Feb 4, 2014

Nonparametric inference of the distribution of fitness effects across functional categories in humans

BioRxiv : the Preprint Server for Biology
Fernando Racimo, Joshua G Schraiber

Abstract

Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE) of segregating single-nucleotide mutations in humans. Unlike previous methods, we do not assume that synonymous mutations are neutral, or rely on fitting the DFE of new nonsynonymous mutations to a particular parametric probability distribution, which is poorly motivated on a biological level. We rely on a previously developed method that utilizes a variety of published annotations (including conservation scores, protein deleteriousness estimates and regulatory data) to score all mutations in the human genome based on how likely they are to be affected by negative selection, controlling for mutation rate. We map this score to a scale of fitness coefficients via maximum likelihood using diffusion theory and a Poisson random field model. We then use our coefficient mapping to quantify the distribution of all scored single-nucleotide polymorphisms in Yoruba and Europeans. Our method serves to approximate the DFE of any type of segregating mutatio...Continue Reading

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Mentioned in this Paper

Gene Polymorphism
Genome
Diffusion Weighted Imaging
Transcription, Genetic
ST2 protein, rat
Site
Genomics
Nucleotides
Na-deacetyl-ferrocenoyl-strychnobrasiline
CTCF gene

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