
48584593
p.Q256*
SNV
+
5-15%
Detected

18
48584602
p.T259fs*4
DEL
+
5-15%
Detected

18
48586262
p.Q311*
SNV
+
5-15%
Detected

18
48586291
p.?
SNV
+
5-15%
Detected

18
48591838
p.Q334R
SNV
+
5-15%
Detected

18
48591847
p.E337G
SNV
+
5-15%
Detected

18
48591855
p.K340E
SNV
+
5-15%
Detected

18
48591865
p.S343*
SNV
+
5-15%
Detected

18
48593405
p.G386R
SNV
+
5-15%
Detected

18
48593465
p.A406T
SNV
+
5-15%
Detected

18
48593475
p.Q410fs*6
INS
+
5-15%
Detected

18
48593495
p.R416G
SNV
+
5-15%
Detected

18
48603032
p.R445*
SNV
+
5-15%
Detected

18
48604682
p.R502G
SNV
+
5-15%
Detected

18
48604697
p.K507E
SNV
+
5-15%
Detected

18
48604754
p.E526*
SNV
+
5-15%
Detected

18
48604769
p.R531R
SNV
+
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

17
7579801
Not Covered
Not Covered
Detected

17
37880220
Detected
Detected
Not Covered

17
37880261
Detected
Detected
Not Covered

17
37880981
Detected
Not Covered
Detected

17
37881332
Detected
Not Detected
Not Covered

17
37881378
Detected
Detected
Not Covered

17
37881440
Detected
Detected
Not Covered

18
48575112
Detected
Not Covered
Not Covered

18
48575183
Detected
Detected
Not Covered

18
48575195
Detected
Detected
Not Covered

18
48575209
Detected
Detected
Not Covered

18
48575671
Detected
Not Covered
Not Covered

18
48581198
Detected
Detected
Not Covered

18
48581229
Detected
Detected
Not Covered

18
48581243
Detected
Detected
Not Covered

18
48584560
Detected
Detected
Not Covered

18
48584593
Detected
Detected
Not Covered

18
48584602
Detected
Detected
Not Covered

18
48586262
Detected
Detected
Not Covered

18
48586291
Detected
Detected
Not Covered

18
48591838
Detected
Detected
Detected

18
48591847
Detected
Detected
Detected

18
48591855
Detected
Detected
Detected

18
48591865
Detected
Detected
Detected

18
48593405
Detected
Detected
Not Covered

18
48593465
Detected
Detected
Not Covered

18
48593475
Detected
Detected
Not Covered

18
48593495
Detected
Detected
Not Covered

18
48603032
Detected
Detected
Not Covered

18
48604682
Detected
Detected
Detected

18
48604697
Detected
Detected
Detected

18
48604754
Detected
Detected
Detected

18
48604769
Detected
Detected
Detected

Chromosome
Position
Reference

19
1207076
TG

19
1220321
T

19
1220371
G

19
1220382
C

19
1220487
G

19
1220502
G

19
1221293
C

19
1221319
C

19
1223125
C

19
3115012
C

19
3118942
A

19
3119239
C

19
17945696
C

19
17948009
G

20
36031631
C

20
57480494
C

20
57484420
C

20
57484596
A

22
24133967
C

22
24133990
C

22
24134006
C

22
24143240
C

22
24145528
C

22
24145582
C

22
24145588
G

22
24145675
G

22
24176353
GC

Chromosome
Position
Alternate

19
1207076
T

19
1220321
C

19
1220371
T

19
1220382
T

19
1220487
T

19
1220502
T

19
1221293
T

19
1221319
T

19
1223125
G

19
3115012
T

19
3118942
T

19
3119239
T

19
17945696
T

19
17948009
A

20
36031631
T

20
57480494
T

20
57484420
T

20
57484596
T

22
24133967
T

22
24133990
A

22
24134006
T

22
24143240
T

22
24145528
CCCGAGGTGCTGGTCCCCAT (SEQ ID NO: 34)

