Effect sizes of somatic mutations in cancer

Vincent L. Cannataro 1, Stephen G. Gaffney1, Jeffrey P. Townsend 1,2,3†

1Department of Biostatistics, Yale University, New Haven, CT, 2Program in Computational Biology and Bioinformatics and 3Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT †To whom correspondence should be addressed.

1

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Cancer growth is fueled by genomic alterations that confer selective advantage to somatic cells 1. A major goal of cancer biology is determining the relative importance of these alterations. Genomic tumor sequence surveys have frequently ranked the importance of genetic substitutions to cancer growth by P value or a false-discovery conversion thereof 2,3. However, P values are thresholds for belief 4, not metrics of effect 5,6. Their frequent misuse as metrics of effect has often and ineffectively been vociferously decried 5,7–9, even in cases when the only attributable mistake was omission of effect sizes 10,11. Here, we draw upon an understanding of the development of cancer as an evolutionary process 12,13 to estimate the effect size of somatic variants. We estimate the effect size of all recurrent single nucleotide variants in 23 cancer types, ranking their relative importance within and between driver genes. Many of the variants with the highest effect size per tumor, such as EGFR L858R in lung adenocarcinoma and BRAF V600E in colon adenocarcinoma, are within genes deemed significantly mutated by existing whole-gene metrics. Quantifying the effect sizes of somatic mutations underlying cancer has immediate significance to the prioritization of clinical decision-making by tumor boards, selection and design of clinical trials, pharmacological targeting, and basic research prioritization.

2

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Since the advent of whole-exome and whole-genome sequencing of tumor tissues, studies of

somatic mutations have revealed the underlying genetic architecture of cancer 14, producing ordered lists

of significantly mutated genes whose ordering implies their relative importance to tumorigenesis and

cancer development. Typically, differentiation of selected mutations from neutral mutations is performed

by quantifying the over-representation of mutations within specific genes in tumor tissue relative to

normal tissue, and disproportionate prevalence of somatic mutations in a gene has been taken as prima

facie evidence of a causative role for that gene. Two quantifications have implicitly ordered the

importance of discovered cancer “driver” genes: the prevalence of the mutation among tumor tissues

sequenced from that tumor type 15,16, the statistical significance (P value) of the disproportionality of

mutation frequency 2, or both 14. Versions of these metrics have shifted from simple ranks by mutation

prevalence in a tumor population 17–19 to calculation of statistical significance of mutation prevalence over

genome-wide context-specific background mutation rates 20–22, to ratios of the prevalence of

nonsynonymous and synonymous mutations 1,23, to P values based on a gene-specific mutation rate and a

diversity of genomic data 3. Although the approaches used to calculate P values have become more

sophisticated, neither prevalence nor P value is an appropriate metric for quantifying the vital role of

genes or their mutations to tumorigenesis and cancer development.

While prevalence of a somatic mutation in a cancer type has important consequences for biomarker

studies 24 and identification of therapeutic population for a targeted therapy 25, there is only a

correlative—rather than causal—link between prevalence of mutation and its contribution to

tumorigenesis and cancer development. The lack of causal linkage is easily seen by considering the

mutated genes that, in spite of their high prevalence in tumor populations, are universally regarded as

false positives. For example, the gene TTN is a structural protein of striated muscle. Because it is long,

because it replicates relatively late in the synthesis phase of mitosis, and because it is inaccessible to

transcription-mediated repair in non-muscle tissues, it has a high mutation rate and is frequently mutated

3

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

in non-sarcoma cancer tissues. While TTN is an extreme example—sometimes showing up at the top of

lists ordered by prevalence of genic mutation 1,3—it exemplifies the problem with using mutation

prevalence as a proxy for importance. Any consideration of whether mutated genes are contributing to

tumorigenesis and cancer development—or of the degree to which they are contributing—must address

the issue of their underlying mutation rate.

The appearance of such biologically implausible genes in ranked mutation lists prompted the

development of increasingly sophisticated statistical approaches designed to “weed out” false-positives

via calculation of a P value that accounted for gene length and background mutation rate. The classical

evolutionary biology approach is to use the frequency of synonymous site mutations in each gene as a

proxy for mutation rate. As in the divergence of species, synonymous site mutations are presumably

neutral (or nearly so) to the success of cancer lineages during the divergence from normal to resectable

tumor. As the number of mutations observed in a given gene is typically much smaller in the somatic

evolution of cancer than is observed in the divergence between most species, use of synonymous sites

within a single gene leads to many genes with zero synonymous mutations in most cancers, and an

ineffective calculation of P value. Alternative approaches currently in use obtain a reasonably robust

estimate of genic mutation rate using correlates such as gene expression levels, chromatin states, and

replication timing, and are largely successful at excluding known false positives 3.

In genomic tumor surveys, the sample size of tumors varies among studies, posing a problem for

comparison of P values within or between cancer types 5,6. An even more serious issue with using P

values for ranking genes or mutations arises from the same source that obviates use of genic mutation

prevalence: the confounding effect of mutation rate. Because the “sample size” of overall mutations in a

gene is dictated by the genic mutation rate, it is much easier for genes with high mutation rates not only to

reach high genic prevalence, but also to reach statistical significance despite small effect sizes. While

approaches accounting for genic mutation rates will eliminate false positives 3, and the P value will serve

4

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

to exclude genes like TTN that have no role in tumorigenesis and cancer development, the rank order by P

value of genes that do have a role in tumorigenesis and cancer development will remain highly affected

by mutation rate. Genes with higher mutation rate will (correctly) be more likely to achieve statistical

significance, and thus will appear deceptively high on a ranked list whose ordering suggests importance in

tumorigenesis and cancer development.

Because genic mutation prevalence and P value inadequately capture importance to tumorigenesis

and cancer development, another metric must be appropriate. To provide an evaluation of the relative

importance of mutations in diverse cancer types to tumorigenesis and cancer development, we called on

an understanding of the development of cancer as an evolutionary process 12,13, and adapted some

straightforward insights from classical evolutionary theory. The cognate metric in evolutionary theory for

quantifying importance to tumorigenesis and cancer development is the selective effect of the mutation on

the cancer lineage. The appropriateness of this metric is fairly easy to recognize. While mutations are the

ultimate source of variation contributing to tumorigenesis, we do not conduct genomic tumor sequence

surveys to discover neutral mutation rates. We conduct them to determine which mutations spread within

cancer tissues because of the effects of mutations on proliferation and survival. Mutation rate is a

confounding phenomenon: when it is high, it also increases prevalence of mutations. Because silent site

substitutions and other correlates of baseline mutation rate provide a means to independently differentiate

silent mutation rate from the impact of natural selection within the tumor, selection intensities can be

estimated, providing the effect sizes of each mutation.

We calculated cancer effect sizes by comparing the rate of observed substitutions to the rate that

substitutions would be expected to arise in the absence of selection 26. In accordance with population

genetic theory, we specify that the rate neutral mutations arise and the rate that they fix as substitutions

within tumors are equivalent 27, and that non-neutral mutations arise at a consistent rate. Thus any

increase in the flux of substitutions among tumors of a particular context above the baseline silent rate

5

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

would be the appropriate estimate of the intensity of selection on that mutation within the tumor

population (Methods).

This calculation yielded cancer effect sizes for all fixed substitutions (Methods, Supplemental

Figure 1, Supplemental Table 1) that quantify contribution to the cancer phenotype within 23 tumor types.

Their relative rank corresponds to their relative importance within the respective tumor types. Several

common known oncogenic substitutions, such as BRAF V600E in COAD and EGFR L858R in LUAD,

and substitutions in known tumor suppressor genes, such as APC in READ and TP53 in HPV-negative

HNSCC, are highly selected, and those genes are also determined as significantly mutated by MutSigCV3.

However, genes determined to be significantly altered in cancer by MutSigCV are well-dispersed within a

large range of site-specific cancer effect sizes (Figure 1), illustrating how discrepant Q values are with

cancer effect size. Several substitutions within genes that are not determined to be significantly

over-mutated via MutSigCV are interspersed among more prevalent substitutions within genes that are

estimated to be significantly mutated, for instance Mastermind-like3 (MAML3) G1069A in READ, a

protein that binds to and stabilizes the DNA-binding complex of the Notch intracellular domain 28 and

Nuclear factor (erythroid derived 2)-like 2 (NFE2L2) R34G in UCEC, a protein that is believed to play a

causative role in squamous cell lung cancer 29,30. Indeed, substitutions in this gene comprise two of the top

three most selected substitutions within our analysis of lung squamous cell carcinoma (Figure 1).

6

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Figure 1. Cancer effect sizes of recurrent somatic substitutions in eight of the 23 cancer types analyzed. Effect sizes greater than 1 × 103 are indicated by ticks along the tumor-type axes. The highest 50 effect sizes are labeled within each tumor. Names of genes that have more than one mutation within or between tumors are uniquely colored. Genes deemed significantly burdened with mutation 3 are depicted by a red circle next to mutation labels, and the prevalence of each substitution is represented by the size of this circle. LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma. UCEC: Uterine corpus endometrial carcinoma; LGG: Brain Lower Grade Glioma; HNSC: Head and neck squamous cell carcinoma, broken into HPV positive and HPV negative tumor samples (methods); COAD: Colon adenocarcinoma; READ: Rectum adenocarcinoma. NCSNV refers to a non-coding single nucleotide variant outside an exon (e.g. 5’ or 3’ UTRs). HPV+ and HPV– HNSCC have been demonstrated to have significantly different genetic architectures 31, thus they are presented separately.

