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 Marrero Rolon; Theresa Scognamiglio; Alain Borczuk; Juan Miguel Mosquera; Qiulu Pan; Andrea Sboner; Mark A Rubin; Olivier Elemento; Hanna Rennert; Helen Fernandes; Wei Song

doi:10.5858/arpa.2019-0162-OA

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

Arch Pathol Lab Med. 2020 Dec 1;144(12):1535-1546. doi: 10.5858/arpa.2019-0162-OA.

Authors

Kyung Park¹, Hung Tran², Kenneth W Eng^{3

2}, Sinan Ramazanoglu^{3

2}, Rebecca M Marrero Rolon¹, Theresa Scognamiglio¹, Alain Borczuk¹, Juan Miguel Mosquera^{1

2}, Qiulu Pan^{1

2}, Andrea Sboner^{3

2}, Mark A Rubin^{1

2}, Olivier Elemento^{3

2}, Hanna Rennert¹, Helen Fernandes¹, Wei Song^{1

2}

Affiliations

¹ From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.
² Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York.
³ Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.

PMID: 32045275
DOI: 10.5858/arpa.2019-0162-OA

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

DNA Copy Number Variations / genetics*
Gene Fusion
Genetic Variation / genetics*
High-Throughput Nucleotide Sequencing / methods*
Humans
Mutagenesis, Insertional
Neoplasms / diagnosis
Neoplasms / genetics*
Polymorphism, Single Nucleotide / genetics
Precision Medicine*
Reproducibility of Results
Sensitivity and Specificity
Sequence Analysis, DNA
Sequence Deletion

Abstract

Publication types

MeSH terms

Grants and funding