Toward automation of germline variant curation in clinical cancer genetics

Abstract

Purpose: Cancer care professionals are confronted with interpreting results from multiplexed gene sequencing of patients at hereditary risk for cancer. Assessments for variant classification now require orthogonal data searches and aggregation of multiple lines of evidence from diverse resources. The clinical genetics community needs a fast algorithm that automates American College of Medical Genetics and Genomics (ACMG) based variant classification and provides uniform results.

Methods: Pathogenicity of Mutation Analyzer (PathoMAN) automates germline genomic variant curation from clinical sequencing based on ACMG guidelines. PathoMAN aggregates multiple tracks of genomic, protein, and disease specific information from public sources. We compared expertly curated variant data from clinical laboratories to assess performance.

Results: PathoMAN achieved a high overall concordance of 94.4% for pathogenic and 81.1% for benign variants. We observed negligible discordance (0.3% pathogenic, 0% benign) when contrasted against expert curated variants. Some loss of resolution (5.3% pathogenic, 18.9% benign) and gain of resolution (1.6% pathogenic, 3.8% benign) were also observed.

Conclusion: Automation of variant curation enables unbiased, fast, efficient delivery of results in both clinical and laboratory research. We highlight the advantages and weaknesses related to the programmable automation of variant classification. PathoMAN will aid in rapid variant classification by generating robust models using a knowledgebase of diverse genetic data ( https://pathoman.mskcc.org).

Keywords: ACMG; cancer; curation; germline; pathogenicity.

Figure 1

A: Distribution of 3513 variants in the test dataset by variant class (IF - Inframe insertion and/or deletion. It alters length but not frame of coding sequence, FS - Frameshifting insertion and/or deletion. It alters length and frame of coding sequence, ESS - Any variant that alters essential splice-site base (+1, +2, −1, −2), EE - Variant that alters the first or last three bases of an exon (i.e., the exon end), but not the frame of the coding sequence, 5PU - Any variant in 5′ untranslated region, SY - Synonymous variant. It does not alter amino acid or coding sequence length, SS5 - Any variant that alters +5 splice-site base but not an ESS base, SS - Any variant that alters splice-site base within the first eight intronic bases flanking exon (i.e., +8 to −8) but not an ESS or SS5 base, SG - Stop-gain (nonsense) variant caused by base substitution, NSY - Nonsynonymous variant. It alters amino acid(s) but not coding sequence length, IM - Variant that alters initiating methionine start codon, 3PU - Any variant in 3′ untranslated region). Figure 1B: Performance of PathoMAN’s variant classification against variant classification from three clinical laboratories – Ambry Genetics, Invitae and GeneDx. Figure 1C: Concordance of PathoMAN and clinical lab results for reported P/LP variants group by penetrance of the gene (1257 variants in 27 genes Supp table S5). Figure 1D: Concordance of PathoMAN and published reports for reported P/LP variants from four cancer studies (300 variants in 55 genes; Mandelker et al – 97 variants, Maxwell et al 40 variants, Pritchard et al – 56 variants and Zhang et al – 107 variants Supp table S7)

Figure 2

A: Utilization of knowledgebase components by PathoMAN during variant curation of test datasets. Figure 2B: Ratio of number of articles per variant across different review status reported in ClinVar.