Genetic architecture of gene expression traits across diverse populations

For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-Eu...

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Published in:PLoS genetics Vol. 14; no. 8; p. e1007586
Main Authors: Mogil, Lauren S., Andaleon, Angela, Badalamenti, Alexa, Dickinson, Scott P., Guo, Xiuqing, Rotter, Jerome I., Johnson, W. Craig, Im, Hae Kyung, Liu, Yongmei, Wheeler, Heather E.
Format: Journal Article
Language:English
Published: United States Public Library of Science 10.08.2018
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ISSN:1553-7404, 1553-7390, 1553-7404
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Abstract For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop.
AbstractList For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop.
For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop.For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop.
For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R.sup.2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at
For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations and subsequent effects on genetic prediction are not well understood, in part due to the historical paucity of GWAS in populations of non-European ancestry. We used data from the MESA (Multi-Ethnic Study of Atherosclerosis) cohort to characterize the genetic architecture of gene expression within and between diverse populations. Genotype and monocyte gene expression were available in individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. We performed expression quantitative trait loci (eQTL) mapping in each population and show genetic correlation of gene expression depends on shared ancestry proportions. Using elastic net modeling with cross validation to optimize genotypic predictors of gene expression in each population, we show the genetic architecture of gene expression for most predictable genes is sparse. We found the best predicted gene in each population, TACSTD2 in AFA and CHURC1 in CAU and HIS, had similar prediction performance across populations with R2 > 0.8 in each population. However, we identified a subset of genes that are well-predicted in one population, but poorly predicted in another. We show these differences in predictive performance are due to allele frequency differences between populations. Using genotype weights trained in MESA to predict gene expression in independent populations showed that a training set with ancestry similar to the test set is better at predicting gene expression in test populations, demonstrating an urgent need for diverse population sampling in genomics. Our predictive models and performance statistics in diverse cohorts are made publicly available for use in transcriptome mapping methods at https://github.com/WheelerLab/DivPop. Most genome-wide association studies (GWAS) have been conducted in populations of European ancestry leading to a disparity in understanding the genetics of complex traits between populations. For many complex traits, gene regulation is critical, given the consistent enrichment of regulatory variants among trait-associated variants. However, it is still unknown how the effects of these key variants differ across populations. We used data from MESA to study the underlying genetic architecture of gene expression by optimizing gene expression prediction within and across diverse populations. The populations with genotype and gene expression data available are from individuals with African American (AFA, n = 233), Hispanic (HIS, n = 352), and European (CAU, n = 578) ancestry. After calculating the prediction performance, we found that many genes that were well predicted in one population are poorly predicted in another. We further show that a training set with ancestry similar to the test set resulted in better gene expression predictions, demonstrating the need to incorporate diverse populations in genomic studies. Our gene expression prediction models and performance statistics are publicly available to facilitate future transcriptome mapping studies in diverse populations.
Audience Academic
Author Liu, Yongmei
Johnson, W. Craig
Guo, Xiuqing
Mogil, Lauren S.
Rotter, Jerome I.
Im, Hae Kyung
Wheeler, Heather E.
Badalamenti, Alexa
Andaleon, Angela
Dickinson, Scott P.
AuthorAffiliation 7 Department of Computer Science, Loyola University Chicago, Chicago, Illinois, United States of America
Emory University, UNITED STATES
4 Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States of America
1 Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
3 Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
5 Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
6 Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
2 Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, United States of America
8 Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, Il
AuthorAffiliation_xml – name: 7 Department of Computer Science, Loyola University Chicago, Chicago, Illinois, United States of America
– name: Emory University, UNITED STATES
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– name: 4 Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States of America
– name: 3 Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
– name: 1 Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
– name: 2 Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, United States of America
– name: 5 Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
– name: 6 Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
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  surname: Mogil
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  orcidid: 0000-0003-4459-6398
  surname: Andaleon
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  orcidid: 0000-0001-7191-1723
  surname: Rotter
  fullname: Rotter, Jerome I.
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  fullname: Liu, Yongmei
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  givenname: Heather E.
  orcidid: 0000-0003-1365-9667
  surname: Wheeler
  fullname: Wheeler, Heather E.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/30096133$$D View this record in MEDLINE/PubMed
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Copyright COPYRIGHT 2018 Public Library of Science
2018 Mogil et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Snippet For many complex traits, gene regulation is likely to play a crucial mechanistic role. How the genetic architectures of complex traits vary between populations...
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SubjectTerms Analysis
Antigens, Neoplasm - genetics
Antigens, Neoplasm - metabolism
Arteriosclerosis
Asthma
Bioinformatics
Biology
Biology and Life Sciences
Biomedical research
Black or African American - genetics
Cell Adhesion Molecules - genetics
Cell Adhesion Molecules - metabolism
Chromosome Mapping
Consortia
Ecology and Environmental Sciences
Ethnicity - genetics
Funding
Gene expression
Gene Expression Regulation
Gene Frequency
Gene mapping
Gene regulation
Generalized linear models
Genetic regulation
Genetics
Genetics, Population
Genome-wide association studies
Genome-Wide Association Study
Genomes
Genomics
Genotypes
Genotyping Techniques
Hispanic or Latino - genetics
Humans
Medicine
Medicine and Health Sciences
Methods
Models, Genetic
Monocytes
Multifactorial Inheritance
Pediatrics
People and Places
Phenotype
Physical Sciences
Population
Population genetics
Prediction models
Principal components analysis
Quantitative Trait Loci
Research and Analysis Methods
Software
Statistical analysis
Studies
Transcriptome
White People - genetics
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Title Genetic architecture of gene expression traits across diverse populations
URI https://www.ncbi.nlm.nih.gov/pubmed/30096133
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https://doaj.org/article/2eb6769fcca84fc1bca33cec87f48f46
http://dx.doi.org/10.1371/journal.pgen.1007586
Volume 14
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