Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization

By K. J. Velde, Joël Kuiper, B. Thompson, J. Plazzer, G. van Valkenhoef, M. Haan, J. Jongbloed, C. Wijmenga, T. Koning, K. Abbott and 6 more. 2015

43 citations recorded by the source corpus.

Next‐generation sequencing in clinical diagnostics is providing valuable genomic variant data, which can be used to support healthcare decisions. In silico tools to predict pathogenicity are crucial to assess such variants and we have evaluated a new tool, Combined Annotation Dependent Depletion (CADD), and its classification of gene variants in Lynch syndrome by using a set of 2,210 DNA mismatch repair gene variants. These had already been classified by experts from InSiGHT's Variant Interpretation Committee. Overall, we found CADD scores do predict pathogenicity (Spearman's ρ = 0.595, P < 0.001). However, we discovered 31 major discrepancies between the InSiGHT classification and the CADD scores; these were explained in favor of the expert classification using population allele frequencies, cosegregation analyses, disease association studies, or a second‐tier test. Of 751 variants that could not be clinically classified by InSiGHT, CADD indicated that 47 variants were worth further study to confirm their putative pathogenicity. We demonstrate CADD is valuable in prioritizing variants in clinically relevant genes for further assessment by expert classification teams.

Subfields: Genetics, Pathology and Forensic Medicine

Citations in the corpus

• CADD: predicting the deleteriousness of variants throughout the human genome (2018, neutral): “This includes variants from clinical studies, like de novo , dominant and recessive variants discovered in family-based sequencing (e.g. 23,25– 28), as well as variants identified in population-based studies (e.g. 29).”