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Series GSE39672 Query DataSets for GSE39672
Status Public on Jul 01, 2013
Title Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Elucidating cytosine modification difference between human populations can enhance our understanding of ethnic specificity in complex traits such as disease predisposition and drug response. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines (LCLs) derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at false discovery rate (FDR) of 1%. CpG sites with greater modification levels in European descents were enriched in the proximal regulatory regions, while those greater in African descents were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained by genetic variation. A substantial proportion of local modification quantitative trait loci (mQTL) exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interaction could be common. Distinct inter-individual correlations were observed between gene expression and cytosine modifications in both proximal promoters and gene bodies, demonstrating a regulatory role of inter-individual variation in cytosine modification. Furthermore, a number of SNPs (single nucleotide polymorphisms) previously identified for complex traits with known racial disparities could be annotated as mQTLs for population-specific CpGs. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.
 
Overall design 60 unrelated CEU and 73 unrelated YRI samples from the HapMap Project were profiled for cytosine modification levels.
 
Contributor(s) Zhang W, Dolan E, Godley L
Citation(s) 23792949, 24943591, 25818895, 26714498
Submission date Jul 26, 2012
Last update date Jul 26, 2019
Contact name Wei Zhang
E-mail(s) weizhan1@uic.edu
Phone 312-413-2024
Organization name University of Illinois
Department Pediatrics & Institute of Human Genetics
Lab Zhang Lab
Street address 840 S. Wood Street
City Chicago
State/province Illinois
ZIP/Postal code 60612
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (133)
GSM977267 HapMap Cytosine Modification NA19147
GSM977268 HapMap Cytosine Modification NA12750
GSM977269 HapMap Cytosine Modification NA18916
Relations
BioProject PRJNA171375

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39672_RAW.tar 183.1 Mb (http)(custom) TAR
GSE39672_matrix_processed.txt.gz 202.4 Mb (ftp)(http) TXT
GSE39672_matrix_signal_intensities.txt.gz 312.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record
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