Oncomine Comprehensive Panel v2 NGS Assay

The extracted DNA was amplified by the Oncomine Comprehensive Panel (OCP) v2 and subjected to NGS using the Ion Torrent S5 system (Life Technologies) according to the vender recommendations.^{13 (link)} The Oncomine Comprehensive assay was developed and its performance characteristics were determined by the Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine at Weill Cornell Medicine/New York-Presbyterian Hospital^{14 (link)} and approved by the New York-State Department of Health (NYS-DOH). The targeted gene panel interrogates 143 unique cancer genes including the hotspots of 73 genes, 49 copy number alteration genes, entire coding regions of 26 genes, and 22 fusion driver genes. The data obtained were analyzed with the Ion Reporter Software 5.6 including Coverage Analysis and Torrent Variant Annotator v2.3 plug-ins. The mutation nomenclature is based on the recommendations from the Human Genome Variation Society (http://www.hgvs.org/mutnomen).

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Nilforoushan N., Liu L., Cheang G., Sui A.C., Andersen J., Finkelman B.S., Liu Y., Nasseri-Nik N., Vang R., Ronnett B.M., Song W, & Xing D. (2022). Mucinous Tumor Coexisting With Mesonephric-like Proliferation/Tumor in the Ovary A Novel Association. The American journal of surgical pathology, 46(8), 1095-1105.

Publication 2022

Ion Torrent S5 system

Assay Cancer genes Clinical laboratory Copy number alteration Genes Hgvs Human genome Medicine Mutation

Corresponding Organization : Johns Hopkins University

Other organizations : Sky Ridge Medical Center, Cornell University, Baptist Hospital of Miami

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Variable analysis

independent variables

Oncomine Comprehensive Panel (OCP) v2 amplification of extracted DNA
Next-generation sequencing (NGS) using the Ion Torrent S5 system

dependent variables

Mutation detection and characterization in 143 unique cancer genes

control variables

The Oncomine Comprehensive assay development and performance characteristics determined by the Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine at Weill Cornell Medicine/New York-Presbyterian Hospital
Approval of the Oncomine Comprehensive assay by the New York-State Department of Health (NYS-DOH)

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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