Haplotype-based inference of the distribution of fitness effects

Author:

Ortega-Del Vecchyo Diego12ORCID,Lohmueller Kirk E234,Novembre John56ORCID

Affiliation:

1. Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 76230, México

2. Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA

3. Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA

4. Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA

5. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA

6. Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA

Abstract

Abstract Recent genome sequencing studies with large sample sizes in humans have discovered a vast quantity of low-frequency variants, providing an important source of information to analyze how selection is acting on human genetic variation. In order to estimate the strength of natural selection acting on low-frequency variants, we have developed a likelihood-based method that uses the lengths of pairwise identity-by-state between haplotypes carrying low-frequency variants. We show that in some nonequilibrium populations (such as those that have had recent population expansions) it is possible to distinguish between positive or negative selection acting on a set of variants. With our new framework, one can infer a fixed selection intensity acting on a set of variants at a particular frequency, or a distribution of selection coefficients for standing variants and new mutations. We show an application of our method to the UK10K phased haplotype dataset of individuals.

Funder

UC MEXUS-CONACYT fellowship

UC-MEXUS CONACYT

NIH

Alejandra Medina-Rivera

Publisher

Oxford University Press (OUP)

Subject

Genetics

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