7

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Current approaches using conservative P values are particularly underpowered to detect genes that

are of high importance to tumorigenesis and cancer development in some cancer cases because the site or

sites conveying the relevant phenotype are mutated at low rates. For instance, FBXW7 R505G was

estimated to have the highest selection intensity in HPV+ HNSCC, and BRAF V600E was estimated to

have the fifth highest selection intensity in LGG, but both of these genes were classified as not

significantly mutated by MutSigCV within these two cancer types. Mutations within these two

well-known oncogenes were estimated to confer large effect sizes, and these genes were determined to be

significantly mutated in other cancer types, yet their degree of influence within HPV+ HNSCC and LGG

is obscured in cancer-wide significance analyses. The relative effect sizes of cancer mutations can inform

nearly every aspect of basic research related to oncology and should play key roles in clinical

decision-making. They should be integrated into clinical decision-making in tumor boards, where they

would provide crucial insight into the relative upper limits of the efficacy of precision-targeted treatments.

They should guide the selection of clinical trials to target small populations that can benefit from targeted

therapeutics developed for other cancer types. They should guide targeted development of new

therapeutics, indicating the upper limit of effect for a perfect therapeutic ameliorating an oncogenic

mutation. Lastly, they should guide the selection of important areas of basic research that have potential

to lead to therapies and cures for cancer. It does not escape our notice that here we only calculate the

effect size of single nucleotide variants. Importantly, effect sizes of other mutational processes, such as

copy number alterations or epigenetic modifications, could be similarly calculated once estimates of

intrinsic mutation rate in the absence of selection are identifiable for these processes.

8

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

METHODS:

Data acquisition and processing:

All data were obtained either from The Cancer Genome Atlas (TCGA) projects downloaded from

the National Cancer Institute’s Genomic Data Commons 32, or from projects part of the Yale-Gilead

collaboration (Supplemental Table 2). All TCGA data used in this analysis were from GDC version

gdc-1.0.0 and relevant UUID are found in Supplemental Table 3.

All TCGA data were first converted to hg19 coordinates using the liftOver function of the

rtracklayer R package33. To obtain consistency between gene symbols used in MutSigCV and in

mutation data, symbols in the MutSigCV default covariates files were mapped to HUGO symbols.

Non-HUGO symbols were mapped using substitutions from the NCBI Gene database using unambiguous

'synonym' matches; unambiguous 'previous symbol' matches; and manual lookups. CDS coordinates for

each gene were obtained from UCSC's hg19 annotation database. The MutSigCV covariates files, and

gene annotation files used in our analyses can be found at

https://github.com/Townsend-Lab-Yale/SNV_selection_intensity. Nucleotide variants one or two

positions apart in the same tumor sample were removed from the analysis to ensure that we analyzed only

single nucleotide variants. Head and neck squamous cell tumors were designated as HPV positive if they

contained greater than 100 HPV RNA viral transcript reads per hundred million (RPHM) 34 and were

designated positive in clinical data obtained from The Broad GDAC Firehose 35, and tumors were

designated HPV negative if they contained less than 100 HPV RNA viral transcript RPHM and were

designated negative in clinical data obtained from The Broad GDAC Firehose.

Calculating mutation rate and selection intensity:

We define the selection intensity of a single nucleotide variant as the ratio of the flux of fixed

mutations to the expected flux of fixed mutations in the absence of selection. We estimate the expected

rate of fixed mutations in the absence of selection by using MutSigCV to calculate the silent mutation rate

9

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

for each gene. We use the median gene expression from cell lines derived from each analyzed tissue type

(Supplemental Table 3) as the MutSigCV expression covariate for that tissue type. We then normalized

this gene-level rate at every site for every mutation across each gene given the specific trinucleotide

mutation profile of the tissue, such that the average rate of mutations among all trinucleotide

combinations in each gene is equal to the average rate calculated by MutSigCV. The trinucleotide profile

of a tissue is calculated as the average of trinucleotide COSMIC signatures among non-recurrent

mutations calculated by the deconstructSigs R package 36 for all tumors with over 50 single

nucleotide variants.

Formally, we define the rate of non-neutral substitutions, as , where N is the,λ μ u(s)N ×

effective population size of the tumor, is the mutation rate of a substitution, and is the probabilityμ (s)u

the mutation fixes within the population, which is a function of the selection coefficient of the mutation, s .

The probability that a silent mutation fixes is the inverse of the population size within which it fixes, and

thus rate of non-neutral substitutions, divided by the rate of neutral substitutions, is or,λμ = Nμ × 1

N

Nμ × u(s)

, the selection intensity and effect size of the mutation. The term selection intensity is used as a(s)N × u

direct parallel to the classic derivation of “scaled selection coefficient” or “selection intensity” in the

population genetics literature 37–40. Because a tumor sequence is a single snapshot in time, we can only

detect one substitution event per site per tumor. To correct for this issue of detection, we define the rate of

substitution, , as the Poisson rate of occurrence of one or more observed fixation events, i.e. the value ofλ

that maximizes , where is the number of tumors without any substitutionλ e ( −λ) n0 × 1 ( − e −λ) n1 n0

at that site and is the number of tumors with the specified substitution at that site. We definen1

substitutions as single nucleotide variants that are observed in tumors from more than one patient

(recurrent) within our dataset, and we calculate the selection intensity of the recurrently mutated

substitutions to minimize the probability of analyzing passenger mutations.

10

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Scripts used to perform this analysis are available online at

https://github.com/Townsend-Lab-Yale/SNV_selection_intensity

References cited

1. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158

(2007).

2. Kan, Z. et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature

466, 869–873 (2010).

3. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated

genes. Nature 499, 214–218 (2013).

4. Evans, D. M. & Purcell, S. Power Calculations in Genetic Studies. Cold Spring Harb. Protoc. 2012,

db.top069559 (2012).

5. Nakagawa, S. & Cuthill, I. C. Effect size, confidence interval and statistical significance: a practical

guide for biologists. Biol. Rev. Camb. Philos. Soc. 82, 591–605 (2007).

6. Hojat, M. & Xu, G. A Visitor’s Guide to Effect Sizes – Statistical Significance Versus Practical

(Clinical) Importance of Research Findings. Adv. Health Sci. Educ. Theory Pract. 9, 241–249

(2004).

7. Gardner, M. J. & Altman, D. G. Confidence intervals rather than P values: estimation rather than

hypothesis testing. Br. Med. J. 292, 746–750 (1986).

8. Goodman, S. A dirty dozen: twelve p-value misconceptions. Semin. Hematol. 45, 135–140 (2008).

9. Hayat, M. J. Understanding statistical significance. Nurs. Res. 59, 219–223 (2010).

10. Sullivan, G. M. & Feinn, R. Using Effect Size-or Why the P Value Is Not Enough. J. Grad. Med.

Educ. 4, 279–282 (2012).

11

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

11. Chavalarias, D., Wallach, J. D., Li, A. H. T. & Ioannidis, J. P. A. Evolution of Reporting P Values in

the Biomedical Literature, 1990-2015. JAMA 315, 1141–1148 (2016).

12. Nowell, P. The clonal evolution of tumor cell populations. Science 194, 23–28 (1976).

13. Crespi, B. & Summers, K. Evolutionary biology of cancer. Trends Ecol. Evol. 20, 545–552 (2005).

14. Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types.

Nature 505, 495–501 (2014).

15. Miki, Y. et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1.

Science 266, 66–71 (1994).

16. Futreal, P. et al. BRCA1 mutations in primary breast and ovarian carcinomas. Science 266, 120–122

(1994).

17. Zang, Z. J. et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations

in cell adhesion and chromatin remodeling genes. Nat. Genet. 44, 570–574 (2012).

18. Kumar, A. et al. Exome sequencing identifies a spectrum of mutation frequencies in advanced and

lethal prostate cancers. Proc. Natl. Acad. Sci. U. S. A. 108, 17087–17092 (2011).

19. Zhao, S. et al. Landscape of somatic single-nucleotide and copy-number mutations in uterine serous

carcinoma. Proc. Natl. Acad. Sci. U. S. A. 110, 2916–2921 (2013).

20. Chapman, M. A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471,

467–472 (2011).

21. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318,

1108–1113 (2007).

22. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science

314, 268–274 (2006).

23. Krauthammer, M. et al. Exome sequencing identifies recurrent somatic RAC1 mutations in

melanoma. Nat. Genet. 44, 1006–1014 (2012).

12

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

24. Lui, V. W. Y. et al. Frequent mutation of the PI3K pathway in head and neck cancer defines

predictive biomarkers. Cancer Discov. 3, 761–769 (2013).

25. Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304,

554 (2004).

26. Cannataro, V. L. et al. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating

the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene in press, (2017).

27. Gillespie, J. H. Population genetics: a concise guide. 2004.

28. Oyama, T. et al. Mastermind-like 1 (MamL1) and mastermind-like 3 (MamL3) are essential for

Notch signaling in vivo. Development 138, 5235–5246 (2011).

29. Sasaki, H. et al. NFE2L2 gene mutation in male Japanese squamous cell carcinoma of the lung. J.

Thorac. Oncol. 5, 786–789 (2010).

30. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous

cell lung cancers. Nature 489, 519–525 (2012).

31. Seiwert, T. Y. et al. Integrative and comparative genomic analysis of HPV-positive and

HPV-negative head and neck squamous cell carcinomas. Clin. Cancer Res. 21, 632–641 (2015).

32. Grossman, R. L. et al. Toward a Shared Vision for Cancer Genomic Data. N. Engl. J. Med. 375,

1109–1112 (2016).

33. Lawrence, M., Gentleman, R. & Carey, V. rtracklayer: an R package for interfacing with genome

browsers. Bioinformatics 25, 1841–1842 (2009).

34. Cao, S. et al. Divergent viral presentation among human tumors and adjacent normal tissues. Sci.

Rep. 6, 28294 (2016).

