RET Variant Reclassification across Demographic Sub-Groups in a Large-Scale Clinical Population.
TL;DR
The expansion of RET germline testing coincided with substantial reclassification of VUSs, highlighting the importance of periodic laboratory reassessment.
Abstract
Background
The expanded use of germline testing panels that include the RET proto-oncogene has identified many variants of uncertain significance (VUSs). It remains poorly understood how many RET VUSs are returned in clinical practice, how many are ultimately reclassified, and which patient populations are affected most.
Methods
We conducted a nationwide retrospective cohort study of individuals tested for RET germline variants between 2017 and 2024 as part of routine clinical diagnostic testing at Ambry Genetics. Samples underwent next-generation sequencing, and variants were reported with their associated five-tier pathogenicity classification. Variant reclassification was measured as a change between initial and updated classification status on a per-variant and per-person basis. Test requisition forms, pedigrees, and clinic notes were used to associate genetic test results with demographic and clinical patient characteristics.
Results
Among 616,077 individuals who underwent RET germline genetic testing that included RET, 969 (0.2%) had a RET PV, and 5516 (0.9%) had a RET VUS. A total of 1607 (29%) individuals with initial RET VUSs were reclassified. Most variants (164/166; 98.8%) and individuals (1605/1607; 99.9%) were reclassified as benign. The prevalence of VUS on initial classification was significantly higher in individuals self-reporting as Asian (1.5%), Black (1.3%), and Hispanic (1%) compared with those self-reporting as White (0.8%). Reclassification reduced the proportion of VUSs within race and ethnicity groups, but relative differences remained statistically significant.
Conclusions
The expansion of RET germline testing coincided with substantial reclassification of VUSs, highlighting the importance of periodic laboratory reassessment. Most reclassifications were benign, which is cautiously reassuring for clinical counseling of patients. Both further characterization of RET variants and society guidance on clinical management of VUS test results are needed as genetic testing continues to expand.