Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants

Abstract

The variant curation guidelines published in 2015 by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) provided the genetics community with a framework to assess variant pathogenicity; however, these rules are not gene specific. Germline pathogenic variants in the CDH1 gene cause hereditary diffuse gastric cancer and lobular breast cancer, a clinically challenging cancer predisposition syndrome that often requires a multidisciplinary team of experts to be properly managed. Given this challenge, the Clinical Genome Resource (ClinGen) Hereditary Cancer Domain prioritized the development of the CDH1 variant curation expert panel (VCEP) to develop and implement rules for CDH1 variant classifications. Here, we describe the CDH1 specifications of the ACMG/AMP guidelines, which were developed and validated after a systematic evaluation of variants obtained from a cohort of clinical laboratory data encompassing ∼827,000 CDH1 sequenced alleles. Comparing previously reported germline variants that were classified using the 2015 ACMG/AMP guidelines to the CDH1 VCEP recommendations resulted in reduced variants of uncertain significance and facilitated resolution of variants with conflicted assertions in ClinVar. The ClinGen CDH1 VCEP recommends the use of these CDH1-specific guidelines for the assessment and classification of variants identified in this clinically actionable gene.

Keywords: ACMG/AMP Variant Curation Guidelines; CDH1; ClinGen; ClinVar; hereditary diffuse gastric cancer; lobular breast cancer.

Figure 1 –

Pilot assessment of CDH1 variants. A – Clinical and population evidence of selected CDH1 missense variants. Red boxes highlight the three missense variants that were demonstrated functionally by RNA analysis to activate cryptic splicing sites; green boxes highlight variants that met benign population allele-frequency cutoffs. Allele frequencies for the selected variants in the ExAC database (~120,000 alleles) and in the cohorts of the three largest data sharing clinical genetic laboratories in the U.S.A. (~827,000 alleles total). B – Laboratory cohort phenotypes associated with each of the specific variants. HDGC = family meets International Gastric Cancer Linkage Consortium (IGCLC) criteria; HDGC-associated tumors = Diffuse Gastric Cancer, Signet Ring Cell tumors (e.g., Krukenberg tumor), Lobular Breast Cancer, but does not meet IGCLC criteria; Others are either reported unaffected or having non-CDH1 tumors (e.g., breast invasive ductal carcinoma). C – Comparing variant classifications from EP or ClinVar submitters and from the original ACMG/AMP criteria versus applying CDH1 evidence code specifications demonstrates a reduction of VUS. P = pathogenic; LP = likely pathogenic; VUS = variant of uncertain significance; LB = likely benign; B = benign. ClinVar assertions were accessed on April 16, 2018. D – E-cadherin schematic representation demonstrating its major domains in relation to the 50 pilot variants curated by the EP. E-cadherin is a highly conserved transmembrane protein that possess a signal peptide, a precursor protein, the extracellular domain, which is the “adhesive” ectodomain composed of tandem cadherin repeats, the transmembrane (TM) domain, and the cytoplasmic domain, which interacts with the armadillo catenins, p120 and β-catenin (Gul et al., 2017). Clinically actionable variants (P, LP) are shown at the top; VUS, LB, and B variants are shown at the bottom.