Using Online Mendelian Inheritance in Man (OMIM) database and the Human Genome Mutation Database (HGMD) Pro 2015.2 for Quantification of the growth in gene-disease and variant-disease associations
Reporter: Aviva Lev-Ari, PhD, RN
Reanalysis of Clinical Exome Data Over Time Could Yield New Diagnoses
NEW YORK (GenomeWeb) – Clinical exomes that are re-evaluated in a systematic way could yield new diagnoses and prove useful to clinicians, according to a study published yesterday in Genetics in Medicine.
A team of researchers from Stanford University set out to examine whether nondiagnostic clinical exomes could provide new information for patients if they were re-examined with current bioinformatics software and knowledge of disease-related variants as presented in the literature.
Clinical exome sequencing yields no diagnosis for about 75 percent of patients evaluated for possible Mendelian disorders, wrote senior author Gill Bejerano and his colleagues. But a reanalysis of exome and phenotypic data from 40 such individuals using current methods identified a definitive diagnosis for four of them — 10 percent — the team said.
In these cases, the causative variant was de novo and found in a relevant autosomal-dominant disease gene. At the time these exomes were first sequenced, the researchers wrote, the existing literature on these causative genes was either “weak, nonexistent, or not readily located.” When the exomes were re-examined by his team, Bejerano noted, the supporting literature was more robust.
At ACMG, Researchers Report Data Re-Analysis, Matchmaking Boosts Solved Exome Cases
In addition to re-analyzing exome data, the researchers have been working on establishing causality for novel candidate disease genes through patient matches. For this, the team has been using the GeneMatcher website, which allows them to find other clinicians and researchers around the world who have patients, or animal models, with mutations in the same genes as their own patients. Through an API developed by the Matchmaker Exchange project, GeneMatcher submitters can also query the PhenomeCentral and Decipher databases. As of March, more than 4,000 genes had been submitted to GeneMatcher from more than 1,300 submitters in 48 countries, and 1,900 matches had been made, Sobreira reported.
Her team has so far submitted data from 104 families, involving 280 genes, and has had 314 matches so far, involving 113 genes. Several cases have been successes, meaning the researchers could establish that a candidate gene is indeed disease causing, and several others are pending, both from Hopkins and from other groups. The total number of solved cases tracing their success to GeneMatcher is currently unknown, Sobreira said, but the organizers are planning to survey submitters about their success rate in the near future.