Molecular Diagnostics

The TP53 VCEP followed ClinGen standard operating procedures (see https://clinicalgenome.org/site/assets/files/3677/clingen_variant-curation_sopv1.pdf). The VCEP formed in 2015 by recruiting international TP53 experts knowledgeable in phenotype, molecular diagnosis and functional processes. Twenty-four members contributed to at least one of three different evidence type working groups: Population/Computational, Functional, and Clinical. Each group reviewed the ACMG/AMP TP53-specifications in detail, incorporated this with critical review of the relevant literature and analyses of relevant data to inform evidence weights, and came to consensus for each specification.
The VCEP members nominated variants for pilot testing the TP53-specific ACMG/AMP guidelines. Specifically, 23 variants were were chosen to cover varying molecular effects and the availability of data to assess the usability of different rule codes. Seven variants from the International Agency on Research in Cancer (IARC) TP53 Database (Bouaoun et al., 2016 (link)) were included for their rich phenotypic information, but had no prior variant classifications. Thirteen variants from the ClinVar database (Landrum et al., 2018 (link)) were used to balance the spectrum of suspected classifications (with annotation at time of study initiation ranging from benign to pathogenic). In addition to evidence available from public databases, case level evidence available from clinical laboratory databases was provided by relevant VCEP members to the biocurators, including information regarding cancer type(s) and family history, familial variant segregation, and de novo observations. Variant classifications (pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB) and benign (B)) were also provided by the nominating VCEP member, which are referred to as prior expert assertions. Of note, variants sourced from ClinVar had assertions submitted by laboratories with representation on our VCEP, so that laboratory’s assertion in 2017 was considered as the prior expert assertion. Each variant was independently curated by two of the collaborating five biocurators using the original ACMG/AMP guidelines and the TP53 specifications to test user interpretability. Only one of the five biocurators had prior experience with the rule specifications during development. The criteria combinations for a given classification tier were followed as originally proposed (Richards et al., 2015 (link)), with the additional combination of very strong plus supporting criteria reaching LP for the TP53-specific guidelines supported by the Tavtigian et al. Bayesian rule combination calculator (Tavtigian et al., 2018 (link)). The resulting classifications were compared between biocurators, against prior assertions by the nominating expert(s) or contributing laboratories, and with ClinVar assertions (Landrum et al., 2018 (link)) when possible. During this phase, the TP53-specific guidelines were refined, and the final draft and results of the application of the evidence codes to the pilot variants was presented to the ClinGen Sequence Variant Interpretation (SVI) Committee for approval.