1. Expression quantitative trait loci (eQTL) mapping in Puerto Rican children
- Author
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Jerome Lin, Juan C. Celedón, Edna Acosta-Pérez, Glorisa Canino, Ting Wang, Wei Chen, John Brehm, Erick Forno, and Nadia Boutaoui
- Subjects
Male ,medicine.medical_specialty ,Adolescent ,Microarray ,Quantitative Trait Loci ,lcsh:Medicine ,Genome-wide association study ,Single-nucleotide polymorphism ,Biology ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,Molecular genetics ,medicine ,Humans ,Genetic Predisposition to Disease ,RNA, Messenger ,Child ,lcsh:Science ,Genotyping ,Genetic association ,Genetics ,Multidisciplinary ,Puerto Rico ,lcsh:R ,Hispanic or Latino ,Asthma ,Gene Expression Regulation ,Expression quantitative trait loci ,Female ,lcsh:Q ,Research Article ,Genome-Wide Association Study - Abstract
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
- Published
- 2015