1. Identifying recent adaptations in large-scale genomic data.
- Author
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Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL, Lander ES, Schaffner SF, and Sabeti PC
- Subjects
- Animals, Bacteria metabolism, Flagellin metabolism, HapMap Project, Humans, NF-kappa B metabolism, Quantitative Trait Loci, Regulatory Elements, Transcriptional, Signal Transduction, Toll-Like Receptor 5 genetics, Toll-Like Receptor 5 metabolism, Genetic Techniques, Genome, Human, Genome-Wide Association Study, Mutation
- Abstract
Although several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 Genomes (1000G) Project and the composite of multiple signals (CMS) test, we investigated 412 candidate signals and leveraged functional annotation, protein structure modeling, epigenetics, and association studies to identify and extensively annotate candidate causal variants. The resulting catalog provides a tractable list for experimental follow-up; it includes 35 high-scoring nonsynonymous variants, 59 variants associated with expression levels of a nearby coding gene or lincRNA, and numerous variants associated with susceptibility to infectious disease and other phenotypes. We experimentally characterized one candidate nonsynonymous variant in Toll-like receptor 5 (TLR5) and show that it leads to altered NF-κB signaling in response to bacterial flagellin. PAPERFLICK:, (Copyright © 2013 Elsevier Inc. All rights reserved.)
- Published
- 2013
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