Open AccessPerformance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome
Author(s) -
Kyung Park,
Hung Tran,
Kenneth Eng,
Sinan Ramazanoglu,
Rebecca M Marrero Rolon,
Theresa Scognamiglio,
Alain Borczuk,
Juan Miguel Mosquera,
Qiulu Pan,
Andrea Sboner,
Mark A. Rubin,
Olivier Elemento,
Hanna Rennert,
Helen Fernandes,
Wei Song
Publication year - 2020
Publication title -
archives of pathology and laboratory medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.79
H-Index - 117
eISSN - 1543-2165
pISSN - 0003-9985
DOI - 10.5858/arpa.2019-0162-oa
Subject(s) - amplicon , dna sequencing , computational biology , context (archaeology) , international hapmap project , amplicon sequencing , copy number variation , biology , deep sequencing , precision oncology , genetics , gene , genome , precision medicine , polymerase chain reaction , human genome , paleontology , 16s ribosomal rna
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 (NCI-MATCH) 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.