35. Broad Institute. Broad Institute TCGA Genome Data Analysis Center (2016): Firehose

stddata__2016_01_28 run. Broad Institute of MIT and Harvard. doi:10.7908/C11G0KM9. (2016).

36. Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S. & Swanton, C. DeconstructSigs:

13

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns

of carcinoma evolution. Genome Biol. 17, 31 (2016).

37. Sawyer, S. A. & Hartl, D. L. Population genetics of polymorphism and divergence. Genetics 132,

1161–1176 (1992).

38. Bustamante, C. D. Population Genetics of Molecular Evolution. in Statistical Methods in Molecular

Evolution 63–99 (Springer New York, 2005).

39. Innan, H. & Kim, Y. Pattern of polymorphism after strong artificial selection in a domestication

event. Proc. Natl. Acad. Sci. U. S. A. 101, 10667–10672 (2004).

40. Parsons, T. L. & Quince, C. Fixation in haploid populations exhibiting density dependence I: The

non-neutral case. Theor. Popul. Biol. 72, 121–135 (2007).

Supplementary Information available online. Acknowledgements: This project was supported by Gilead Sciences, Inc. We also thank the Yale High Performance Computing Center for providing computational resources. Author contributions : VLC and JPT designed the analyses. VLC performed the analyses with assistance from SGG. JPT, VLC, and SGG wrote the manuscript. Author Information: The authors declare no competing financial interests. Correspondence and requests for materials should be addressed to jeffrey.townsend@yale.edu.

14

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

Supplemental figure 1 legend: Selection intensities of recurrent somatic substitutions in 23 cancers. BLCA: Bladder Urothelial Carcinoma; BRCA: Breast invasive carcinoma; Cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD: Colon adenocarcinoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and neck squamous cell carcinoma, broken into HPV+ and HPV- tumor samples using criteria described within the Methods section; KIRC: Kidney renal clear cell carcinoma; LAML: Acute Myeloid Leukemia; LGG: Brain Lower Grade Glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SKCM: Skin Curaneous Melanoma, broken into primary skin tumors and metastatic skin tumors; STAD: Stomach adenocarcinoma; THCA: Thyroid carcinoma; UCEC: Uterine corpus endometrial carcinoma.

15

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint

I III I III I III I II III I III III IIII IIII II III I II I II IIII I I I II I II IIIII III I I I I II II II III III II III I I IIII I IIIII II I III II III I IIII II I IIIII I I III I I III III II II I II II IIII II II I II II II I II IIII II I II I II III IIII I II II III III I IIII II II II III II IIII I I II III III III II III IIII I II II IIIII I IIIII IIII I I II I II III II I I IIIII I II III II II I II IIII II I II II II I II I III III II III III III I II II III II II III II IIII I I I I I III III II I IIII II II III II II II I II II III II II I III III II IIII I III II III I II I IIII I II II I III II I III III III I III III II I II II II I I III III I IIIIII II I II I III I II III III II II II I II I III IIII III IIII II I

III II IIII I I IIIII II II I I II II III III II II IIIII IIIII I III II I I I I III I III II I II II I II II I II I II II II IIII II II II I III II I II I II II I I IIII I III II I II II I III III I I I III II II II I II III II I II I III III II II I II II III I III III I I II I II III III I I II I I I II II II II II I I III III II II I I II III II I II I I II III I III II III III II III III II III IIIII I I II III II I II IIII IIIII I III IIII I II II III II II IIII II III III II I III I II II II I IIII III III I I II II II II II II II II III I III II II I IIII II I III III II III II III II II III II II I II II I II I III III I II III I

III II III III I III III III I I III II III I III III I I II II IIII III II IIII I II II IIII II III I III I II II II I II II I II I II II I II II II II III III II II III I II II III IIII I III III I II III IIII I I III IIIIIII III I II II I III I II I II I II II II II III I II II II III I I I IIIIII I III II I II I I III III I III I II I I II III III III II III II IIII II I II I II III II III III I II II I II IIII IIII III II I II IIIIII

I I III I III II II I III I III II I I II II IIIIIII I II II II II IIII II III III I I II I IIIII I I II IIII II I I III I II II I II I III III IIIII II II II II III I II I II III II I III II II I II II I II I IIII IIII II II I II III I IIII IIII III II I II I III III II III I IIII I IIII I III III II I I I I II III II II II I I III I III I I II II III III II II I II II I II I I II II III III I II I II II III III IIIII I II III II I I III III II II II II I IIII II IIII II III II II II I II IIII II I III III II I I II III I III I II I I II IIII I I II IIII III IIII I III II I II I II I II III I II II I I II I III I IIII I III II I II I II I III I II I IIII I I I II III IIIII I II I I II II IIIII II III II IIII I IIII IIII II II II I II I I II II I III I I II II II I III III I II I III III I III I II I III II II I IIII II I IIII I IIII II II I III III IIII I IIII I I II I III III II I III IIII III II III II II II II III II I IIII I II II II III II II II III II III I III III II II II III II III I II III II IIII I III

II I IIII III III I IIII I II II II I II II III I III II III I IIIII I II IIII IIII II II IIIIII III I II I II I III II II II II II II II I II II III IIII II II II II I II III I II I III II II II II I II II II II II I II I I II II II III

I IIIII III I I I III I II I II II I III III I I I I II II III II I III I II I I IIII I I II II II I I II I I II II II I III II II IIII I II II II I II III III II II II I II I IIII I II I IIII II II II II I II IIII I I II II IIII II II IIIII I I III III III II I III II III I I II I II II II II II I III II II I III II II II

IIIIII II II II II

I III I I III II III I IIII II II I II IIII II II II II I IIII I I III II III I I II II I I I I II I II III II I II II I I I II III II II III I IIIIII I IIII IIII IIII I II I II I IIII II II II III I II II IIII II I I II IIII IIII IIII II II I II I II I III II III II IIII I II II I I II I II II III III II I I II II I I IIIII I II II I II I III I II

I IIII I II I I II I II II II I I II III I II II II

I II III III I IIII III I II IIII II I II III III

II III I III III II II III I IIII II I III I I III I II II II I III I II I I I IIII III II II II III I I III II II II I I I II I II II I II II II II II II II II II II II III I II II I III II I I II II III

I I I II II I II III II III I I II I II I II II II III II II I III IIII I III I III I II III II I I II II III I III II I III II III II I II II II I IIII II I II I II III I III II I II I II I I IIII II I I II I II II III I II I III IIII III II I IIII I I IIII II II IIII II II II I I II I III II I III III I I III I III I I I IIII I II III III III I II I IIII I I II II I II II I I IIII II I III II I IIII IIII I I I I II I II II II II II III II I III II II I II II III I III III II II III I I IIII I II II I I III II I IIII II II I II II II III II II I II II I II I II III III II III III II I I I II II III III IIIII II II II II III II II I II I III I IIII II I II II II I II I

IIII I III I IIII III I II II II I III II II II II II IIII II I I I III II I II II II II II I III II II I I I II II I II I I IIII I II III I II II II II III II I I II I II I II I II IIII II III II II II I II I II III IIII III II III IIIII I II I III II III I I IIII I II II IIIIII II I II II II II II IIII III II II I II II II II II II II I IIII I II II I III III I I II III I II II I I IIIII I III I II II II II II IIIIII I II II I III II III II I II I II II II IIIII I I III I II I I IIII I II II III II II I II I I II II III II I II II II II III III I III II I III I II I II II III I III II I I II II III I II II II II IIIIII III I I III III I II IIIII I IIIIII I I II IIII IIII III III II I I III II II I III I III II III I II II III I III I I II I I II II II III I II I III II I III III III II I III II II I

II II III III II II I III III III II I I II II I I II III I II II III I III II I I II I II I II II II I I III IIIII I II I II I II II II IIIII II II II II II I II I I IIIII I III II I II IIIII III II I IIII III II I IIIII I II III I II II II IIIIII III I I III II II III II II IIII II I III I I II II II I III III I I II II III II IIII III II II IIII I IIII I II I II I IIII II III II I I III I I II III I IIIII II II I IIIII III IIII II II II III II II I I IIIII III II II III II I III III I I I II I II II II I IIII IIII II IIIII II I II III IIII II II III I III II II II I II II I I I IIII I II I III III III I III II I III I II I I II II II II III I II III II II III II II I I II III II II I II I II II I II II III III II I I IIII II III I III III II II II II II I I II III I II I III I II II I II II

I I III I II II I II III II I I II II IIII IIII III I II II I IIII II I II III II I II II I I III I I I I II I II III II II II I IIII II II II III III III III III II II II I II II II IIII III II II I II II III II III II I II II II III II III I I II I II III I II II II II I III II I II II II II IIIII II I II II IIII I I II I II I II I II III II II II I IIII III II I II II I I III I I II IIII II II II I II IIII II I II II I III I IIII II I II I I II II II II II II III III I I II

I II I I I II III III II I I II II II II II I II III I I I III II I III IIII I I III I III II I I III IIII

I II III I II II II IIIII II III I II II II II III III II I I III II I II I II I I III III IIII III II II III

III II I II IIIII I I I I IIIII III I I III II III I II IIIIII I III I II III II I I II I II I III II I I III I IIII II I II I II II I III II I II I IIII II II I II II III IIII III I I I I III II I III I I III IIIII III II II I I II II II I II II IIII III I IIII III I II II II III III II I II II II II II I II I III II II III I II II II II I II II IIII I II II III II IIIII II III I III IIII I I III I IIII II II II IIII IIII I II IIIII II II II II II I III I I I III III I II II III I III I III III IIII III II II I II I II II II II II II II II II I III III II I III II II II II II II I I III III I III II II II I II II II II II III I I II I III III I II II II II II II I III II II III II III II I II II I I I II II II II I II II II I III I II I II I I I II I II II II I III I

