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Effect sizes of somatic mutations in cancer

View ORCID ProfileVincent L. Cannataro, View ORCID ProfileStephen G. Gaffney, View ORCID ProfileJeffrey P. Townsend
doi: https://doi.org/10.1101/229724
Vincent L. Cannataro
1Department of Biostatistics, Yale University, New Haven, CT,
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Stephen G. Gaffney
1Department of Biostatistics, Yale University, New Haven, CT,
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Jeffrey P. Townsend
1Department of Biostatistics, Yale University, New Haven, CT,
2Program in Computational Biology and Bioinformatics
3Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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Abstract

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 thereof2,3. However, P values are thresholds for belief4, not metrics of effect5,6. 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 06, 2017.
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Effect sizes of somatic mutations in cancer
Vincent L. Cannataro, Stephen G. Gaffney, Jeffrey P. Townsend
bioRxiv 229724; doi: https://doi.org/10.1101/229724
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Effect sizes of somatic mutations in cancer
Vincent L. Cannataro, Stephen G. Gaffney, Jeffrey P. Townsend
bioRxiv 229724; doi: https://doi.org/10.1101/229724

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