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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
The Journal of molecular diagnostics : JMD, 2014, January 2014, 2014-Jan, 2014-01-00, 20140101, Volume: 16, Issue: 1Journal Article
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.
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