I III II II IIII III II II III IIII IIII III I I IIII IIIIII I II II II I III II III II II III II I I II I I I IIII III II I II I II II III II I II III III II I II I I III II I III II II II II I II II IIIII II II II II III II II I I II I IIIIII II I III II II II I II I III III II I II II II II I III IIIII II II II III I II II I II II I II II IIII I III II I II II III IIII II I III I II I I IIII II I II II II II IIII I III I II I III II II I II III I I II II II I II IIIII I I IIII II II II I I II I IIIII II II IIII I III II I III III I I III I II II III II II I II II III I I III II III I I II II III I II II II III II II I I IIII III I II II III I II III I III I I II II I I II II I II III II I IIII III III I I II II II I I I I II II III I II I III I II I I I I IIII I II I II II II I IIII I III II I II I I II IIII III IIII III II I II II II I II IIIII III I I IIIII II I II I III II III I II II II III II II II II IIIII I I I III I III III I II II I I I II II II III II II III II I I I I II III I II III II I III II III III III I II II I IIII III II I III II I III I II II I IIII III I II I II II II IIIII IIII II II II III IIII II II II I II II II II I II I II I I III II I II I III III II I IIII I I III III II III II IIIII I II II I I IIIII I I III I IIII II III IIII I II I III I I III III I IIII II III IIIII II II II II II III II IIII II III II II II I II II I II I III II II II I III I I II I I III I II III III II III I II I II I II II II II IIII III I III III I IIII I II II III I II II III II I II II II III I IIII II I III II II I I II III I I II I I III I III I III III II I III I II III III II I II III III II II I II IIII I II II III I III II II II III IIIII I I IIII III I I II I IIIII II II I II II II II II I I II I III II I II I II II I I III II II II I III II I II II I II III III I II I II I IIII I III I I IIII II I II III I II I II II I IIIII III I IIII I I I II II III IIII III II III III II I III I I III II II II II II III I II I III II I II II II II II II II II IIII I I II II I II II I II II IIII II II II I III II IIII III IIII I I III I II III III II I III I III I III II II II I II I II III III II I IIIII II III III I II I III I IIIII II I II I III II IIII II III IIII I III IIII I III I III III I II III I III II II III III III II II I IIIII II I III I I I II I II I II IIII I I II II II I II III III II III II II I II I II II II I I II II IIII II III I I III I II II I I II II I II II II III II II II II I I II III II II II I IIII II I III IIII III I III III II II II IIII II IIII II I I

II I I II I II I II III I I III II I II I III II IIII III I II IIIII I II I I III I I III I I I I II II I I II I II II III III II II III II III II II IIIII I I II I III I II III I II II III II I II III I II III II II III II II I II I II I I I III III II IIII I II I

I II II I II II I III IIII IIIII II II II II I I II IIII II III II III II II IIII II III I IIIII I III III I I IIII I I II I IIII II IIII II II I III IIII III II II II I IIII I I II I I I II II II II I I IIIII III I II III I II I I I II II I II II I II II II IIIIIII I II III I IIII II III III I III III III II II I II II II II I II I II I IIII II I I II II II I IIII II II I II II III II II II I II I III IIII III I I I IIII I III II I I IIII I III II II II II I II I III III II II IIII I IIII I II III III I II II I II II I I I III III III III I II III I II II I III IIIII III II II II II II II II II I III I III II II III I II I III I I II III I II I III I II I IIII I III II I IIII II I II II III II III

I II II I II III II IIII III I II I III II III

I I II III II III III I IIII IIII II I II II I III I IIII II II I I II II III III I IIIII III III II I III I II I II I I II I II II III III II II II II I III III I II II II II III I III II I III IIIII II I III III IIII I I III I II I IIII I I II I I II I III I III III III I II II II II I I II I I II II II III III IIIII II I I II III II I II II I II II I III II IIII III I II II IIII I III I II II II II II II III I I II II II I IIII III II I II I II II I II II II II IIIII II II II I III II I II II I II I I I III III III II II I I III III I III II I III II II I I II I II I I III II III II II III II II I III III III III I I I III III III III I I I II II I II II I III I III II III II III II II IIIII I I IIII II II III III II IIII I II III III III III II I II I III I IIII II I I I IIIII I IIII I II I II II II II II III I III II I I III I I II II I I I III III II I II IIII II I I III I III III II III II II II II I IIII II II III I I IIII III II II III II II II III II II II I II II III III II IIII II III III I II II III I III IIIII I I III II III III II I III III IIII IIII I II I I III I II IIII I IIIII I III I III I III II I III II II II I II I IIII I I II II I II I IIIII II I II III IIIII I IIIII III I IIII I III II II I II I II I II II II II I IIII I III I II II I II I II II II II III II III I II III II IIII I II II I III I II I II I II I III II I III I II I II I II I II I II II III III I I III II III IIIII II I III II III III III I II III II I II II I I III II III II IIII II I I II I II II III I I I I IIII I I III I I III III I III II I II III I IIIII I I I IIII I II I III I III III I I II II I II III IIIII III II IIIII IIIII I II II II II III III I I III II III II I IIII II I IIII III I II II II I II I IIII III II II I I I I II I II I I II I II III II IIII IIII III I I III II I II III II I III II I II II I IIIII II III II II I IIIII II III II II III III II I II III I III I II II II II II IIIII II II I II I II II II II I II II II II IIII I I III I III II I I I II II I IIII I III IIIII III I I IIIII III II III II III III I III II I III III II II II IIIII II I II I I III II I I II II II I II

