Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer

Abstract

Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.

Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions

“…For sequencing, genome coverage differs between WGS, WES, and targeted gene panel assays. WGS covers the whole genome, WES covers the entire exome coding region, and targeted gene panels cover specified areas that may or may not include tumor suppressor genes, driver genes, or intronic regions . Moreover, the size and location of the capture region differs between targeted gene panel assays.…”

“…WGS covers the whole genome, WES covers the entire exome coding region, and targeted gene panels cover specified areas that may or may not include tumor suppressor genes, driver genes, or intronic regions. 4,60,61 Moreover, the size and location of the capture region differs between targeted gene panel assays. It is important to carefully consider the panel size and composition for accurate TMB assessment.…”

Clinical sequencing: From raw data to diagnosis with lifetime value

“…Genes of interest, so‐called gene panels, can be enriched and sequenced simultaneously by TS, which serves as an inexpensive and rapid first‐tier test with compatibility to benchtop short‐read sequencers (eg, Illumina MiSeq/NextSeq and Thermo Fisher Scientific Ion PGM/Proton) and with especially high read depth of targeted regions (Table ). Consequently, TS enables sequence variant detection in samples with very low non‐reference allele frequencies caused by germline mosaics or clonal complexity of tumors . Moreover, the use of disease‐related gene panels facilitates the interpretation of detected sequence variants and minimizes the chance of incidental findings .…”

“…Consequently, TS enables sequence variant detection in samples with very low non-reference allele frequencies caused by germline mosaics or clonal complexity of tumors. 3,4 Moreover, the use of disease-related gene panels facilitates the interpretation of detected sequence variants and minimizes the chance of incidental findings. 5 According to the guidelines and recommendations of the American College of Medical Genetics and Genomics (ACMG), only genes with a scientifically sufficiently supported role in disease should be included in a clinical gene panel.…”

The impact of hereditary cancer gene panels on clinical care and lessons learned

“…As the cost of sequencing continues to drop, WES has been considered as an alternative to panels. Targeted gene panels have some advantages over WES in terms of average mean read depth and coverage of genes of interest ( Feliubadaló et al 2017 ). Turnaround time is shorter with targeted gene panels because the amount of data to analyze is considerably less.…”