Format

Send to

Choose Destination
J Mol Diagn. 2014 Jan;16(1):56-67. doi: 10.1016/j.jmoldx.2013.08.004. Epub 2013 Nov 2.

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

Author information

1
Department of Laboratory Medicine, University of Washington, Seattle, Washington. Electronic address: cpritch@uw.edu.
2
Department of Laboratory Medicine, University of Washington, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington.
3
Department of Laboratory Medicine, University of Washington, Seattle, Washington.
4
Department of Laboratory Medicine, University of Washington, Seattle, Washington; Department of Pathology, University of Washington, Seattle, Washington.
5
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington.
6
Department of Pathology, University of Washington, Seattle, Washington.
7
Department of Genome Sciences, University of Washington, Seattle, Washington.
8
Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington.
9
Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois.
10
Department of Genome Sciences, University of Washington, Seattle, Washington; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington.

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.

PMID:
24189654
PMCID:
PMC3873496
DOI:
10.1016/j.jmoldx.2013.08.004
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center