FB

XW

7 R

425G

ZY

G11

B R

257P

HR

AS

G13

R

EIF

3I R

77P

TB

C1D

12 N

CS

NV

TP

53 D

259V

RA

BE

P2

V35

2L

FG

FR

3 S

249C

BIR

C6

R47

13L

SO

RB

S1

G13

3R

ER

BB

3 V

104L

EX

OC

4 S

21*

EV

I2A

NC

SN

V

NF

E2L

2 R

34G

TB

C1D

12 N

CS

NV

HR

AS

Q61

L

WD

R83

E69

Q

FG

FR

3 Y

373C

PR

DM

16 E

271Q

PIK

3CA

H10

47R

PIK

3CA

H10

47L

NC

OA

6 K

905N

TP

53 L

257Q

HAV

CR

2 N

CS

NV

KR

AS

G12

D

GA

R1

R13

P

TP

53 R

248Q

DS

T N

CS

NV

GT

F2I

RD

1 P

307A

ER

CC

2 N

238S

FAM

82B

R6G

SE

NP

3 N

CS

NV

FG

FR

3 S

371C

GN

A13

R20

0G

MD

GA

2 R

955G

C2o

rf16

E26

8K

HR

AS

Q61

K

PS

D3

NC

SN

V

FG

FR

3 K

650E

FG

FR

3 G

370C

GA

D2

NC

SN

V

HIS

T1H

3B R

132G

WN

K1

R34

1G

TT

N N

CS

NV

SC

AM

P1

NC

SN

V

RB

1CC

1 I4

33V

KC

NK

2 S

6W

ELF

3 E

262Q

KD

M6A

NC

SN

V

KR

AS

G12

V

RA

B11

FIP

5 T

246P

MIN

A N

CS

NV

PIK

3CA

H10

47R

C10

orf7

6 Q

267K

US

P40

NC

SN

V

SF

3B1

K70

0E

EX

OC

4 S

21L

TP

53 Y

220S

FAM

189A

2 I2

41I

TP

53 R

273L

PD

E4D

IP N

CS

NV

KIA

A05

28 R

181Q

PLE

KH

M1

NC

SN

V

LDH

AL6

B N

CS

NV

TP

53 R

342P

MY

LK3

NC

SN

V

TP

53 I1

95T

PIK

3CA

H10

47L

ZM

YM

1 N

CS

NV

TP

53 F

113C

CN

TN

AP

3 N

CS

NV

MLL

3 E

640*

ZN

F69

2 N

CS

NV

MY

L5 R

46P

VP

S13

C T

3732

M

TP

53 L

194R

FR

MD

7 N

CS

NV

US

O1

E61

0Q

AK

AP

9 N

CS

NV

HE

ATR

6 L1

62P

PPA

RG

L24

2V

C1o

rf12

9 N

CS

NV

ER

BB

2 L7

55S

GAT

A3

M29

4K

CD

H1

Q23

*

TP

53 Y

220C

TP

53 H

179R

TP

53 H

193R

PIK

3CA

N34

5K

ZN

F61

1 N

CS

NV

SE

C31

A R

242L

ALD

OA

NC

SN

V

SU

PT

6H D

130Y

PIK

3CA

E54

5A

C12

orf6

9 N

CS

NV

TP

53 N

CS

NV

MY

O15

A K

2535

M

TP

53 H

193L

AK

T1

E17

K

STA

R N

CS

NV

FB

XW

7 R

505G

NO

D2

P17

7R

ST

MN

3 N

CS

NV

ALD

OA

NC

SN

V

ZN

F33

5 N

CS

NV

ME

D12

D23

Y

AN

KR

D20

A4

NC

SN

V

GA

BPA

NC

SN

V

HN

RN

PR

NC

SN

V

TH

AP

1 N

CS

NV

FB

XW

7 R

479G

SIG

LEC

7 Q

309R

TP

63 K

188M

CE

LF4

NC

SN

V

TC

F20

NC

SN

V

PP

P1R

16B

NC

SN

V

CA

CN

G7

V19

7G

C12

orf4

3 E

28Q

TR

MT

2A R

167P

LMN

B2

NC

SN

V

RB

M39

NC

SN

V

ZN

F65

8 N

443K

FAM

155A

NC

SN

V

ST

6GA

L1 N

CS

NV

AK

T1

NC

SN

V

PIK

3CA

C42

0R

CC

ND

1 P

287T

HIS

T2H

2AC

R30

P

GT

F3C

4 F

317F

EP

300

W14

36R

PIK

3CA

H10

47R

HIS

T1H

2AL

R30

P

FAT

2 N

CS

NV

RO

CK

1 N

CS

NV

PR

R22

NC

SN

V

NF

E2L

2 E

82D

KR

AS

G12

D

PIK

3CA

E54

5K

KR

AS

G12

V

ZN

F70

6 I8

N

CA

MK

2D N

CS

NV

BT

G1

NC

SN

V

FAM

19A

5 N

CS

NV

OB

P2B

NC

SN

V

NX

F1

NC

SN

V

IQS

EC

2 P

1185

P

C8o

rf59

NC

SN

V

DE

NN

D4A

R81

4H

MA

PK

1 E

322K

ER

CC

6 E

272K

BR

AF

V60

0E

TP

53 A

159P

AB

CF

3 R

269G

VN

1R5

K35

7M

KR

AS

G12

V

KR

AS

G12

A

KR

AS

G12

D

AP

C K

1370

*

CG

RE

F1

NC

SN

V

ZC

3H11

A M

752T

PIK

3CA

E54

5K

PC

BP

1 L1

00Q

AP

C S

940*

PO

LDIP

3 C

320W

RU

FY

3 N

CS

NV

PIK

3CA

H10

47R

KR

AS

G12

R

ITP

RIP

L2 N

CS

NV

TR

ER

F1

V11

66D

MO

RC

2 N

CS

NV

KR

AS

G12

C

AP

C E

1408

*

GN

G11

NC

SN

V

DS

P I8

38S

TM

ED

4 N

CS

NV

ZN

F18

9 R

392I

GP

R98

S49

92A

PIK

3CA

V34

4G

OR

6C65

L11

2I

NP

NT

NC

SN

V

KR

AS

G13

D

PC

DH

11Y

NC

SN

V

SP

DY

E6

D26

1E

AB

CA

6 T

772A

AP

C E

1397

*

NR

AS

G13

R

ME

P1B

K39

6N

GT

F2B

NC

SN

V

TC

F7L

2 S

46*

TM

EM

132E

A11

G

AP

C Y

935*

AP

C Q

1378

*

PT

PR

K N

915T

AP

C E

941*

PIK

3CA

E54

5A

RB

AK

S99

A

CN

TN

AP

3 N

CS

NV

EYA

2 G

77A

DN

AJC

22 H

30Q

NU

P10

7 T

45A

TP

53 R

175G

AD

AM

TS

3 N

CS

NV

AN

XA

8 N

CS

NV

TP

53 N

CS

NV

PIK

3CA

H10

47L

AR

F6

NC

SN

V

CD

C42

BPA

P67

5T

SU

PT

6H D

130Y

ST

6GA

L1 N

CS

NV

RN

F4

NC

SN

V

TP

53 P

278A

TP

53 C

135F

TP

53 Y

220C

ST

RN

3 N

CS

NV

SLC

38A

11 N

CS

NV

TP

53 R

248Q

RB

BP

8 G

810V

TP

53 C

275F

TP

53 C

176F

RE

RE

NC

SN

V

TP

53 E

198*

TP

53 E

294*

TP

53 R

175H

AM

PH

NC

SN

V

SLI

TR

K6

NC

SN

V

TP

53 R

248W

TT

N T

2290

4P

PIK

3CA

E54

5K

TR

IM13

NC

SN

V

KP

NB

1 L5

52F

NT

RK

3 N

CS

NV

AB

CB

1 K

915T

TP

53 R

213*

DN

AH

10 D

1128

Y

PH

AC

TR

1 N

CS

NV

TP

53 R

282W

GB

E1

F55

1V

HD

AC

4 F

746L

TP

53 R

273C

C10

orf7

6 Q

267K

MB

TP

S1

L77M

ER

BB

2 V

777L

TP

53 R

273H

HE

ATR

7B2

K14

96T

ELA

VL3

NC

SN

V

TP

53 R

196*

TP

53 R

342*

AS

PH

NC

SN

V

AS

PH

NC

SN

V

SN

AI1

NC

SN

V

NE

XN

M38

6R

C10

orf3

5 N

CS

NV

LLG

L1 A

462P

CN

R1

Y27

5S

FH

OD

1 N

CS

NV

DH

X40

E12

1*

BR

AF

V60

0E

FH

L1 K

17Q

SIA

H2

NC

SN

V

AC

TC

1 K

330*

TP

53 Y

220C

NR

AS

Q61

L

GA

BR

A6

V32

F

SID

T2

A63

2P

RG

AG

1 N

CS

NV

TP

53 H

179R

LSS

V48

9G

PIG

O N

CS

NV

PIA

S3

NC

SN

V

EG

FR

G59

8V

PR

DM

11 N

182H

PT

EN

G13

2D

EG

FR

T26

3P

LY6E

NC

SN

V

TP

53 Y

234C

PIK

3R1

G37

6R

TP

53 C

238F

PIK

3R1

NC

SN

V

EG

FR

S64

5C

CT

SA

E42

7D

PT

EN

S17

0N

DA

PK

1 V

1134

A

PD

CD

2L E

344*

EG

FR

A28

9D

TP

53 V

216M

TP

53 C

275Y

PIK

3R1

K37

9N

MU

C2

Y19

77Y

TB

X1

D24

7Y

MLX

NC

SN

V

MU

C6

T10

15M

FAM

120A

H91

8Q

TP

53 R

248Q

EG

FR

A28

9V

DQ

X1

R50

5H

FB

XO

33 S

401R

AN

KR

D17

G17

42G

KC

NT

2 Q

1038

H

TP

53 R

175H

PIK

3CA

M1V

FB

XW

7 R

505G

FG

FR

3 S

249C

MY

H7

E14

9K

IFN

GR

1 R

123*

DH

X15

R39

9H

PIK

3CA

E54

5K

EP

300

D13

99N

PIK

3CA

E54

2K

PIK

3CA

R88

Q

MA

PK

1 E

322K

MU

C16

E14

09Q

ALP

K3

Q86

0Q

PC

DH

A6

S60

8S

CO

L6A

6 L1

125L

TP

53 R

283P

TP

53 E

298*

CC

DC

50 N

CS

NV

TP

53 R

110L

TP

53 V

157F

TP

53 R

196P

TP

53 H

193L

TP

53 H

193P

FB

XW

7 R

505G

HR

AS

G13

R

TP

53 L

201*

TP

53 Y

163C

PIK

3CA

H10

47R

TP

53 R

158L

TP

53 R

337L

TP

53 Y

220C

TP

53 Y

236C

TP

53 R

280G

TM

TC

2 T

409R

TP

53 H

