Clinical OMICS

NOV-DEC 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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30 Clinical OMICs November/December 2017 Data & Informatics T he mystery of how subtle differ- ences in our DNA give rise to both our unique traits as well as a variety of diseases is one that thousands of scientists around the world are trying to solve. The Genotype-Tissue Expres- sion (GTEx) Consortium, is one of a handful of ambitious endeavors aimed at answering this question. Launched in 2010, its goal is to identify and cata- log genetic variants related to changes in gene expression—dubbed expres- sion quantitative trait loci (eQTLs)—in tissues across the entire human body. "Over the last decade or so, there have been many studies that have linked genetic variants to a wide range of traits, but many of these were found in regions of the genome that are far away from genes, so it was difficult to link them to disease mechanisms that would allow for better diagnoses and treatment," said Michelle Ward, a postdoctoral researcher in Yoav Gilad's lab at the University of Chi- cago. "What GTEx starts to provide is a way of linking genetic variants to the genes that they're regulating." In 2015, the GTEx group, which includes researchers across multiple research centers, released a pilot data- set that included the results of gene expression analyses on the post-mor- tem tissues collected from 237 donors. The latest version of their atlas, which was released in October, contains more than 7000 samples from 449 indi- viduals. These include 44 different tis- sues types throughout the entire body, including the brain, lungs, muscles, and whole blood. "None of this would be have been possible without the tissue donors, their families, and the bio-specimen collection sites," said GTEx member Casey Brown, a genetics professor at the University of Pennsylvania. "We're all extremely grateful." Novel Insights Along with releasing the dataset, the GTEx group also published new find- ings based on the data in a series of four Nature papers in October. "Being the largest study of this kind, they've been able to ask questions that have been difficult to answer in the past," Ward said. For example, in one study, the team observed that across the broad spectrum of analyzed tissues, genetic variation was influencing the expres- sion of most protein-coding genes. Although most variants affecting expression were located nearby the impacted gene, some were as far away as on a different chromosome. The nearby variants, dubbed cis-QTLs, were much more common—research- ers identified more than 150,000—and were found in a wider variety of tis- sues than the more distant trans-QTLs, which numbered in the hundreds. However, Brown noted, because the current dataset is still statistically underpowered when it comes to ana- lyzing trans-QTLs, more tissue will need to be analyzed in order to fully characterize them. In addition, the researchers discov- ered that around half of all trait-asso- From Form to Function The GTEx Project Sheds New Light on the Links between Gene Expression and Regulation By Diana Kwon A GTEx community meeting, which was open to all members of the scientific community . Biocat La BioRegió de Catalunya

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