Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

被引：432

作者：

Van Allen, Eliezer M. ^{[1
,2
]}

Wagle, Nikhil ^{[1
,2
]}

Stojanov, Petar ^{[1
,2
]}

Perrin, Danielle L. ^{[2
]}

Cibulskis, Kristian ^{[2
]}

Marlow, Sara ^{[1
,2
]}

Jane-Valbuena, Judit ^{[1
,2
]}

Friedrich, Dennis C. ^{[2
]}

Kryukov, Gregory ^{[2
]}

Carter, Scott L. ^{[2
]}

McKenna, Aaron ^{[2
,3
]}

Sivachenko, Andrey ^{[2
]}

Rosenberg, Mara ^{[2
]}

Kiezun, Adam ^{[2
]}

Voet, Douglas ^{[2
]}

Lawrence, Michael ^{[2
]}

Lichtenstein, Lee T. ^{[2
]}

Gentry, Jeff G. ^{[2
]}

Huang, Franklin W. ^{[1
,2
]}

Fostel, Jennifer ^{[2
]}

Farlow, Deborah ^{[2
]}

Barbie, David ^{[1
]}

Gandhi, Leena ^{[1
]}

Lander, Eric S. ^{[2
]}

Gray, Stacy W. ^{[1
]}

Joffe, Steven ^{[1
,4
]}

Janne, Pasi ^{[1
]}

Garber, Judy ^{[1
]}

MacConaill, Laura ^{[1
,5
]}

Lindeman, Neal ^{[1
,5
]}

Rollins, Barrett ^{[1
]}

Kantoff, Philip ^{[1
]}

Fisher, Sheila A. ^{[2
]}

Gabriel, Stacey ^{[2
]}

Getz, Gad ^{[2
,6
,7
]}

Garraway, Levi A. ^{[1
,2
]}

机构：

[1] Harvard Univ, Sch Med, Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02115 USA

[2] Broad Inst MIT & Harvard, Cambridge, MA USA

[3] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[4] Childrens Hosp Boston, Boston, MA USA

[5] Brigham & Womens Hosp, Dept Pathol, Boston, MA 02115 USA

[6] Massachusetts Gen Hosp, Dept Pathol, Boston, MA 02114 USA

[7] Massachusetts Gen Hosp, Ctr Canc, Boston, MA USA

来源：

NATURE MEDICINE | 2014年 / 20卷 / 06期

基金：

美国国家卫生研究院;

关键词：

SOMATIC MUTATIONS; LUNG-CANCER; LANDSCAPE; PLATFORM; CATALOG; GENOME; ERA;

D O I：

10.1038/nm.3559

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

Translating whole-exome sequencing (WES) for prospective clinical use may have an impact on the care of patients with cancer; however, multiple innovations are necessary for clinical implementation. These include rapid and robust WES of DNA derived from formalin-fixed, paraffin-embedded tumor tissue, analytical output similar to data from frozen samples and clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival formalin-fixed, paraffin-embedded 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 out of 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.

引用

页码：682 / 688

页数：7

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