179R

HR

AS

G13

V

EP

HA

3 T

802R

TP

53 R

175H

TP

53 N

CS

NV

TP

53 Y

234C

HR

AS

G12

C

TP

53 R

249S

TP

53 R

282W

CD

KN

2A D

108Y

MA

P2

E86

5*

TP

53 E

294*

TP

53 R

213*

EP

HA

2 S

419*

H3F

3B K

37M

TP

53 C

242F

TP

53 C

238F

TP

53 P

151S

TP

53 V

272M

RA

C1

A17

8V

ITG

B1

D15

8N

CD

KN

2A R

80*

TP

53 N

CS

NV

TP

53 R

196*

TP

53 R

248W

TP

53 R

248Q

TP

53 S

106R

TP

53 P

278S

TP

53 R

273C

TP

53 R

306*

AR

HG

AP

9 N

CS

NV

VH

L S

68*

VH

L S

65*

SE

TD

2 W

1782

*

SIP

A1L

3 G

777A

VH

L L1

69P

VH

L N

78D

VH

L I1

51T

ZN

F38

4 N

CS

NV

SP

SB

3 G

241R

VH

L H

115N

HN

F1B

N30

2K

VH

L L1

28H

VH

L L1

84P

VH

L N

CS

NV

VH

L V

130F

VH

L N

CS

NV

VH

L E

173*

VH

L L1

88P

VH

L L1

58V

BA

K1

R76

W

VH

L N

131K

VH

L N

CS

NV

VH

L R

161*

MTO

R T

1977

R

VH

L W

88*

ALL

C T

83M

PB

RM

1 R

710*

GP

M6A

A50

V

BA

P1

M1I

GA

LNT

6 P

311P

ED

IL3

T34

3M

PB

RM

1 R

850*

NX

PH

4 K

272K

KIT

D81

6V

C1o

rf85

NC

SN

V

TE

T1

N11

34I

KR

AS

G12

V

RIM

S4

V86

L

FLT

3 D

835Y

GA

RT

E94

8G

IDH

1 R

132C

NS

MA

F L

710F

HIS

T1H

2AE

K12

8M

CH

ST

15 N

CS

NV

AR

HG

AP

30 H

1042

H

IDH

2 R

140Q

CA

CN

G7

V19

7G

FLT

3 D

835E

ALO

X12

B N

670T

NR

AS

G13

D

GA

LNT

8 N

CS

NV

ELA

C2

NC

SN

V

IDH

1 R

132H

DN

MT

3A R

882C

MTA

2 N

CS

NV

ZD

HH

C13

S24

2G

PR

DM

2 M

1397

L

DN

MT

3A R

882H

NR

AS

G12

D

C3A

R1

I116

T

CD

4 N

CS

NV

RA

PH

1 K

296M

RU

NX

1 R

201*

IDH

2 R

172K

RU

NX

1 R

162G

AS

B17

W38

R

KR

TAP

12−4

A59

T

RB

BP

4 E

330K

IDH

1 R

132G

IDH

1 R

132S

IDH

1 R

132H

EG

FR

R25

2P

BR

AF

V60

0E

TP

53 R

273L

IDH

1 R

132C

GR

IA4

K29

5E

TP

53 R

158S

CIC

R15

12L

TP

53 Q

136E

TP

53 H

179D

EG

FR

R32

4L

TP

53 Y

220C

TP

53 H

179R

TP

53 R

273C

IDH

2 R

172K

NO

TC

H1

R44

8L

PIK

3CA

H10

47R

IDH

2 R

172W

EG

FR

L62

R

PIK

3CA

M10

43V

PIK

3CA

K11

1E

TP

53 F

270S

PIK

3CA

G11

8D

TP

53 T

155N

TP

53 Y

236C

PIK

3CA

E45

3K

EG

FR

G59

8V

TP

53 C

275F

TP

53 H

193R

TP

53 M

237V

TP

53 M

246V

IDH

2 R

172M

PIK

3R1

N56

4D

C10

orf7

6 R

419*

IDH

2 R

172G

TP

53 V

173L

TP

53 Y

163C

TP

53 R

280K

KR

T13

R20

1C

SD

HA

M1V

TP

53 P

151S

NR

AS

Q61

R

PIK

3CA

E54

2K

PT

PN

11 A

72D

TP

53 R

248Q

ZB

TB

20 N

650S

PLC

G1

E11

63K

CN

OT

4 N

463S

BA

Z2A

R16

42L

ATP

9A N

56I

MY

O7A

S63

W

CD

163L

1 L1

296P

DN

M2

E37

8D

CT

NN

B1

I35S

ZN

F26

4 E

368*

FAM

13C

P20

1Q

RA

LGA

PB

R61

1P

NE

B D

4097

H

C14

orf3

9 V

463L

TE

RT

NC

SN

V

CT

NN

B1

H36

P

NX

F1

R34

2G

FO

XO

1 S

22W

NLR

P6

D44

1H

HC

N4

NC

SN

V

CT

NN

B1

D32

V

CT

NN

B1

S45

P

ES

YT

2 R

569H

CT

NN

B1

S37

A

IL17

RE

L C

23W

ATP

1A1

N40

5T

LRR

C16

B N

CS

NV

CT

NN

B1

D32

G

CT

NN

B1

K33

5I

FAM

193A

L85

2F

OD

F2

E67

6A

PPA

RA

I171

L

TP

53 C

277*

FG

D6

A51

3G

DU

SP

8 T

316M

DB

N1

D41

V

FAM

124B

R47

P

BR

AP

L41

6V

CT

NN

B1

S33

C

TR

PC

4AP

L48

1V

GJC

1 A

37P

TP

53 R

249S

TP

53 V

157F

SP

HK

1 P

417A

TP

53 R

248L

KIA

A03

55 Q

121P

PLA

2G3

K30

5*

UG

T2B

10 D

120H

FE

M1C

L26

6V

ALD

H1L

2 F

107S

ZD

HH

C1

A29

1P

US

P49

I345

L

CT

NN

B1

N38

7K

EG

FR

L85

8R

CT

NN

B1

S37

F

FAM

71A

R30

*

WD

R60

E10

6K

WA

PAL

D42

3N

CT

NN

B1

S45

F

CD

1A N

CS

NV

ZM

PS

TE

24 S

261F

CT

NN

B1

S37

C

BR

AF

V60

0E

GN

AL

P72

P

OR

2W5

H21

4Y

KR

AS

G12

A

CT

NN

B1

G34

V

AK

R1B

15 Q

212H

TD

O2

Q19

7H

HE

ATR

1 F

1877

V

RP

L6 K

221Q

SH

AN

K3

G62

1G

MB

OAT

2 L3

23F

KR

AS

G12

D

AG

AP

7 I5

81I

BR

AF

N58

1S

KR

AS

G12

V

KR

AS

G12

C

EG

FR

G71

9A

PF

KF

B1

R18

6L

EG

FR

L62

R

PT

PR

U P

559S

SM

AR

CC

2 E

855K

CP

SF

1 S

285L

BC

OR

N14

59S

BR

AF

G46

9A

BC

L9L

G98

0C

PIK

3CA

N34

5K

PIK

3CA

H10

47R

FLR

T3

G19

7C

C4B

NC

SN

V

SO

S1

N23

3Y

MU

C2

P24

11H

TP

53 A

159P

TP

53 V

157L

FLR

T3

E49

8K

RA

B8A

NC

SN

V

RE

V1

NC

SN

V

PIK

3CA

E54

5K

TT

C17

R41

3L

RA

D50

D69

Y

KE

AP

1 D

479G

AR

HG

EF

9 R

338L

TP

53 Y

234S

NF

E2L

2 R

34P

NF

E2L

2 R

34G

STO

N1

NC

SN

V

TP

53 V

157F

FR

MD

4B R

900L

TP

53 R

175G

TP

53 E

298*

TP

53 R

158L

TP

53 G

245C

SLC

24A

1 V

455G

ME

GF

8 R

2514

L

CD

KN

2A D

108Y

TT

N R

1073

0G

TP

53 R

273L

TP

53 Y

163C

MD

GA

2 T

517P

MID

N E

122Q

TP

53 Y

234C

TP

53 Y

220C

HO

ME

Z L

306P

TP

53 A

159P

TAF

9 N

CS

NV

NP

R2

E21

1*

LOX

HD

1 T

1789

N

PR

KA

G1

NC

SN

V

DS

T N

CS

NV

CH

D8

E59

9K

CD

KN

2A D

84G

TP

53 N

CS

NV

IQS

EC

2 G

613C

CO

L5A

2 G

936W

DD

R2

D17

1Y

FB

XW

7 R

505G

TP

53 T

125T

TP

53 N

131I

CD

KN

2A D

84Y

NF

E2L

2 G

31A

RO

RC

H49

0P

TP

53 R

248L

C20

orf9

4 T

180R

CLN

3 G

206S

TP

53 Y

236C

TP

53 K

305*

TP

53 Q

144P

C11

orf6

3 K

685M

SLC

45A

2 S

97C

EP

300

D13

99N

TP

53 R

282W

SE

RP

INA

11 R

150P

MO

N2

NC

SN

V

MG

RN

1 G

64A

CO

L14A

1 N

CS

NV

BD

NF

NC

SN

V

PIK

3CD

V23

3G

TOP

BP

1 N

CS

NV

CA

SD

1 N

CS

NV

TP

53 V

157F

TP

53 I2

51S

CC

DC

66 Q

379E

TP

53 I1

95T

RS

F1

NC

SN

V

TP

53 R

273L

RP

S16

NC

SN

V

PD

ILT

Y47

6*

GA

BPA

NC

SN

V

FR

MD

7 N

CS

NV

MA

P2

NC

SN

V

TOP

2A T

215P

PIK

3R4

G60

9D

MA

ML3

G10

69A

CY

P4F

2 A

182G

TP

53 Y

163C

TP

53 Y

220C

SY

TL4

NC

SN

V

TP

53 R

175H

LDH

AL6

B N

CS

NV

UX

S1

V10

5L

TP

53 R

248Q

TP

53 L

194R

NR

IP1

NC

SN

V

TP

53 R

248W

FAM

83H

P70

A

PR

KG

2 N

CS

NV

TF

M45

I

FB

XO

10 S

950T

UT

P20

L38

4H

PN

N S

443A

LRR

C16

B T

804P

UB

E3C

NC

SN

V

SO

RB

S1

NC

SN

V

NR

AS

Q61

R

TP

53 Y

234C

TP

53 S

241F

TP

53 M

237K

RP

F1

F26

7S

TP

53 Q

192*

C1o

rf12

9 N

CS

NV

TP

53 N

CS

NV

TP

53 P

177R

KR

AS

G12

R

KR

AS

G12

V

KR

