Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios

Elife. 2020 Mar 30:9:e48714. doi: 10.7554/eLife.48714.

Abstract

The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells. However the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that determines the selective coefficients of individual driver mutations from dN/dS estimates. We then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1-5%). This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and measures the DFE of mutations in human tissues.

Keywords: cancer evolution; computational biology; distribution of fitness effects; dn/ds; genetics; genomics; human; population genetics; somatic evolution; systems biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clonal Evolution*
  • Esophagus / cytology
  • Evolution, Molecular*
  • Genetic Fitness*
  • Humans
  • Models, Theoretical
  • Mutation*
  • Phylogeny
  • Receptor, Notch1 / genetics
  • Skin / cytology
  • Tumor Suppressor Protein p53 / genetics

Substances

  • NOTCH1 protein, human
  • Receptor, Notch1
  • TP53 protein, human
  • Tumor Suppressor Protein p53