Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

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Author
Allen, Eliezer M. Van
Stojanov, Petar
Perrin, Danielle L.
Cibulskis, Kristian
Marlow, Sara
Friedrich, Dennis C.
Kryukov, Gregory
Carter, Scott L.
McKenna, Aaron
Sivachenko, Andrey
Rosenberg, Mara
Kiezun, Adam
Voet, Douglas
Lawrence, Michael
Lichtenstein, Lee T.
Gentry, Jeff G.
Fostel, Jennifer
Farlow, Deborah
Joffe, Steven
Fisher, Sheila A.
Gabriel, Stacey
Note: Order does not necessarily reflect citation order of authors.
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https://doi.org/10.1038/nm.3559Metadata
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Allen, E. M. V., N. Wagle, P. Stojanov, D. L. Perrin, K. Cibulskis, S. Marlow, J. Jane-Valbuena, et al. 2013. “Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine.” Nature medicine 20 (6): 682-688. doi:10.1038/nm.3559. http://dx.doi.org/10.1038/nm.3559.Abstract
Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048335/pdf/Terms of Use
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http://nrs.harvard.edu/urn-3:HUL.InstRepos:13581165
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