Performance characteristics of a targeted sequencing platform for simultaneous detection of single nucleotide variants, insertions/deletions, copy number alterations, and gene fusions in cancer genome

Kyung Park, Hung Tran, Kenneth W. Eng, Sinan Ramazanoglu, Rebecca M.Rolon Marrero, Theresa Scognamiglio, Alain Borczuk, Juan Miguel Mosquera, Qiulu Pan, Andrea Sboner, Mark A. Rubin, Olivier Elemento, Hanna Rennert, Helen Fernandes, Wei Song

Research output: Contribution to journalArticlepeer-review

Abstract

Context. - An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. Objective. - To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCIMATCH) trial. Design. - Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. Results. - High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/ deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. Conclusions. - This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.

Original languageEnglish (US)
Pages (from-to)1535-1546
Number of pages12
JournalArchives of Pathology and Laboratory Medicine
Volume144
Issue number12
DOIs
StatePublished - Dec 2020
Externally publishedYes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology

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