| Literature DB >> 31490007 |
Bradford Coffee1, Hannah C Cox1, Ryan Bernhisel1, Susan Manley1, Karla Bowles1, Benjamin B Roa1, Debora Mancini-DiNardo1.
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.Entities:
Keywords: Li-Fraumeni syndrome; TP53; acquired somatically; hereditary pan-cancer gene panel; next-generation sequencing; pathogenic variant
Mesh:
Substances:
Year: 2019 PMID: 31490007 PMCID: PMC6972517 DOI: 10.1002/humu.23910
Source DB: PubMed Journal: Hum Mutat ISSN: 1059-7794 Impact factor: 4.878
Figure 1Follow‐up testing schema. The possible interpretations of follow‐up test results are provided for family testing and fibroblast testing in the proband
Figure 2(a) Age at diagnosis and (b) age at testing for individuals with an apparent germline TP53 PV identified by hereditary cancer genetic testing. Results are stratified according to the results of follow‐up testing
Summary of TP53 follow‐up testing and interpretation
| Follow‐up test result interpretation | |||||
|---|---|---|---|---|---|
| Follow‐up testing performed | Confirmed germline | Likely germline | Somatic | Inconclusive/uninformative | Total |
| Family testing only | 15 (28.8%) | 13 (25.0%) | 0 | 24 (46.2%) | 52 |
| Fibroblast testing only | 0 | 14 (56.0%) | 9 (36.0%) | 2 (8.0%) | 25 |
| Family and fibroblast testing | 4 (19.0%) | 10 (47.6%) | 6 (28.6%) | 1 (4.8%) | 21 |
| Total | 19 (19.4%) | 37 (37.8%) | 15 (15.3%) | 27 (27.6%) | 98 |
Fibroblast testing results were inconclusive when initial testing showed an allele frequency consistent with a germline variant, but the ratio of wild‐type to PV allele in the fibroblast sample was significantly skewed from the expected 50:50 ratio. Family member testing was considered uninformative when the TP53 PV was not detected in the tested family member.
Figure 3Allele frequencies for (a) somatic TP53 PVs (N = 15) and (b) confirmed germline (N = 19) and likely germline (N = 37) TP53 PVs. Only sequence variants are included. NGS, next‐generation sequencing; PV, pathogenic variant
Clinical Li–Fraumeni syndrome (LFS) classification, stratified by TP53 follow‐up testing result
| Follow‐up test result interpretation | ||||
|---|---|---|---|---|
| Confirmed germline/likely germline ( | Somatic ( | Inconclusive/uninformative ( | Unknown | |
| Did not meet clinical criteria for LFS | 33 (58.9%) | 12 (80.0%) | 18 (66.7%) | 86 (69.9%) |
| Met Chompret criteria for LFS | 23 (41.1%) | 3 (20.0%) | 9 (33.3%) | 37 (30.1%) |
| Met classic criteria for LFS | 0 | 0 | 0 | 0 |
Includes individuals for whom no follow‐up testing was performed.