Geographical genomics of human leukocyte gene expression variation in southern Morocco

Youssef Idaghdour; Wendy Czika; Kevin V. Shianna; Sang H. Lee; Peter M. Visscher; Hilary C. Martin; Kelci Miclaus; Sami J. Jadallah; David B. Goldstein; Russell D. Wolfinger; Greg Gibson

doi:10.1038/ng.495

Geographical genomics of human leukocyte gene expression variation in southern Morocco

Youssef Idaghdour, Wendy Czika, Kevin V. Shianna, Sang H. Lee, Peter M. Visscher, Hilary C. Martin, Kelci Miclaus, Sami J. Jadallah, David B. Goldstein, Russell D. Wolfinger, Greg Gibson

Research output: Contribution to journal › Article › peer-review

Abstract

Studies of the genetics of gene expression can identify expression SNPs (eSNPs) that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment of transcripts involved in ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples: cis eSNPs (P <10 ^-08) were identified for 346 genes, and trans eSNPs (P <10 ^-11) for 10 genes. All of these associations were consistent both across the three sample locations and after controlling for ancestry and relatedness. No evidence of large-effect trans-acting mediators of the pervasive environmental influence was found; instead, genetic and environmental factors acted in a largely additive manner.

Original language	English (US)
Pages (from-to)	62-67
Number of pages	6
Journal	Nature Genetics
Volume	42
Issue number	1
DOIs	https://doi.org/10.1038/ng.495
State	Published - Jan 2010

ASJC Scopus subject areas

Genetics

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title = "Geographical genomics of human leukocyte gene expression variation in southern Morocco",

abstract = "Studies of the genetics of gene expression can identify expression SNPs (eSNPs) that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment of transcripts involved in ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples: cis eSNPs (P <10 -08) were identified for 346 genes, and trans eSNPs (P <10 -11) for 10 genes. All of these associations were consistent both across the three sample locations and after controlling for ancestry and relatedness. No evidence of large-effect trans-acting mediators of the pervasive environmental influence was found; instead, genetic and environmental factors acted in a largely additive manner.",

author = "Youssef Idaghdour and Wendy Czika and Shianna, {Kevin V.} and Lee, {Sang H.} and Visscher, {Peter M.} and Martin, {Hilary C.} and Kelci Miclaus and Jadallah, {Sami J.} and Goldstein, {David B.} and Wolfinger, {Russell D.} and Greg Gibson",

note = "Funding Information: We thank all of the study participants in Agadir, Ighrem and Boutroch, and numerous individuals who facilitated sample collection, in particular the Idaghdour family. D. Ge and A. Motsinger-Reif provided timely computational support, and we also thank S.Biswas and J.Akey for providing HapMap genotypes.Funding for the study was provided by the University of Queensland.Y.I.was supported by a Fulbright Fellowship and G.G. by an ARC Australian Professorial Fellowship.",

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AU - Idaghdour, Youssef

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AU - Visscher, Peter M.

AU - Martin, Hilary C.

AU - Miclaus, Kelci

AU - Jadallah, Sami J.

AU - Goldstein, David B.

AU - Wolfinger, Russell D.

AU - Gibson, Greg

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Geographical genomics of human leukocyte gene expression variation in southern Morocco

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