Non-Public Variant Reporting Hampers Consistency of Sequence Interpretation Between Labs

Discrepancies in the interpretation of variants between laboratories occurs in more than half the samples, according to a study published in the January issue of Genetics in Medicine. Alarmingly, many of these discrepant interpretations could significantly affect diagnosis or recommendations for clinical care. Standardization of variant interpretation could benefit from expansion of publicly available variant catalogs through mandatory reporting, standards for the use of investigative algorithms, and inclusion of predicted protein consequences in variant and clinical databases, the authors suggest.

The Collagen Diagnostic Laboratory (CDL; Seattle, Wash.), is a research and clinical laboratory specializing in heritable connective-tissue disorders. It commonly receives requests to provide "second opinion" on variants identified by outside laboratories (OLs). Over a 14-month period, CDL received 38 of these requests for interpretation. Interpretations by the two laboratories were compared and discrepancies were assessed. OL reports were reviewed for sources and tools used in interpretation to understand the reason for discordance between the labs.

The researchers found that the original genetic testing was completed in five private commercial laboratories (20 sample inquiries), six academic laboratories (12 sample inquiries), and six unidentified laboratories. Gene interrogation at the OL used exome sequencing (n = 6), next-generation sequencing panel (n = 17), single-gene Sanger sequencing (n = 8), or unknown methodology (n = 7). The types of variants identified included missense (n = 28), intronic (n = 6), in-frame duplications (n = 2), and synonymous (n = 1).

Interpretations between the laboratories were concordant in 11 cases (29 percent). Discrepancies were classified as moderate in 11 instances (29 percent) and significant in 16 (42 percent). In just over half (13 of 25) of cases classified by an OL as a variant of unknown significance, CDL interpreted the variant as either definitively benign or pathogenic. Factors that were identified as potential causes of the discrepancies included private data not shared in a public database (n = 9); publicly available allele frequency data not referenced and used as evidence (n = 5); and important aspects of protein structure and function that were not taken into account (n = 13).

"Of the genes interrogated in the OL inquiries, 80 percent of recorded ClinVar pathogenic entries were submitted by the CDL, which reflects a low submission rate for genes associated with heritable connective-tissue disorders to date by other laboratories," writes lead author Melanie Pepin, from University of Washington, Seattle. "With time, the increased availability of variant data should decrease discrepant interpretations among laboratories that result because data are available to only one source. However, submission of all accrued variants from prior years and decades of testing faces the logistical challenge of insufficient laboratory resources to allocate to the task of manual curation and submission."

Takeaway: Discrepancies between laboratories in the interpretation of variants are common and can affect clinical care. Lack of data sharing of variant information is responsible for many of these interpretation discrepancies.