AS

G12

D

KR

AS

Q61

H

TP

53 V

143E

KR

AS

Q61

R

EE

F2

Y45

7*

TP

53 Y

220C

TP

53 C

275F

TP

53 H

179R

TM

EM

218

NC

SN

V

TP

53 E

294*

IGF

N1

S19

76S

ATP

1B1

E15

4E

TP

53 H

179Y

CD

KN

2A H

83Y

TP

53 R

248W

TP

53 R

213*

TP

53 R

282W

SM

AD

4 S

144*

SM

AD

4 E

520*

TP

53 R

248Q

AB

CA

13 A

2368

V

CD

KN

2A R

80*

SM

AD

4 Q

289*

TP

53 R

175H

GN

AS

R84

4C

TP

53 R

196*

TP

53 G

245S

SM

AD

4 R

361C

TP

53 R

273C

PLE

KH

H1

V86

6M

GN

AS

R84

4H

PX

DN

L R

235Q

TP

53 R

306*

TP

53 R

337C

TR

A2A

R94

*

CD

KN

2A R

58*

CO

L5A

1 P

657L

PLE

KH

A4

R22

5W

TP

53 R

273H

AB

CG

4 T

494M

SLC

12A

6 R

319H

TG

FB

R1

R48

7Q

EH

BP

1L1

A97

7A

OD

Z3

R22

28H

TT

N N

2692

7N

CD

KL4

V10

6I

ER

BB

2 V

842I

RS

PO

1 A

146A

SP

OP

Y87

S

SP

OP

W13

1G

SP

OP

F13

3C

SP

OP

F13

3V

SP

OP

F10

2V

CU

L3 M

305R

SP

OP

F10

2C

SP

OP

Y87

N

TP

53 Y

163H

SP

OP

F10

2S

TP

53 C

141G

SP

OP

F13

3I

RH

OA

L22

R

SP

OP

F13

3L

PC

DH

19 R

395*

SP

OP

Y87

C

SP

OP

W13

1L

TP

53 N

239D

BR

AF

G46

9A

SP

OP

W13

1R

ME

D12

V12

23L

HR

AS

Q61

R

CT

NN

B1

T41

A

TP

53 G

279E

ME

D12

L12

24F

MLL

3 Y

4440

C

AC

P1

NC

SN

V

PIK

3CA

H10

47R

TP

53 R

248Q

PIK

3CA

E54

2K

PO

U2F

1 R

401H

IDH

1 R

132C

C11

orf2

4 A

395V

AK

T1

E17

K

TP

53 G

245S

BD

KR

B1

G11

5R

CAT

SP

ER

G D

966D

TP

53 R

282W

DN

AH

10 R

3649

W

PY

GL

S80

9L

GG

T5

G49

0R

ME

CO

M R

915Q

TP

53 R

175H

CN

OT

3 E

20K

CD

H23

S12

50S

TLR

7 P

147L

ITG

AL

R83

0C

HT

T A

805V

HE

Y2

C24

9C

PAR

VG

A96

T

AP

C E

1209

*

AP

C E

1322

*

AP

C C

1270

*

AP

C K

1165

*

MA

ML3

G10

69A

AP

C E

1353

*

AP

C Q

1367

*

AP

C Q

1378

*

AP

C Q

1406

*

AP

C E

1397

*

AP

C Q

1429

*

AP

C E

1309

*

AP

C S

1327

*

AP

C S

1356

*

AP

C R

1114

*

AP

C R

876*

AP

C E

1306

*

AP

C Q

1338

*

AP

C R

1450

*

AP

C R

302*

AP

C R

213*

NP

HS

1 D

1208

Y

PC

BP

1 L1

00Q

KR

AS

G12

V

AP

C R

216*

C8A

S42

1Y

SLC

5A8

E55

9*

HE

ATR

1 L1

256I

TOP

2A E

1035

*

CC

DC

18 N

CS

NV

AP

1M1

N15

5H

KR

AS

G12

A

AP

C R

283*

AP

C R

348*

AP

C R

564*

AR

ID1A

R19

89*

TP

53 I1

95T

GY

LTL1

B V

553G

PC

YT

1A F

263C

PC

BP

1 L1

02Q

KR

AS

G12

D

NA

A25

S60

6Y

ATP

10B

L76

1H

PD

CD

6IP

R32

7Q

RF

X6

R86

6Q

EYA

2 G

77A

KR

AS

G12

C

TR

PM

7 R

1862

C

AB

CB

1 R

286I

GO

LGB

1 V

1309

L

NR

AS

Q61

R

NR

AS

Q61

K

NR

AS

Q61

L

AP

RT

R87

G

NR

AS

G13

R

BR

AF

V60

0E

CS

DE

1 F

700V

IPM

K L

254V

NR

AS

G12

R

NR

AS

Q61

H

SN

X7

E36

4A

AN

KR

D32

L69

1R

NR

AS

G12

V

SD

CB

P T

268A

EP

RS

I820

L

DH

X32

R51

S

AN

O9

D47

3A

SY

TL2

NC

SN

V

AR

HG

EF

2 R

609G

ZN

F83

0 R

239S

FAM

120A

I302

K

TM

2D3

Y13

6S

KIA

A01

00 R

952L

PPA

T E

11D

SC

UB

E3

L427

V

CD

K4

R24

S

UC

KL1

D47

3H

CP

SF

1 Y

1164

H

TR

IM59

I353

M

FAM

151A

V31

D

US

PL1

A43

5G

PLE

KH

G4B

D33

0A

GP

RA

SP

1 D

145V

SLC

6A2

R21

6G

GC

G N

CS

NV

EIF

4G3

E18

9*

CU

BN

R22

4G

BR

AF

N58

1T

MB

NL3

NC

SN

V

TP

MT

V22

0A

STA

T5A

L35

5P

SLC

25A

46 L

221Q

NR

4A3

NC

SN

V

TLL

2 N

CS

NV

DD

X47

G12

8R

AB

CA

6 N

CS

NV

PIP

4K2A

NC

SN

V

TR

PV

2 L1

27V

CT

RB

2 N

CS

NV

MT

MR

6 F

75C

BR

AF

V60

0E

KIT

K64

2E

NR

AS

Q61

R

NR

AS

Q61

L

RP

S27

NC

SN

V

NR

AS

Q61

K

BR

AF

K60

1E

GN

AQ

Q20

9P

CD

YL2

D31

2E

P2R

Y11

NC

SN

V

BA

GE

2 N

CS

NV

TT

N N

CS

NV

C5

R12

06C

AB

CF

1 R

844*

SN

AP

91 D

723N

SIP

A1L

2 S

1472

L

TP

53 R

342*

CO

L5A

3 N

CS

NV

ZN

F99

NC

SN

V

DD

X27

NC

SN

V

TT

N N

CS

NV

TT

N N

CS

NV

PP

IAL4

A N

CS

NV

SLC

30A

8 L2

90P

TT

N H

1509

3H

KIA

A11

99 G

722E

AQ

P12

B T

16I

CY

P4F

12 P

367S

ZN

F76

8 A

488A

A2M

R14

7C

SA

RS

2 N

CS

NV

AR

NT

S32

1F

MD

N1

A23

8V

CO

L12A

1 R

1414

*

AM

D1

R21

0C

FO

LH1

NC

SN

V

AM

Y1C

K29

3K

RA

C1

P29

S

NS

FL1

C N

CS

NV

MA

GE

A11

S20

8L

DH

TK

D1

P84

2L

SE

RP

INA

1 N

CS

NV

ALP

PL2

G44

8R

GD

F2

F33

6F

RE

G1B

NC

SN

V

RA

SA

L2 P

146L

SY

DE

1 F

703F

NP

HP

1 R

347*

BU

B1

R67

7C

SLC

4A10

R41

0C

AR

ID5B

A10

09G

LHC

GR

NC

SN

V

MA

CC

1 N

CS

NV

RH

OA

Y42

S

VM

O1

NC

SN

V

GA

BR

E N

CS

NV

TT

N N

CS

NV

RN

F17

5 S

215G

PIK

3CA

H10

47R

TT

N N

CS

NV

PIK

3CA

N34

5K

ZC

3H4

E77

9Q

CD

H1

D25

4Y

ZB

TB

7A K

424T

DE

K S

288T

OLI

G2

S88

A

IQS

EC

2 G

283A

TP

53 C

176F

DR

G2

R38

L

KC

NH

2 G

149A

C8B

L13

8R

GN

G7

N45

K

ZD

HH

C8

P45

7A

KR

AS

G12

D

DO

CK

10 K

935M

TP

53 Y

220C

ITG

B1

L378

I

INS

IG2

I63F

CAV

1 N

CS

NV

CT

NN

B1

D32

H

AR

HG

AP

1 N

154I

ZM

YM

5 V

60D

TM

CC

1 N

CS

NV

ER

BB

2 D

769Y

C1o

rf9

NC

SN

V

PIK

3CA

E54

5K

ER

BB

2 N

CS

NV

C8o

rf42

W89

G

DE

FB

104A

E25

A

TP

53 P

151T

MLH

1 R

659*

ER

BB

2 S

310F

RP

L5 M

208T

ZH

X3

N24

9K

WT

1 N

CS

NV

NA

LCN

NC

SN

V

DK

K2

NC

SN

V

GA

RT

Q24

1R

STA

G1

A11

6T

TP

53 V

272M

BR

AF

V60

0E

NR

AS

Q61

R

ST

XB

P3

NC

SN

V

MR

PS

16 N

CS

NV

HR

AS

Q61

R

NR

AS

Q61

K

INT

S2

Y57

8N

SPA

CA

3 N

CS

NV

EIF

1AX

NC

SN

V

MA

RC

H4

NC

SN

V

GN

B2L

1 N

CS

NV

BR

AF

K60

1E

EIF

1AX

G9R

KR

AS

G12

V

KIA

A11

09 V

825F

PLC

L1 V

442I

ATP

6V0A

1 N

CS

NV

PM

PC

B N

CS

NV

EIF

1AX

G9D

HR

AS

Q61

K

MC

PH

1 K

645N

DN

AH

10 I1

660M

TB

C1D

12 N

CS

NV

OG

T P

120L

CC

2D2B

NC

SN

V

PP

P2R

1A A

273V

NU

P93

Q15

*

AK

T1

E17

K

DG

CR

8 E

518K

TB

C1D

12 N

CS

NV

TP

53 Q

192*

OR

52E

2 A

251A

PT

EN

R13

0G

SP

I1 N

CS

NV

NF

E2L

2 R

34G

FG

FR

2 S

252W

VN

1R5

K35

7M

AR

ID1A

R22

36P

PP

P2R

1A P

179R

XPA

NC

SN

V

C2C

D4A

NC

SN

V

CN

O N

CS

NV

MB

D2

NC

SN

V

ST

X5

NC

SN

V

AB

HD

14A

F19

1C

GC

SH

