Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes

JCO Clin Cancer Inform. 2019 Oct;3:1-12. doi: 10.1200/CCI.19.00077.

Abstract

Purpose: Clinical targeted sequencing panels are important for identifying actionable variants for patients with cancer; however, existing approaches do not provide transparent and rationally designed clinical panels to accommodate the rapidly growing knowledge within oncology.

Materials and methods: We used the Clinical Interpretations of Variants in Cancer (CIViC) database to develop an Open-Sourced CIViC Annotation Pipeline (OpenCAP). OpenCAP provides methods to identify variants within the CIViC database, build probes for variant capture, use probes on prospective samples, and link somatic variants to CIViC clinical relevance statements. OpenCAP was tested using a single-molecule molecular inversion probe (smMIP) capture design on 27 cancer samples from 5 tumor types. In total, 2,027 smMIPs were designed to target 111 eligible CIViC variants (61.5 kb of genomic space).

Results: When compared with orthogonal sequencing, CIViC smMIP sequencing demonstrated a 95% sensitivity for variant detection (n = 61 of 64 variants). Variant allele frequencies for variants identified on both sequencing platforms were highly concordant (Pearson's r = 0.885; n = 61 variants). Moreover, for individuals with paired tumor and normal samples (n = 12), 182 clinically relevant variants missed by orthogonal sequencing were discovered by CIViC smMIP sequencing.

Conclusion: The OpenCAP design paradigm demonstrates the utility of an open-source and open-access database built on attendant community contributions with peer-reviewed interpretations. Use of a public repository for variant identification, probe development, and variant interpretation provides a transparent approach to build dynamic next-generation sequencing-based oncology panels.

MeSH terms

  • Biomarkers, Tumor / genetics*
  • Computational Biology / methods*
  • DNA Mutational Analysis / methods
  • DNA Probes / genetics*
  • Databases, Genetic
  • Genetic Variation
  • High-Throughput Nucleotide Sequencing / methods
  • High-Throughput Nucleotide Sequencing / standards*
  • Humans
  • Molecular Sequence Annotation / methods*
  • Molecular Sequence Annotation / standards
  • Molecular Targeted Therapy
  • Neoplasms / diagnosis
  • Neoplasms / genetics*
  • ROC Curve
  • Software Design

Substances

  • Biomarkers, Tumor
  • DNA Probes