Study says genetic test results benefit from re-analysis as genomics research accelerates

Nov. 6, 2018

Decades of genetic research linking variants to specific diseases or treatment, along with the diagnoses of patients whose genetic variants help clinicians provide the best care. But as genetic research progresses, what a particular variant means for a patient can change. If clinicians don’t keep pace, patients could fall behind.

A new study published in the journal JAMA Pediatrics quantifies how quickly new research could benefit patients. Jason Park, an associate professor of pathology at UT Southwestern, and other researchers found that the interpretation of over 30% of variants associated with childhood epilepsy changed based on new research over the course of five years.

Park concludes that clinicians should review patients’ genetic data against the most current research every two years to keep pace with new advances.

How does genetics research progress? It starts with geneticists identifying a variant in a gene that’s associated with a disease, like epilepsy. Initially, they don’t know what the variant means, so they classify it as a variant of unknown significance. It might contribute to the disease, making it pathogenic, or it might not, making it benign. Only further research can reveal a variant’s classification.

Most gene variants fall in the unknown category, simply because they haven’t been studied closely enough. According to Park, only about 20% of genetic tests for epilepsy yield a clinically significant finding. This percentage will likely tip up as the pace of genetics research accelerates. For example, ClinVar, a public database where researchers can report new variants, saw its numbers skyrocket from less than 50,000 variants in 2013 to over 600,000 in 2018.

To understand what this surge means for patients, the researchers examined 309 local cases of genetic testing for epilepsy that occurred between 2012 and 2015. They re-analyzed the genetic results based on current research and found that over a third of patients had a variant reclassified, and 12% had a change in interpretation that could lead to better epilepsy treatment.

Park was somewhat surprised at how many variants changed. “I didn’t expect it to be quite that high,” said Park. Most variants moved from unknown significance to benign. But that information can still be helpful to clinicians as they decide on treatment.

Gene tests are playing an increasingly integral role in how patients are diagnosed and treated. In this photo essay, experts at UT Southwestern and Children’s Health lead us through the basic steps of how a patient s DNA sample is analyzed in the laboratory to determine which genetic abnormalities are causing their disease.

Park thinks this study supports the idea that our interpretation of variants is dynamic. “As the important work of studying individual genes continues, clinicians need to be updating regularly because the pace of research is high enough that interpretations could change quickly,” said Park.

Not all fields will have a similar pace of change. For example, because scientists know more about the genes that cause cystic fibrosis, or breast cancer, re-analysis likely won’t change a clinician’s interpretation.

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