Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors

Abstract

Importance: Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown.

Objective: To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors.

Design: Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic children's hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record.

Main outcomes and measures: Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations.

Results: Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%).

Conclusions and relevance: Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

Figure 1. Categories of Mutation Results Included in Clinical Tumor and Germline Whole-Exome Sequencing Reports

Reported categories of somatic mutations (A) and germline mutations (B) are shown. Germline testing for autosomal recessive carrier mutations was performed if requested by the parents at the time of study enrollment. PCG indicates pharmacogenetic; VUS, variant of uncertain significance. The image in panel B was adapted from the study by Scollon et al, an open access article. For more information on the categorization of TSC2 frameshift as a category II mutation, see Perry et al, Krueger et al, and Iyer et al.

Figure 2. Somatic Mutations Detected Among Study Participants

A, Highest category of somatic mutation per participant identified by tumor whole-exome sequencing (WES). Data for the subsets of children with central nervous system (CNS) tumors (n = 40) and non-CNS tumors (n = 81) are shown in addition to the entire patient cohort with tumor samples available (n = 121). I indicates category I mutation; II, category II mutation; III, category III mutation; IV, category IV or no mutation. B, Genes targeted by recurrent somatic mutations in patients for whom tumor WES was performed.

Figure 3. Combined Yield of Tumor and Germline Whole-Exome Sequencing (WES)

Mutations with known or potential clinical implications identified by tumor and germline WES of children with newly diagnosed solid tumors. Each slice represents a different patient undergoing both tumor and germline sequencing (n = 121), and each concentric ring a category of somatic or germline mutation.