Dataset Information

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

ABSTRACT:

In this paper (Gibbs et al., 2010, PMID: 20485568) we describe a comprehensive assessment of the correlation between common genetic variability across the human genome, gene expression and DNA methylation, within human brain. We studied the cerebellum, frontal cortex, temporal cortex and pons regions of 150 individuals (600 tissue samples). In each tissue we assessed 27,578 DNA methylation sites and the expression level of 22,184 genes. Our research shows that DNA methylation and RNA expression patterns differ between brain regions. Further we show that DNA genotype is correlated with gene expression and DNA methylation, particularly when the genetic variation is close to the DNA methylation site or gene.

PROVIDER: phs000249.v1.p1 | EGA |

REPOSITORIES: EGA

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Publications

Empirical threshold values for quantitative trait mapping.

Churchill G A GA Doerge R W RW

Genetics 19941101 3

The detection of genes that control quantitative characters is a problem of great interest to the genetic mapping community. Methods for locating these quantitative trait loci (QTL) relative to maps of genetic markers are now widely used. This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects. An empirical method is described, based on the concept of a permutation test, for estimating threshold val ...[more]

PMID: 7851788

Publication: 1/32

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Project description:A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We describe a set of integrated experiments designed to investigate the effects of common genetic variability on DNA methylation, mRNA expression and microRNA (miRNA) expression in four distinct human brain regions. We show that brain tissues may be readily distinguished based on methylation status or expression profile. We find an abundance of genetic cis regulation mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation. We observe that the largest magnitude effects occur across distinct brain regions. We believe these data, which we have made publicly available, will be useful in understanding the biological effects of genetic variation. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249.v1.p1 Because of our interest in genomic regulation of expression and neurological disorders we embarked upon a series of experiments to provide a brain region-specific contextual framework for genetic and epigenetic regulation of gene expression. We obtained frozen brain tissue from the cerebellum, frontal cortex, pons and temporal cortex from 150 subjects (total 600 tissue samples). We undertook four separate assays across this series; first, genome-wide SNP genotyping; second, assay of >27,000 CpG methylation sites in each of the four brain regions; third, mRNA expression profiling of >22,000 transcripts in all four brain regions; and, fourth, miRNA expression profiling of 735 miRNA transcripts. Here we discuss the results of these experiments, particularly in the context of integrated datasets to define expression and CpG methylation quantitative trait loci (eQTL and methQTL) and detailing differences and similarities across brain regions.

Dataset Information

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

Publications

Empirical threshold values for quantitative trait mapping.

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