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Expression Quantitative Trait Loci (eQTL) mapping in Puerto Rican children

Chen, W and Brehm, JM and Lin, J and Wang, T and Forno, E and Acosta-Pérez, E and Boutaoui, N and Canino, G and Celedón, JC (2015) Expression Quantitative Trait Loci (eQTL) mapping in Puerto Rican children. PLoS ONE, 10 (3).

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Abstract

© 2015 Chen et al. Background: Expression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics. Methods: We performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ∼15 K transcripts and ∼1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes. Results: We identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list. Conclusions: We present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Chen, Wwei.chen@pitt.eduWEC47
Brehm, JMjmb270@pitt.eduJMB270
Lin, Jjel146@pitt.eduJEL146
Wang, T
Forno, Eerf30@pitt.eduERF30
Acosta-Pérez, E
Boutaoui, Nnab86@pitt.eduNAB86
Canino, G
Celedón, JC
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorHsu, Yi-HsiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 27 March 2015
Date Type: Publication
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Journal or Publication Title: PLoS ONE
Volume: 10
Number: 3
DOI or Unique Handle: 10.1371/journal.pone.0122464
Institution: University of Pittsburgh
Schools and Programs: Graduate School of Public Health > Human Genetics
School of Medicine > Immunology
Refereed: Yes
Date Deposited: 23 Aug 2016 13:57
Last Modified: 02 Feb 2019 16:58
URI: http://d-scholarship.pitt.edu/id/eprint/28492

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