Prevalence and characteristics of likely-somatic variants in cancer susceptibility genes among individuals who had hereditary pan-cancer panel test... - PubMed - NCBI

Prevalence and characteristics of likely-somatic variants in cancer susceptibility genes among individuals who had hereditary pan-cancer panel test... - PubMed - NCBI

Cancer Genet. 2019 Apr 13. pii: S2210-7762(18)30555-6. doi: 10.1016/j.cancergen.2019.04.005. [Epub ahead of print]

Prevalence and characteristics of likely-somatic variants in cancer susceptibility genes among individuals who had hereditary pan-cancer panel testing.

Slavin TP1, Coffee B2, Bernhisel R2, Logan J2, Cox HC2, Marcucci G3, Weitzel J4, Neuhausen SL5, Mancini-DiNardo D2.

Author information

Abstract

Next-generation sequencing (NGS) hereditary pan-cancer panel testing can identify somatic variants, which exhibit lower allele frequencies than do germline variants and may confound hereditary cancer predisposition testing. This analysis examined the prevalence and characteristics of likely-somatic variants among 348,543 individuals tested using a clinical NGS hereditary pan-cancer panel. Variants showing allele frequencies between 10% and 30% were interpreted as likely somatic and identified in 753 (0.22%) individuals. They were most frequent in TP53, CHEK2 and ATM, commonly as C-to-T transitions. Among individuals who carried a likely-somatic variant and reported no personal cancer history, 54.2% (78/144) carried a variant in TP53, CHEK2 or ATM. With a reported cancer history, this percentage increased to 81.1% (494/609), predominantly in CHEK2 and TP53. Their presence was associated with age (OR=3.1, 95% CI 2.5, 3.7; p<0.001) and personal history of cancer (OR=3.3, 95% CI 2.7, 4.0; p<0.001), particularly ovarian cancer. Germline ATM pathogenic variant carriers showed significant enrichment of likely-somatic variants (OR=2.8, 95% CI 1.6, 4.9; p = 0.005), regardless of cancer status. The appearance of likely-somatic variants is consistent with clonal hematopoiesis, possibly influenced by cancer treatment. These findings highlight the precision required of diagnostic laboratories to deliver accurate germline testing results.

Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

KEYWORDS:

Clonal hematopoiesis; Hereditary pan-cancer panel testing; Next-generation sequencing; Somatic variant

PMID:

 

31056428

 

DOI:

 

10.1016/j.cancergen.2019.04.005