Whole Exome Sequencing May Skip Large Segments of DNA

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A reanalysis of samples from three major US sequencing labs showed that whole exome testing sometimes didn’t adequately analyze more than a quarter of genes, and significant variation exists between labs. The reanalysis, which was done by researchers at University of Texas Southwestern Medical Center, showed that, on average, the labs adequately examined only 34%, 66%, and 69% percent (respectively) of the exome. The new study was published in Clinical Chemistry today.

This finding suggests doctors and patients should question the results of negative sequencing tests. “Many of the physicians who order these tests don’t know this is happening,” said Jason Park, M.D., Ph.D., one of the study’s authors and associate professor of pathology at UT Southwestern. “Many of their patients are young kids with neurological disorders, and they want to get the most complete diagnostic test. But they don’t realize whole exome sequencing may miss something that a more targeted genetic test would find.”

In this study, researchers re-analyzed 36 patients’ exome tests conducted between 2012 and 2016—12 from each of the three national clinical laboratories—and found starkly contrasting results and inconsistency with which genes were completely analyzed. A gene was not considered completely analyzed unless the lab met an industry-accepted threshold for adequate analysis of all DNA that encodes protein, which is defined as sequencing that segment at least 20 times per test.

Notably, less than 1.5% of the genes were completely analyzed in all 36 samples. A review of one lab’s tests showed 28% of the genes were never adequately examined and only 5% were always covered. Another lab consistently covered 27% of the genes.

Park said the process of fully analyzing the approximately 18,000 genes in an exome is inherently difficult and prone to oversights. “And things really start to fall apart when you start thinking about using these tests to rule out a disease,” he said. “A negative exome result is meaningless when so many of the genes are not thoroughly analyzed.”

Currently, about half of whole exome testing does not pinpoint a mutation. But according to this study’s results, negative findings may sometimes be an oversight and not a correct diagnosis. This study built upon previous research that showed similar gaps and disparities in whole genome sequencing.

“When we saw this data we made it a regular practice to ask the labs about coverage of specific genes,” said Garrett Gotway, M.D., Ph.D., a clinical geneticist at UT Southwestern who is the corresponding author of the study. “I don’t think you can expect complete coverage of 18,000 genes every time, but it’s fair to expect 90% or more.”

Gotway says he hopes the findings will prompt more physicians to ask labs about which genes were covered and push for improved consistency in testing quality. He also encourages physicians – even before ordering the test – to consider whether whole exome sequencing is the best approach for the patient.

“Clinical exomes can be helpful in complex cases, but you probably don’t need one if a kid has epilepsy and doesn’t have other complicating clinical problems,” Gotway said. “There’s a decent chance the exome test will come back negative and the parents are still left wondering about the genetic basis for their child’s disease.”

In those cases, Gotway suggests ordering a smaller genetic test that completely analyzes a panel of genes associated with that disease. He says they’re less expensive and just as likely to help physicians find answers.

For example, the chances of detecting an epileptic disorder from any of the 36 tests varied widely depending on which genes were analyzed. One lab conducted several patient tests that fully examined more than three quarters of the genes associated with epilepsy, but the same lab had three other patient samples in which less than 40% were completely analyzed.

Three tests from another lab came in at under 20%.

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