22
24145582
T

22
24145588
A

22
24145675
C

22
24176353
G

Chromosome
Position
Length
Mutation ID
Gene

19
1207076
1
COSM21212
STK11

19
1220321
1
gDNA27
STK11

19
1220371
1
COSM21570
STK11

19
1220382
1
COSM27316
STK11

19
1220487
1
COSM20944
STK11

19
1220502
1
COSM25229
STK11

19
1221293
1
COSM29005
STK11

19
1221319
1
COSM21355
STK11

19
1223125
1
COSM21360
STK11

19
3115012
1
COSM21651
GNA11

19
3118942
1
COSM52969
GNA11

19
3119239
1
gDNA28
GNA11

19
17945696
1
COSM34213
JAK3

19
17948009
1
COSM34214
JAK3

20
36031631
1
COSM1227526
SRC

20
57480494
1
COSM244725
GNAS

20
57484420
1
COSM27887
GNAS

20
57484596
1
COSM27888
GNAS

22
24133967
1
COSM1002
SMARCB1

22
24133990
1
COSM991
SMARCB1

22
24134006
1
COSM24595
SMARCB1

22
24143240
1
COSM992
SMARCB1

22
24145528
19
COSM51386
SMARCB1

22
24145582
1
COSM993
SMARCB1

22
24145588
1
COSM999
SMARCB1

22
24145675
1
gDNA30
SMARCB1

22
24176353
1
COSM1057
SMARCB1

Chromosome
Position
Mutation CDS

19
1207076
c.169delG

19
1220321
c.465 − 51T > C

19
1220371
c.465 − 1G > T

19
1220382
c.475C > T

19
1220487
c.580G > T

19
1220502
c.595G > T

19
1221293
c.816C > T

19
1221319
c.842C > T

19
1223125
c.1062C > G

19
3115012
c.547C > T

19
3118942
c.626A > T

19
3119239
c.771C > T

19
17945696
c.2164G > A

19
17948009
c.1715C > T

20
36031631
c.1460C > T

20
57480494
c.489C > T

20
57484420
c.601C > T

20
57484596
c.680A > T

22
24133967
c.118C > T

22
24133990
c.141C > A

22
24134006
c.157C > T

22
24143240
c.472C > T

22
24145528
c.566_567ins19

22
24145582
c.601C > T

22
24145588
c.607G > A

22
24145675
c.601 + 66G > C

22
24176353
c.1148delC

Mutation

Target
Sanger

Chromosome
Position
Mutation AA
Type
Strand
Frequency
Detection*

19
1207076
p.E57fs*7
DEL
+
5-15%
Detected

19
1220321
p.(=)
SNV
+
genomic
Not Covered

19
1220371
p.?
SNV
+
5-15%
Detected

19
1220382
p.Q159*
SNV
+
5-15%
Detected

19
1220487
p.D194Y
SNV
+
5-15%
Detected

19
1220502
p.E199*
SNV
+
5-15%
Detected

19
1221293
p.Y272Y
SNV
+
5-15%
Detected

19
1221319
p.P281L
SNV
+
5-15%
Detected

19
1223125
p.F354L
SNV
+
5-15%
Detected

19
3115012
p.R183C
SNV
+
5-15%
Detected

19
3118942
p.Q209L
SNV
+
5-15%
Detected

19
3119239
p.T257T
SNV
+
genomic
Not Covered

19
17945696
p.V722I
SNV
−
5-15%
Detected

19
17948009
p.A572V
SNV
−
5-15%
Detected

20
36031631
p.P487L
SNV
+
5-15%
Detected

20
57480494
p.Y163Y
SNV
+
5-15%
Detected

20
57484420
p.R201C
SNV
+
5-15%
Detected

20
57484596
p.Q227L
SNV
+
5-15%
Detected

22
24133967
p.R40*
SNV
+
5-15%
Detected

22
24133990
p.Y47*
SNV
+
5-15%
Detected

22
24134006
p.R53*
SNV
+
5-15%
Detected

22
24143240
p.R158*
SNV
+
5-15%
Detected

22
24145528
p.L191fs*26
INS
+
5-15%
Detected

22
24145582
p.R201*
SNV
+
5-15%
Detected

22
24145588
p.A203T
SNV
+
5-15%
Detected

22
24145675
p.(=)
SNV
+
genomic
Not Covered

22
24176353
p.P383fs
DEL
+
5-15%
Detected

CHPv2
TSACP
TSTP

Chromosome
Position
Detection
Detection
Detection

19
1207076
Detected
Detected
Detected

19
1220321
Detected
Not Covered
Detected

19
1220371
Detected
Not Covered
Detected

19
1220382
Detected
Not Covered
Detected

19
1220487
Detected
Detected
Not Covered

19
1220502
Detected
Detected
Not Covered

19
1221293
Detected
Detected
Detected

19
1221319
Detected
Detected
Detected

19
1223125
Detected
Detected
Detected

19
3115012
Not Covered
Detected
Not Covered

19
3118942
Detected
Detected
Not Covered

19
3119239
Not Covered
Detected
Not Covered

19
17945696
Detected
Detected
Not Covered

19
17948009
Detected
Detected
Not Covered

20
36031631
Not Covered
Not Covered
Detected

20
57480494
Not Covered
Not Covered
Detected

20
57484420
Detected
Detected
Detected

20
57484596
Detected
Not Covered
Not Covered

22
24133967
Detected
Detected
Not Covered

22
24133990
Detected
Detected
Not Covered

22
24134006
Detected
Detected
Not Covered

22
24143240
Detected
Detected
Not Covered

22
24145528
Not Detected
Not Covered
Not Covered

22
24145582
Detected
Detected
Not Covered

22
24145588
Detected
Detected
Not Covered

22
24145675
Not Covered
Detected
Not Covered

22
24176353
Detected
Detected
Not Covered