Prevalence of actionable mutations and copy number alterations and the price of a genomic testing panel
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Chan Shen1,2, Funda Meric-Bernstam3, Xiaoping Su4, John Mendelsohn5,6, Sharon Giordano1
1Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
2Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
3Departments of Investigational Cancer Therapeutics and Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
4Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
5Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
6Center for Health and Biosciences, Baker Institute, Rice University, Houston, TX, USA
Chan Shen, email: [email protected]
Keywords: genomic testing panel, cancer, costs, mutations, copy number alterations
Received: March 28, 2016 Accepted: August 24, 2016 Published: September 13, 2016
Interest in genomic testing for the selection of cancer therapy is growing. However, the cost of genomic testing has not been well studied. We sought to determine the price of identifying mutations and copy number alterations (CNAs) in theoretically actionable genes across multiple tumor types. We reviewed data from The Cancer Genome Atlas to determine the frequency of alterations in nine tumor types. We used price information from a commonly used commercial genomic testing platform (FoundationOne) to determine the price of detecting mutations and CNAs in different types of tumors. Although there are large variations in the prevalence by tumor type, when the detection of both mutations and CNAs was considered overall, most patients had at least one alteration in a potentially actionable gene (84% overall, range 51%- 98% among tumor types assessed). The corresponding average price of identifying at least one alteration per patient ranges from $5,897 to $11,572. Although the frequency of mutations and CNAs in actionable genes differs by tumor type, most patients have an actionable genomic alteration detectable by a commercially available panel. Determining CNAs as well as mutations improves actionability and reduces the price of detecting an alteration.
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