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.

TitlePerformance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome.
Publication TypeJournal Article
Year of Publication2020
AuthorsPark K, Tran H, Eng KW, Ramazanoglu S, Rolon RMMarrero, Scognamiglio T, Borczuk A, Mosquera JMiguel, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W
JournalArch Pathol Lab Med
Volume144
Issue12
Pagination1535-1546
Date Published2020 12 01
ISSN1543-2165
KeywordsDNA Copy Number Variations, Gene Fusion, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Mutagenesis, Insertional, Neoplasms, Polymorphism, Single Nucleotide, Precision Medicine, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, DNA, Sequence Deletion
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 (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.

DOI10.5858/arpa.2019-0162-OA
Alternate JournalArch Pathol Lab Med
PubMed ID32045275
Grant ListP50 CA211024 / CA / NCI NIH HHS / United States
U24 CA210989 / CA / NCI NIH HHS / United States
Related Faculty: 
Andrea Sboner, Ph.D. Hanna Rennert, Ph.D. Juan Miguel Mosquera, M.D. Theresa Scognamiglio, M.D.

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