Targeted next-generation DNA sequencing of paired tumor and normal DNA to reveal frequent actionable germline alterations.

Abstract

11575 Background: Targeted next-generation DNA sequencing of paired tumor and normal DNA samples allows for detection of biologically relevant variants in the tumor with significantly greater accuracy than tumor-only sequencing. In addition, this approach presents with the opportunity of unveiling previously unknown cancer predisposition traits in a patient’s germline DNA. Methods: We sought to determine the rate of pathogenic germline alterations in 546 consecutive pediatric and adult patients who underwent molecular profiling using the UCSF 500 assay, a hybrid capture-based DNA sequencing assay targeting the coding regions of ~500 cancer-related genes, TERT promoter, select introns from 40 genes (for detection of gene fusions and other structural variants), and intergenic regions at regular intervals along each chromosome (for chromosomal copy number and LOH assessment). Results: Pathogenic germline alterations were found in 89/546 patients (16.3%), including 25 pediatric and 64 adult cases. Germline variants were identified in 37 genes with MUTYH (n = 15, 17%), CHEK2 (n = 10, 11%), BRCA2 (n = 9, 10%), BRCA1 (n = 5, 6%), TP53 (n = 5, 5%), and APC (n = 4, 5%) being altered most frequently. Loss of heterozygosity of genes affected in the germline was seen in tumor DNA 37 (42%) cases, highlighting their likely role as drivers of tumorigenesis. Clinically relevant germline findings not associated with increased cancer risk were identified in 6 (7%) of the cases, for example a COL1A1 mutation associated with Ehlers-Danlos Syndrome. In In 73 (82%) of the cases, pathogenic germline alterations were new findings and genetic counseling was recommended. A possible, previously unknown, role of germline mutations was found in some instances, including a TSC2 germline mutation in a patient with hybrid oncocytoma/chromophobe tumor (HOCT) with loss of the normal TSC2 allele in the tumor. Conclusions: Our data suggest that paired tumor/normal DNA analysis uncovers actionable heritable traits in a substantial fraction of patients and represents the preferred approach to analyzing malignancies in children and adults.