Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens

Colin C. Pritchard, Stephen J. Salipante, Karen Koehler, Christina Smith, Sheena Scroggins, Brent Wood, David Wu, Ming K. Lee, Suzanne Dintzis, Andrew Adey, Yajuan Liu, Keith D. Eaton, Renato Martins, Kari Stricker, Kim A. Margolin, Noah Hoffman, Jane E. Churpek, Jonathan F. Tait, Mary Claire King, Tom Walsh

Research output: Contribution to journalArticle

149 Citations (Scopus)

Abstract

Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥10% tumor cells. In clinical samples with ≥10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.

Original languageEnglish (US)
Pages (from-to)56-67
Number of pages12
JournalJournal of Molecular Diagnostics
Volume16
Issue number1
DOIs
StatePublished - Jan 2014
Externally publishedYes

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Gene Rearrangement
Mutation
Neoplasms
Genes
High-Throughput Nucleotide Sequencing
Gene Dosage
Molecular Pathology
Gene Amplification
Point Mutation
Acute Myeloid Leukemia
Paraffin
Formaldehyde
Melanoma
Patient Care
Nucleotides
Therapeutics

ASJC Scopus subject areas

  • Molecular Medicine
  • Pathology and Forensic Medicine

Cite this

Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. / Pritchard, Colin C.; Salipante, Stephen J.; Koehler, Karen; Smith, Christina; Scroggins, Sheena; Wood, Brent; Wu, David; Lee, Ming K.; Dintzis, Suzanne; Adey, Andrew; Liu, Yajuan; Eaton, Keith D.; Martins, Renato; Stricker, Kari; Margolin, Kim A.; Hoffman, Noah; Churpek, Jane E.; Tait, Jonathan F.; King, Mary Claire; Walsh, Tom.

In: Journal of Molecular Diagnostics, Vol. 16, No. 1, 01.2014, p. 56-67.

Research output: Contribution to journalArticle

Pritchard, CC, Salipante, SJ, Koehler, K, Smith, C, Scroggins, S, Wood, B, Wu, D, Lee, MK, Dintzis, S, Adey, A, Liu, Y, Eaton, KD, Martins, R, Stricker, K, Margolin, KA, Hoffman, N, Churpek, JE, Tait, JF, King, MC & Walsh, T 2014, 'Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens', Journal of Molecular Diagnostics, vol. 16, no. 1, pp. 56-67. https://doi.org/10.1016/j.jmoldx.2013.08.004
Pritchard, Colin C. ; Salipante, Stephen J. ; Koehler, Karen ; Smith, Christina ; Scroggins, Sheena ; Wood, Brent ; Wu, David ; Lee, Ming K. ; Dintzis, Suzanne ; Adey, Andrew ; Liu, Yajuan ; Eaton, Keith D. ; Martins, Renato ; Stricker, Kari ; Margolin, Kim A. ; Hoffman, Noah ; Churpek, Jane E. ; Tait, Jonathan F. ; King, Mary Claire ; Walsh, Tom. / Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. In: Journal of Molecular Diagnostics. 2014 ; Vol. 16, No. 1. pp. 56-67.
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AU - Wu, David

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AU - Liu, Yajuan

AU - Eaton, Keith D.

AU - Martins, Renato

AU - Stricker, Kari

AU - Margolin, Kim A.

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