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Identifying genetic variants that affect viability in large cohorts

Hakhamanesh Mostafavi, Tomaz Berisa, Molly Przeworski, Joseph K. Pickrell
doi: https://doi.org/10.1101/085969
Hakhamanesh Mostafavi
1Department of Biological Sciences, Columbia University, New York, NY, USA
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Tomaz Berisa
2New York Genome Center, New York, NY, USA
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Molly Przeworski
1Department of Biological Sciences, Columbia University, New York, NY, USA
3Department of Systems Biology, Columbia University, New York, NY, USA
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Joseph K. Pickrell
1Department of Biological Sciences, Columbia University, New York, NY, USA
2New York Genome Center, New York, NY, USA
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Abstract

A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to test whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Aging (GERA) cohort and to the parents of participants in the UK Biobank. In the GERA cohort, the top signal is the APOE ε4 allele (P < 10−15), whereas in the UK Biobank, the strongest signals are detected in males only, and are for variants near CHRNA3 (P~4×10−8) as well as set of genetic variants that influence heart disease and lipid levels. We suggest that gene-by-environment interactions have altered the genetic architecture of viability in these two cohorts.

Footnotes

  • ↵* These authors co-supervised this project.

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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 November 10, 2016.
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Identifying genetic variants that affect viability in large cohorts
Hakhamanesh Mostafavi, Tomaz Berisa, Molly Przeworski, Joseph K. Pickrell
bioRxiv 085969; doi: https://doi.org/10.1101/085969
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Identifying genetic variants that affect viability in large cohorts
Hakhamanesh Mostafavi, Tomaz Berisa, Molly Przeworski, Joseph K. Pickrell
bioRxiv 085969; doi: https://doi.org/10.1101/085969

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