Database Management Systems study with AMPLICON data on dbGaP (17 participants)

phs001890 — Single Molecule Molecular Inversion Probe Capture Developed Using CIViC

<p>This study evaluated the use of the <a href="https://civicdb.org">Clinical Interpretations of Variants in Cancer database (CIViC)</a> to develop an <a href="http://opencap.org">Open-sourced CIViC Annotation Pipeline (OpenCAP)</a>. OpenCAP is a resource that allows users to develop a clinical capture panel that can be linked back to clinical summaries within the CIViC database. This method for capture panel development and variant annotation was tested using 27 cancer samples from 5 tumor subtypes with original exome or genome sequencing. Specifically, using OpenCAP, 111 variants were identified as relevant for the capture panel and 2,027 smMIPs were designed to target these variants. The smMIPs panel design was employed on all samples to validate the capture panel design. When compared to original sequencing, the CIViC smMIPs capture panel demonstrated a 95% sensitivity for variant detection (n = 61 variants). Additionally, the CIViC smMIPs capture panel identified 182 additional clinically relevant variants that had been missed on original sequencing.</p>