K16

9Q

SS

X2I

P N

CS

NV

RA

B6A

NC

SN

V

ME

TT

L14

R29

8P

P2R

Y13

NC

SN

V

TS

PAN

10 P

115A

SO

X17

S40

3I

ZB

TB

6 T

357I

CB

R3

NC

SN

V

RS

RC

1 S

239Y

FB

XW

7 R

505G

CN

O N

CS

NV

FO

LH1B

NC

SN

V

SO

S1

N23

3Y

DD

X1

NC

SN

V

CN

O N

CS

NV

B2M

NC

SN

V

MO

RC

3 R

896P

C16

orf9

1 N

CS

NV

PC

MT

D1

R16

2Q

PO

LE P

286R

AR

L6IP

6 N

CS

NV

PIK

3CA

H10

47L

LTV

1 R

377*

MU

C2

E26

12K

C2C

D4A

NC

SN

V

INS

M1

NC

SN

V

INS

M1

NC

SN

V

JUN

D N

CS

NV

TM

EM

37 E

165K

DLE

U7

NC

SN

V

ZN

F75

A R

134I

ZN

F75

A R

181I

SO

CS

2 R

96Q

AD

O N

CS

NV

GB

X2

NC

SN

V

AU

P1

NC

SN

V

FB

XW

7

HR

AS

TB

C1D

12

TP

53

FG

FR

3

SO

RB

S1

EX

OC

4

NF

E2L

2

TB

C1D

12

HR

AS

FG

FR

3

PIK

3CA

PIK

3CA

TP

53

KR

AS

TP

53

DS

T

FG

FR

3

MD

GA

2

HR

AS

FG

FR

3

FG

FR

3

TT

N

KR

AS

PIK

3CA

C10

orf7

6

EX

OC

4

TP

53

TP

53

LDH

AL6

B

TP

53

TP

53

PIK

3CA

TP

53

CN

TN

AP

3

MLL

3

TP

53

FR

MD

7

C1o

rf12

9

ER

BB

2

CD

H1

TP

53

TP

53

TP

53

PIK

3CA

ALD

OA

SU

PT

6H

PIK

3CA

TP

53

TP

53

AK

T1

FB

XW

7

ALD

OA

ME

D12

GA

BPA

FB

XW

7

CA

CN

G7

ST

6GA

L1

AK

T1

PIK

3CA

EP

300

PIK

3CA

NF

E2L

2

KR

AS

PIK

3CA

KR

AS

NX

F1

IQS

EC

2

MA

PK

1

BR

AF

TP

53

VN

1R5

KR

AS

KR

AS

KR

AS

AP

C

PIK

3CA

PC

BP

1

AP

C

PIK

3CA

KR

AS

KR

AS

AP

C

PIK

3CA

KR

AS

AB

CA

6

AP

C

NR

AS

AP

C

AP

C

AP

C

PIK

3CA

CN

TN

AP

3

EYA

2

TP

53

TP

53

PIK

3CA

SU

PT

6H

ST

6GA

L1

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TT

N

PIK

3CA

AB

CB

1

TP

53

DN

AH

10

TP

53

TP

53

C10

orf7

6

ER

BB

2

TP

53

TP

53

TP

53

AS

PH

AS

PH

BR

AF

TP

53

NR

AS

TP

53

EG

FR

PT

EN

EG

FR

TP

53

PIK

3R1

TP

53

PIK

3R1

EG

FR

PT

EN

EG

FR

TP

53

TP

53

PIK

3R1

MU

C2

FAM

120A

TP

53

EG

FR

TP

53

PIK

3CA

FB

XW

7

FG

FR

3

PIK

3CA

EP

300

PIK

3CA

PIK

3CA

MA

PK

1

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

FB

XW

7

HR

AS

TP

53

TP

53

PIK

3CA

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

HR

AS

TP

53

TP

53

TP

53

HR

AS

TP

53

TP

53

CD

KN

2A

MA

P2

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

RA

C1

ITG

B1

CD

KN

2A

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

TP

53

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

VH

L

PB

RM

1

PB

RM

1

KIT

KR

AS

FLT

3

GA

RT

IDH

1

IDH

2

CA

CN

G7

FLT

3

NR

AS

IDH

1

DN

MT

3A

DN

MT

3A

NR

AS

RU

NX

1

IDH

2

RU

NX

1

IDH

1

IDH

1 IDH

1

EG

FR

BR

AF

TP

53

IDH

1

TP

53

TP

53

TP

53

EG

FR

TP

53

TP

53

TP

53

IDH

2

PIK

3CA

IDH

2

EG

FR

PIK

3CA

PIK

3CA

TP

53

PIK

3CA

TP

53

TP

53

PIK

3CA

EG

FR

TP

53

TP

53

TP

53

TP

53

IDH

2

PIK

3R1

C10

orf7

6

IDH

2

TP

53

TP

53

TP

53

TP

53

NR

AS

PIK

3CA

TP

53

CT

NN

B1

CT

NN

B1

NX

F1

CT

NN

B1

CT

NN

B1

CT

NN

B1

LRR

C16

B

CT

NN

B1

CT

NN

B1

TP

53

CT

NN

B1

TP

53

TP

53

TP

53

CT

NN

B1

EG

FR

CT

NN

B1

CT

NN

B1

CT

NN

B1

BR

AF

KR

AS

CT

NN

B1

HE

ATR

1

KR

AS

BR

AF

KR

AS

KR

AS

EG

FR

EG

FR

CP

SF

1

BR

AF

PIK

3CA

PIK

3CA

FLR

T3

SO

S1

MU

C2

TP

53

TP

53

FLR

T3

PIK

3CA

TP

53

NF

E2L

2

NF

E2L

2

TP

53

TP

53

TP

53

TP

53

TP

53

CD

KN

2A

TT

N

TP

53

TP

53

MD

GA

2

TP

53

TP

53

TP

53

DS

T

CD

KN

2A

TP

53

IQS

EC

2

FB

XW

7

TP

53

TP

53

CD

KN

2A

NF

E2L

2

TP

53

TP

53

TP

53

TP

53

EP

300

TP

53

TP

53

TP

53

TP

53

TP

53

GA

BPA

FR

MD

7

MA

P2

TOP

2A

MA

ML3

TP

53

TP

53

TP

53

LDH

AL6

B

TP

53

TP

53

TP

53

LRR

C16

B

SO

RB

S1

NR

AS

TP

53

TP

53

TP

53

TP

53

C1o

rf12

9

TP

53

TP

53

KR

AS

KR

AS

KR

AS

KR

AS

TP

53

KR

AS

TP

53

TP

53

TP

53

TP

53

TP

53

CD

KN

2A

TP

53

TP

53

TP

53

SM

AD

4

SM

AD

4

TP

53

CD

KN

2A

SM

AD

4

TP

53

GN

AS

TP

53

TP

53

SM

AD

4

TP

53

GN

AS

TP

53

TP

53

CD

KN

2A

TP

53

TT

N

ER

BB

2

SP

OP

SP

OP

SP

OP

SP

OP

SP

OP

SP

OP

SP

OP

TP

53

SP

OP

TP

53

SP

OP

RH

OA

SP

OP

SP

OP

SP

OP

TP

53

BR

AF

SP

OP

ME

D12

HR

AS

CT

NN

B1

TP

53

ME

D12

MLL

3

PIK

3CA

TP

53

PIK

3CA

IDH

1

AK

T1

TP

53

TP

53

DN

AH

10

TP

53

AP

C

AP

C

AP

C

AP

C

MA

ML3

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

AP

C

PC

BP

1

KR

AS

AP

C

HE

ATR

1

TOP

2A

KR

AS

AP

C

AP

C

AP

C

AR

ID1A

TP

53

PC

BP

1

KR

AS

EYA

2

KR

AS

AB

CB

1

NR

AS

NR

AS

NR

AS

NR

AS

BR

AF

NR

AS

NR

AS

NR

AS

FAM

120A

CP

SF

1

BR

AF

AB

CA

6

BR

AF

KIT

NR

AS

NR

AS

NR

AS

BR

AF

TT

N

TP

53

TT

N

TT

N

TT

N

RA

C1

RH

OA

TT

N

PIK

3CA

TT

N

PIK

3CA

CD

H1

IQS

EC

2

TP

53

KR

AS

TP

53

ITG

B1

CT

NN

B1

ER

BB

2

PIK

3CA

ER

BB

2

TP

53

ER

BB

2

GA

RT

TP

53

BR

AF

NR

AS

HR

AS

NR

AS

EIF

1AX

BR

AF

EIF

1AX

KR

AS

EIF

1AX

HR

AS

DN

AH

10

TB

C1D

12

PP

P2R

1A

AK

T1

TB

C1D

12

TP

53

PT

EN

NF

E2L

2

VN

1R5

AR

ID1A

PP

P2R

1A

C2C

D4A

CN

O

FB

XW

7

CN

O

SO

S1

CN

O

PIK

3CA

MU

C2

C2C

D4A

INS

M1

INS

M1

ZN

F75

A

ZN

F75

A

nTCGA = 137

nTCGA = 143

nTCGA = 184

nTCGA = 178 nYG = 50

nTCGA = 336

nTCGA = 289 nYG = 56

nTCGA = 393

nTCGA = 399

nTCGA = 364 nYG = 41

nTCGA = 412

nTCGA = 65

nTCGA = 412

nTCGA = 436

nTCGA = 437

nTCGA = 495

nTCGA = 508

nTCGA = 492 nYG = 22

nTCGA = 363 nYG = 156

nTCGA = 104 nYG = 47

nTCGA = 530 nYG = 23

nTCGA = 492 nYG = 108

nTCGA = 567 nYG = 108

nTCGA = 986

READ

LAML

ESCA

PAAD

KIRC

CESC

GBM

COAD

LIHC

BLCA

HPV+ HNSC

HPV− HNSC

OV

STAD

PRAD

LGG

THCA

SKCMM

SKCMP

UCEC

LUSC

LUAD

BRCA

103104105106107

Selection intensity

Tum

or ty

pe

Q value

Q ≤ 0.1

Q > 0.1

Prevalence

0.60

0.40

0.20

0.10

0.05

0.01

Supplemental Figure 1

.CC-BY-NC 4.0 International licenseis made available under aThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It. https://doi.org/10.1101/229724doi: bioRxiv preprint