Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes

Abstract

Genome- and exome-sequencing costs are continuing to fall, and many individuals are undergoing these assessments as research participants and patients. The issue of secondary (so-called incidental) findings in exome analysis is controversial, and data are needed on methods of detection and their frequency. We piloted secondary variant detection by analyzing exomes for mutations in cancer-susceptibility syndromes in subjects ascertained for atherosclerosis phenotypes. We performed exome sequencing on 572 ClinSeq participants, and in 37 genes, we interpreted variants that cause high-penetrance cancer syndromes by using an algorithm that filtered results on the basis of mutation type, quality, and frequency and that filtered mutation-database entries on the basis of defined categories of causation. We identified 454 sequence variants that differed from the human reference. Exclusions were made on the basis of sequence quality (26 variants) and high frequency in the cohort (77 variants) or dbSNP (17 variants), leaving 334 variants of potential clinical importance. These were further filtered on the basis of curation of literature reports. Seven participants, four of whom were of Ashkenazi Jewish descent and three of whom did not meet family-history-based referral criteria, had deleterious BRCA1 or BRCA2 mutations. One participant had a deleterious SDHC mutation, which causes paragangliomas. Exome sequencing, coupled with multidisciplinary interpretation, detected clinically important mutations in cancer-susceptibility genes; four of such mutations were in individuals without a significant family history of disease. We conclude that secondary variants of high clinical importance will be detected at an appreciable frequency in exomes, and we suggest that priority be given to the development of more efficient modes of interpretation with trials in larger patient groups.

Figure 1

Filtering Criteria Used for Coding-Variant Interpretation Variants were filtered for quality with MPG scores and coverage, frequency in ClinSeq and minor allele frequency in dbSNP, and data present in the Human Gene Mutation Database (HGMD) and locus specific databases (LSDBs) for each gene when available. Variants were determined to be benign, pathogenic, or of unknown significance (VUSs).

Figure 2

Box and Whisker Plots Showing Base Coverage for 37 Cancer-Associated Genes across a Cohort of 572 Probands The MIM numbers for these genes are listed in Table 1.

Figure 3

Characterization of 572 Variants by Pathogenicity Class Variants were graded from 1 to 5 with a modified version of an established scale; 1 is benign, and 5 is pathogenic. Variants that failed quality filters were defined as class 0. VUSs were defined as classes 2–4. Class 2 included variants highly likely to be benign, class 4 included variants highly likely to be pathogenic, and others were assigned to class 3.

Figure 4

Family Histories for Selected Variants The pathogenicity classes ascribed to variants detected in the probands of each family are as follows: class 5 for BRCA1 and BRCA2 variants in families A, B, and C and class 3 for the CDH1 variant in family D. The diamond symbol indicates relatives of probands in some families so that these families can remain anonymous. Of note, a first-degree relative and a second-degree relative of the proband in family D were diagnosed with prostate cancer; however, these individuals were from separate lineages, and prostate cancer is not thought to be a part of hereditary diffuse gastric cancer syndrome.