Effects of cis and trans genetic ancestry on gene expression in African Americans.
Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be...
Main Authors: | , , , , , , |
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Format: | Journal article |
Language: | English |
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Public Library of Science
2008
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_version_ | 1797064885443493888 |
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author | Price, A Patterson, N Hancks, D Myers, S Reich, D Cheung, V Spielman, R |
author_facet | Price, A Patterson, N Hancks, D Myers, S Reich, D Cheung, V Spielman, R |
author_sort | Price, A |
collection | OXFORD |
description | Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be due to non-genetic (e.g., environmental) effects. Here, we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that individuals from this population inherit variable proportions of two continental ancestries. We first relate gene expression levels in individual African Americans to their genome-wide proportion of European ancestry. The results provide strong evidence of a genetic contribution to expression differences between European and African populations, validating previous findings. Second, we infer local ancestry (0, 1, or 2 European chromosomes) at each location in the genome and investigate the effects of ancestry proximal to the expressed gene (cis) versus ancestry elsewhere in the genome (trans). Both effects are highly significant, and we estimate that 12+/-3% of all heritable variation in human gene expression is due to cis variants. |
first_indexed | 2024-03-06T21:20:42Z |
format | Journal article |
id | oxford-uuid:4158d31a-540d-4603-839c-07cd5cd2063a |
institution | University of Oxford |
language | English |
last_indexed | 2024-03-06T21:20:42Z |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | dspace |
spelling | oxford-uuid:4158d31a-540d-4603-839c-07cd5cd2063a2022-03-26T14:43:13ZEffects of cis and trans genetic ancestry on gene expression in African Americans.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:4158d31a-540d-4603-839c-07cd5cd2063aEnglishSymplectic Elements at OxfordPublic Library of Science2008Price, APatterson, NHancks, DMyers, SReich, DCheung, VSpielman, RVariation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be due to non-genetic (e.g., environmental) effects. Here, we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that individuals from this population inherit variable proportions of two continental ancestries. We first relate gene expression levels in individual African Americans to their genome-wide proportion of European ancestry. The results provide strong evidence of a genetic contribution to expression differences between European and African populations, validating previous findings. Second, we infer local ancestry (0, 1, or 2 European chromosomes) at each location in the genome and investigate the effects of ancestry proximal to the expressed gene (cis) versus ancestry elsewhere in the genome (trans). Both effects are highly significant, and we estimate that 12+/-3% of all heritable variation in human gene expression is due to cis variants. |
spellingShingle | Price, A Patterson, N Hancks, D Myers, S Reich, D Cheung, V Spielman, R Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title | Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title_full | Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title_fullStr | Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title_full_unstemmed | Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title_short | Effects of cis and trans genetic ancestry on gene expression in African Americans. |
title_sort | effects of cis and trans genetic ancestry on gene expression in african americans |
work_keys_str_mv | AT pricea effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT pattersonn effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT hancksd effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT myerss effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT reichd effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT cheungv effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans AT spielmanr effectsofcisandtransgeneticancestryongeneexpressioninafricanamericans |