Prevalence of Variant Reclassification Following Hereditary Cancer Genetic Testing

Abstract

Importance: Variant reclassification is an important component of hereditary cancer genetic testing; however, there are few published data quantifying the prevalence of reclassification.

Objective: Retrospective cohort study of individuals who had genetic testing from 2006 through 2016 at a single commercial laboratory.

Design, setting, and participants: A retrospective cohort of individuals who had genetic testing between 2006 and 2016 at a single commercial laboratory was assessed. Variants were classified as benign, likely benign, variant of uncertain significance, likely pathogenic, or pathogenic. Retrospective chart reviews were conducted for patients from the University of Texas Southwestern (UTSW) Medical Center.

Exposures: Hereditary cancer genetic testing.

Main outcomes and measures: Frequency of and time to amended reports; frequency and types of variant reclassification.

Results: From 2006 through 2018, 1.45 million individuals (median [interquartile range] age at testing, 49 years [40.69-58.31 years], 95.6% women) had genetic testing, and 56.6% (n = 821 724) had a personal history of cancer. A total of 1.67 million initial tests were reported and 59 955 amended reports were issued due to variant reclassification. Overall, 6.4% (2868 of 44 777) of unique variants were reclassified. Reclassification to a different clinical category was rare among unique variants initially classified as pathogenic or likely pathogenic (0.7%, 61 of 9112) or benign or likely benign (0.2%, 15 of 8995). However, 7.7% (2048 of 26 670) of unique variants of uncertain significance were reclassified: 91.2% (1867 of 2048) were downgraded to benign or likely benign (median time to amended report, 1.17 years), 8.7% (178 of 2048) were upgraded to pathogenic or likely pathogenic variants (median time to amended report, 1.86 years). Because most variants were observed in more than 1 individual, 24.9% (46 890 of 184 327) of all reported variants of uncertain significance were reclassified.

Conclusions and relevance: Following hereditary cancer genetic testing at a single commercial laboratory, 24.9% of variants of uncertain significance were reclassified, which included both downgrades and upgrades. Further research is needed to assess generalizability of the findings for other laboratories, as well as the clinical consequences of the reclassification as a component of a genetic testing program.

Figure.. Year-Specific Time to Reclassification

For amended reports sent due to variant reclassification, the time to the amended report is shown according to the year of the initial report. Pan-cancer panel testing was introduced in 2013. Prior to 2013, all amended reports were for single-syndrome testing. The median time for each year is indicated by the thick horizontal line and the interquartile range is indicated by the box. The error bars represent 1.5 times the interquartile range. Data points beyond error bars represent outlying points.