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Database links genetic variants to effects on expression

11 May 2015

By Dr Charlotte Warren-Gash

Appeared in BioNews 801

International scientists from the Genotype-Tissue Expression (GTEx) project have created a new database to study how genetic variants affect gene activity in different body tissues.

The new resource is intended to help scientists better understand how the thousands of disease-associated genetic variants identified in genome-wide association studies (GWAS) alter disease risk in healthy people.

Pilot phase results, published in a set of papers in Science, show how DNA variants create similar gene-expression patterns within tissues across individuals.

Researchers sequenced mRNA in over 1,600 samples from 43 tissue types of 175 individuals. They also used a method called expression quantitative trait locus (eQTL) analysis, which shows the association between a genetic variant and the level of activity of a specific gene in a particular tissue. This comprehensive analysis revealed that around half of the genetic variants had common activity across the nine tissue types studied. It also identified a subset of variants with tissue-specific effects.

In a companion paper focused on gene expression, Dr Roderic Guigo from the Centre for Genomic Regulation in Barcelona, Spain, and colleagues, showed that there is more variation in gene expression across tissues than across individuals. They found that any inter-individual variation tended to correlate with age, sex and ethnicity. Meanwhile, a second companion paper investigated the effect of protein-truncating gene variants on gene activity in different tissues.

'It's a very impressive set of analyses where they are correlating mutations and haplotypes with gene expression in a way I haven’t really seen before,' commented Dr Mathias Uhlen of Sweden's Royal Institute of Technology, who was not involved in the studies, to The Scientist. 'It's a landmark paper for sure.'

Some commentators caution, however, that we are unlikely to see this type of genetic information used in personalised medicine for decades.

In a perspective accompanying the Science papers, Professor Greg Gibson from the Georgia Institute of Technology writes: 'Although there is justifiable excitement about the ability of DNA sequencing to identify the causes of congenital abnormalities, to predict the progression of tumors, and to personalise the prescription of drugs, the static genome has its limitations.

'If, 20 years from now, gene expression profiling is incorporated side-by-side with genotype analysis as a standard component of medical diagnostics, the GTEx project will be seen to have brought us closer to realisation of this vision.'

The GTEx project is funded by the National Institutes of Health and aims to collect samples from autopsy and organ donations of around 900 deceased donors. It will compare whole genome sequence variation with RNA sequencing data across more than 50 tissue types, and the data is expected to be available within the next two years.

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