| Title | 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. |
| Publication Type | Journal Article |
| Year of Publication | 2020 |
| Authors | Park 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 |
| Journal | Arch Pathol Lab Med |
| Date Published | 2020 Feb 11 |
| ISSN | 1543-2165 |
| 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. |
| DOI | 10.5858/arpa.2019-0162-OA |
| Alternate Journal | Arch. Pathol. Lab. Med. |
| PubMed ID | 32045275 |
| Grant List | P50 CA211024 / CA / NCI NIH HHS / United States R01 CA194547 / CA / NCI NIH HHS / United States |