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. 2016 May 5;98(5):801-817.
doi: 10.1016/j.ajhg.2016.02.024.

Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer

Kara N Maxwell  1 , Steven N Hart  2 , Joseph Vijai  3 , Kasmintan A Schrader  4 , Thomas P Slavin  5 , Tinu Thomas  3 , Bradley Wubbenhorst  6 , Vignesh Ravichandran  3 , Raymond M Moore  2 , Chunling Hu  7 , Lucia Guidugli  7 , Brandon Wenz  6 , Susan M Domchek  8 , Mark E Robson  9 , Csilla Szabo  10 , Susan L Neuhausen  11 , Jeffrey N Weitzel  5 , Kenneth Offit  9 , Fergus J Couch  7 , Katherine L Nathanson  12
Affiliations

Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer

Kara N Maxwell et al. Am J Hum Genet. .

Abstract

Sequencing tests assaying panels of genes or whole exomes are widely available for cancer risk evaluation. However, methods for classification of variants resulting from this testing are not well studied. We evaluated the ability of a variant-classification methodology based on American College of Medical Genetics and Genomics (ACMG) guidelines to define the rate of mutations and variants of uncertain significance (VUS) in 180 medically relevant genes, including all ACMG-designated reportable cancer and non-cancer-associated genes, in individuals who met guidelines for hereditary cancer risk evaluation. We performed whole-exome sequencing in 404 individuals in 253 families and classified 1,640 variants. Potentially clinically actionable (likely pathogenic [LP] or pathogenic [P]) versus nonactionable (VUS, likely benign, or benign) calls were 95% concordant with locus-specific databases and Clinvar. LP or P mutations were identified in 12 of 25 breast cancer susceptibility genes in 26 families without identified BRCA1/2 mutations (11%). Evaluation of 84 additional genes associated with autosomal-dominant cancer susceptibility identified LP or P mutations in only two additional families (0.8%). However, individuals from 10 of 253 families (3.9%) had incidental LP or P mutations in 32 non-cancer-associated genes, and 9% of individuals were monoallelic carriers of a rare LP or P mutation in 39 genes associated with autosomal-recessive cancer susceptibility. Furthermore, 95% of individuals had at least one VUS. In summary, these data support the clinical utility of ACMG variant-classification guidelines. Additionally, evaluation of extended panels of cancer-associated genes in breast/ovarian cancer families leads to only an incremental clinical benefit but substantially increases the complexity of the results.

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Figures

Figure 1
Figure 1
Use of A Methodology Based on ACMG Variant-Classification Guidelines to Identify Variants in 180 Clinically Relevant Genes in Individuals with Breast Cancer (A) Heat map showing the individual attributes leading to the raw and final calls of well-curated locus-specific database (LSDB)-classified pathogenic variants found by exome sequencing in individuals at high risk for breast and/or ovarian cancer. Genes are separated into those associated with AD cancer susceptibility, those associated with AR cancer susceptibility, and non-cancer-associated genes. The 28 possible attributes leading to our calls and the method of determination are described in Table S2. (B) Pie charts showing the percentage of all variants found in LSDBs in each of nine possible categories of call comparisons between raw and final calls and LSDBs; likely benign (LB) and benign (B) were considered one call, and likely pathogenic (LP) and pathogenic (P) were considered one call. AD Cancer: genes associated with AD cancer susceptibility. AR Cancer: genes associated with AR cancer susceptibility.Non-cancer: non-cancer-associated genes, (C) Pie charts showing the percentage of all LSDB-classified variants with concordant and discordant raw and final calls based on potential actionability, where B, LB, and VUS (variant of uncertain significance) calls were considered clinically nonactionable and LP and P calls were considered potentially clinically actionable. (D) Heat map showing the individual attributes leading to raw and final calls of clinically relevant variants, i.e., LP or P variants in all genes and truncating variants called VUSs in genes where loss of function is the mechanism of pathogenesis.
Figure 2
Figure 2
Rates of Calls According to ACMG Guidelines in 180 Genes in Individuals with Breast Cancer (A) Overview of the distribution of the five variant classifications in all genes, known or proposed breast cancer susceptibility (BC) genes, genes associated with AD cancer susceptibility, genes associated with AR inherited cancer susceptibility, and non-cancer-associated genes. Breast cancer: genes associated with breast cancer susceptibility; AD Cancer: genes associated with AD cancer susceptibility; AR cancer: genes associated with AR cancer susceptibility; non-cancer: non-cancer-associated genes. (B) Bar plot showing the absolute number of VUSs and LP and P variants in genes with at least one LP or P mutation in BC genes. (C) Bar plot showing the absolute number of VUSs and LP and P variants in genes with at least one LP or P mutation in genes associated with (a/w) AD cancer susceptibility. (D) Bar plot showing the absolute number of VUSs and LP and P variants in genes with at least one LP or P mutation in genes associated with (a/w) AR cancer susceptibility. (E) Bar plot showing the absolute number of VUSs and LP and P variants in genes with at least one LP or P mutation in non-cancer-associated genes. (B–E) F = final calls; R = raw calls.
Figure 3
Figure 3
Variation in Mutation Rate in AD Cancer Susceptibility Genes in Families Affected by Breast or Ovarian Cancer (A) Breakdown of the number of LP or P mutations identified in 389 individuals representing 243 families without identified BRCA1/2 mutations. a/w: associated with. (B) Proportion of families that did not have identified BRCA1/2 mutations and that fit the three main inclusion criteria: history of familial breast cancer (FBC), history of early-onset breast cancer (EOBC), and history of both breast and ovarian cancer (Br/Ov) along with high-risk breast cancer susceptibility gene mutations, ATM or CHEK2 mutations, or mutations in the rest of the genes associated with AD cancer susceptibility. ∗p < 0.05, ∗∗p < 0.01. (C) Percentage of families with VUSs (gray bars) in indicated genes and percentage of families with LP or P mutations (black bars) in indicated genes, additive from top to bottom. AD non-syndromic: genes associated with AD cancer susceptibility not associated with other syndromic features; AD syndromic: genes associated with AD cancer susceptibility syndromes. (D) N-fold increase in the rate of identification of families with LP or P mutations and VUSs as the number of assayed genes associated with AD cancer susceptibility increases. (E) Bar plot showing the distribution of individuals with one and up to six or more VUSs identified in the study.
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