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Researchers to Use EMRs to Discover New Disease Associations

November 25, 2013
by Rajiv Leventhal
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Researchers from Vanderbilt University Medical Center and co-authors from four other U.S. institutions from the Electronic Medical Records (EMRs) and Genomics (eMERGE) Network are using the EMR in conjunction with genetic data to discover new disease associations.

The first large-scale phenome-wide association study (PheWAS) was released on November 25 in the journal Nature Biotechnology. Traditional genetic studies start with one phenotype and look at one or many genotypes; PheWAS does the inverse by looking at many diseases for one genetic variant or genotype.

“This study broadly shows that we can take decades of off-the-shelf electronic medical record data, link them to DNA, and quickly validate known associations across hundreds of previous studies,” lead author Josh Denny, M.D., Vanderbilt associate professor of biomedical informatics and medicine, said in a statement.  “And, at the same time, we can discover many new associations.”

Researchers used genotype data from 13,835 individuals of European descent, exhibiting 1,358 diseases collectively. The team then ran PheWAS on 3,144 single-nucleotide polymorphisms (SNP’s), checking each SNP’s association with each of the 1,358 disease phenotypes.

As a result, study authors reported 63 previously unknown SNP-disease associations, the strongest of which related to skin diseases. “The key result is that the method works,” Denny said. “This is a robust test of PheWAS across all domains of disease, showing that you can see all types of phenotypes in the electronic medical record—cancers, diabetes, heart diseases, brain diseases, etc.—and replicate what’s known about their associations with various SNPs.”

Denny said PheWAS would be unworkable without the eMERGE Network, which has now expanded to nine sites with DNA samples from about 51,000 individuals linked to medical records. Vanderbilt is the coordinating center for eMERGE, which is a National Institutes of Health (NIH)-organized and funded consortium of U.S. medical research institutions,



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