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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Population genomics of human gene expression
Barbara E Stranger1, Alexandra C Nica, Matthew S Forrest
1The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Nature Genetics
|September 18, 2007
Summary
Genetic variation significantly impacts gene expression, with most regulatory variations found close to genes (cis). These findings enhance our understanding of human traits and diseases.
Area of Science:
- Human Genomics
- Gene Expression Regulation
- Population Genetics
Background:
- Genetic variation is a key driver of differences in gene expression.
- Understanding the genetic basis of gene expression variation is crucial for human health.
- Previous studies have hinted at the heritability of gene expression.
Purpose of the Study:
- To comprehensively map genetic variants associated with gene expression variation.
- To investigate the extent and nature of cis- and trans-regulatory variation.
- To explore methodologies for analyzing gene expression variation.
Main Methods:
- Gene expression profiling of Epstein-Barr virus-transformed lymphoblastoid cell lines from 270 HapMap individuals.
- Genome-wide association analysis of over 2.2 million common single nucleotide polymorphisms (SNPs) against gene expression levels.
- Replication analysis in independent populations to validate association signals.
Main Results:
- Gene expression is confirmed to be heritable, with population differentiation aligning with prior research.
- Identified at least 1,348 genes with cis-regulatory signals and 180 with trans-regulatory signals.
- Replication rates were 37% for cis and 15% for trans signals, supporting a prevalence of cis-regulatory variation.
Conclusions:
- The human genome harbors a substantial amount of cis-regulatory variation influencing gene expression.
- While trans-acting regulatory variation is less frequently detected, it may play a significant role in phenotypic variation.
- The study advances analytical methods for dissecting gene expression variation.
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