A substantial proportion of apparently heterozygous TP53 pathogenic variants detected with a next‐generation sequencing hereditary pan‐cancer panel are acquired somatically. Issue 1 (23rd September 2019)

• Record Type: Journal Article
• Authors: Coffee, Bradford; Cox, Hannah C.; Bernhisel, Ryan; Manley, Susan; Bowles, Karla; Roa, Benjamin B.; Mancini‐DiNardo, Debora
• Is Part Of: Human mutation. Volume 41:Issue 1(2020)
• Page Start: 203
• Page End: 211
• Publication Date: 2019-09-23
• Subjects: acquired somatically -- hereditary pan‐cancer gene panel -- Li–Fraumeni syndrome -- next‐generation sequencing -- pathogenic variant -- TP53; Human chromosome abnormalities -- Periodicals; Mutation (Biology) -- Periodicals; 616.04205
• DOI: 10.1002/humu.23910
• Languages: English
• ISSNs: 1059-7794

Abstract

Abstract: Previous analysis of next‐generation sequencing (NGS) hereditary pan‐cancer panel testing demonstrated that approximately 40% of TP53 pathogenic and likely pathogenic variants (PVs) detected have NGS allele frequencies between 10% and 30%, indicating that they likely are acquired somatically. These are seen more frequently in older adults, suggesting that most result from normal aging‐related clonal hematopoiesis. For this analysis, apparent heterozygous germline TP53 PV carriers (NGS allele frequency 30–70%) were offered follow‐up testing to confirm variant origin. Ninety‐eight probands had samples submitted for follow‐up family member testing, fibroblast testing, or both. The apparent heterozygous germline TP53 PV was not detected in 32.6% (15/46) of submitted fibroblast samples, indicating that it was acquired somatically, either through clonal hematopoiesis or via constitutional mosaicism. Notably, no individuals with confirmed germline or likely germline TP53 PVs met classic Li–Fraumeni syndrome (LFS) criteria, only 41% met Chompret LFS criteria, and 59% met neither criteria, based upon provider‐reported personal and family cancer history. Comprehensive reporting of TP53 PVs detected using NGS, combined with follow‐up analysis to confirm variant origin, is advised for clinical testing laboratories. These findings underscore the investment required to provide individuals and family members with clinically accurate genetic test results pertaining to their LFS risk. Abstract : In next‐generation sequencing (NGS) hereditary cancer panel testing, TP53 pathogenic variants whose NGS allele frequencies might appear consistent with those expected for germline variants, but the variant might be acquired somatically. Confirming TP53 variant origin can markedly impact medical management for tested individuals and their family members. The report highlights the need for a conservative approach to initial reporting of TP53 ‐positive findings, along with investment in follow‐up testing to deliver clinically accurate results.