DOI: 10.1101/479394Nov 28, 2018Paper

Development of a precision oncology single molecule molecular inversion probe (smMIP) panel using a community-consensus approach

BioRxiv : the Preprint Server for Biology
Erica K. BarnellObi L. Griffith

Abstract

Clinical targeted sequencing panels are important for identifying actionable variants for cancer patients, however, there are currently no strategies to create impartial and rationally-designed panels to accommodate rapidly growing knowledge within the field. Here we use the Clinical Interpretations of Variants in Cancer database (CIViC) in conjunction with single-molecule molecular inversion probe (smMIP) capture to provide a dynamic and accurate capture panel targeting clinically relevant variants in cancer. In total, 2,027 smMIPs were designed to target 111 eligible CIViC variants. The total genomic region covered by the panel was 61.5 kb. When compared to existing genome or exome sequencing results (n = 27 cancer samples from 5 tumor types), the CIViC smMIP capture panel demonstrated a 95% sensitivity for variant detection (n = 61/64 variants). Variant allele frequency for variants identified on both sequencing platforms were highly concordant (Pearson correlation = 0.885; n = 61 variants). Moreover, for individuals with paired tumor/normal samples (n = 12), 182 clinically relevant variants missed by original sequencing were discovered by the CIViC smMIPs panel. This panel demonstrates the utility of an open-sourced databas...Continue Reading

Related Concepts

Malignant Neoplasms
Genome
Neoplasms
Probes
Oncologic
Protein Isoforms
Gene Mutant
Analysis
Nucleic Acid Sequencing
Small Molecule

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