PurposeBlood/saliva DNA is thought to represent the germline in genetic cancer risk assessment. Cases with pathogenic TP53 variants detected by multi-gene panel tests (MGPT) are often discordant with Li-Fraumeni Syndrome (LFS), raising concern about misinterpretation of acquired aberrant clonal expansions (ACE) with TP53 variants as germline results.MethodsPathogenic TP53 variants with abnormal next-generation sequencing (NGS) metrics (e.g., decreased ratio [<25%] of mutant to wild-type allele, >2 detected alleles) were selected from a CLIA laboratory testing cohort. Alternate tissues and/or close relatives were tested to discern between ACE and germline status. Clinical data and LFS testing criteria were examined.ResultsAmong 114,630 MGPT and 1,454 TP53 gene-specific analyses, abnormal NGS metrics were observed in 20% of 353 TP53 positive results, and ACE was confirmed for 91% of cases with ancillary materials, most due to clonal hematopoiesis. Only four met Chompret criteria. ACE cases were older (50 years vs 33.7; P = 0.02) and were more frequent among MGPT (66/285; 23.2%) vs TP53 gene-specific tests (6/68; 8.8%, P = 0.005).ConclusionACE confounds germline diagnosis, may portend hematologic malignancy, and may result in unwarranted clinical interventions. Ancillary testing to confirm germline status should precede Li-Fraumeni syndrome management.

BackgroundMultigene panels can be a cost- and time-effective alternative to sequentially testing multiple genes, especially with a mixed family cancer phenotype. However, moving beyond our single-gene testing paradigm has unveiled many new challenges to the clinician. The purpose of this article is to familiarize the reader with some of the challenges, as well as potential opportunities, of expanded hereditary cancer panel testing.MethodsWe include results from 348 commercial multigene panel tests ordered from January 1, 2014, through October 1, 2014, by clinicians associated with the City of Hope’s Clinical Cancer Genetics Community of Practice. We also discuss specific challenging cases that arose during this period involving abnormalities in the genes: CDH1, TP53, PMS2, PALB2, CHEK2, NBN, and RAD51C.ResultsIf historically high risk genes only were included in the panels (BRCA1, BRCA2, MSH6, PMS2, TP53, APC, CDH1), the results would have been positive only 6.2% of the time, instead of 17%. Results returned with variants of uncertain significance (VUS) 42% of the time.ConclusionThese figures and cases stress the importance of adequate pre-test counseling in anticipation of higher percentages of positive, VUS, unexpected, and ambiguous test results. Test result ambiguity can be limited by the use of phenotype-specific panels; if found, multiple resources (the literature, reference laboratory, colleagues, national experts, and research efforts) can be accessed to better clarify counseling and management for the patient and family. For pathogenic variants in low and moderate risk genes, empiric risk modeling based on the patient’s personal and family history of cancer may supersede gene-specific risk. Commercial laboratory and patient contributions to public databases and research efforts will be needed to better classify variants and reduce clinical ambiguity of multigene panels.

For nonbenign variants in cancer-related genes, the rates at which reclassifications are issued vary by ancestry in ways that differ between BRCA1/2 and other genes.