Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

被引：1698

作者：

Frampton, Garrett M. ^{[1
]}

Fichtenholtz, Alex ^{[1
]}

Otto, Geoff A. ^{[1
]}

Wang, Kai ^{[1
]}

Downing, Sean R. ^{[1
]}

He, Jie ^{[1
]}

Schnall-Levin, Michael ^{[1
]}

White, Jared ^{[1
]}

Sanford, Eric M. ^{[1
]}

An, Peter ^{[1
]}

Sun, James ^{[1
]}

Juhn, Frank ^{[1
]}

Brennan, Kristina ^{[1
]}

Iwanik, Kiel ^{[1
]}

Maillet, Ashley ^{[1
]}

Buell, Jamie ^{[1
]}

White, Emily ^{[1
]}

Zhao, Mandy ^{[1
]}

Balasubramanian, Sohail ^{[1
]}

Terzic, Selmira ^{[1
]}

Richards, Tina ^{[1
]}

Banning, Vera ^{[1
]}

Garcia, Lazaro ^{[1
]}

Mahoney, Kristen ^{[1
]}

Zwirko, Zac ^{[1
]}

Donahue, Amy ^{[1
]}

Beltran, Himisha ^{[2
,3
,4
]}

Mosquera, Juan Miguel ^{[3
,4
,5
]}

Rubin, Mark A. ^{[3
,4
,5
]}

Dogan, Snjezana ^{[6
]}

Hedvat, Cyrus V. ^{[6
]}

Berger, Michael F. ^{[6
]}

Pusztai, Lajos ^{[7
]}

Lechner, Matthias ^{[8
]}

Boshoff, Chris ^{[8
]}

Jarosz, Mirna ^{[1
]}

Vietz, Christine ^{[1
]}

Parker, Alex ^{[1
]}

Miller, Vincent A. ^{[1
]}

Ross, Jeffrey S. ^{[1
,9
]}

Curran, John ^{[1
]}

Cronin, Maureen T. ^{[1
]}

Stephens, Philip J. ^{[1
]}

Lipson, Doron ^{[1
]}

Yelensky, Roman ^{[1
]}

机构：

[1] Fdn Med, Cambridge, MA USA

[2] Cornell Univ, Weill Med Coll, Dept Med, Div Hematol & Med Oncol, New York, NY 10021 USA

[3] Weill Cornell Med Coll, Inst Precis Med, New York, NY USA

[4] New York Presbyterian Hosp, New York, NY USA

[5] Cornell Univ, Weill Med Coll, Dept Pathol & Lab Med, New York, NY 10021 USA

[6] Mem Sloan Kettering Canc Ctr, Dept Pathol, New York, NY 10021 USA

[7] Yale Univ, Sch Med, Yale Canc Ctr, Genet & Genom Program, New Haven, CT USA

[8] UCL, UCL Canc Inst, London, England

[9] Albany Med Coll, Dept Pathol & Lab Med, Albany, NY 12208 USA

来源：

NATURE BIOTECHNOLOGY | 2013年 / 31卷 / 11期

基金：

奥地利科学基金会; 英国惠康基金;

关键词：

NEGATIVE BREAST-CANCER; TUMOR SAMPLES; MUTATIONAL PROCESSES; DRUG-SENSITIVITY; LUNG-CANCER; GENES; IMMUNOHISTOCHEMISTRY; IDENTIFICATION; AMPLIFICATION; LANDSCAPE;

D O I：

10.1038/nbt.2696

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. Here we describe a test based on massively parallel DNA sequencing to characterize base substitutions, short insertions and deletions (indels), copy number alterations and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens. We implemented a practical validation strategy with reference samples of pooled cell lines that model key determinants of accuracy, including mutant allele frequency, indel length and amplitude of copy change. Test sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%). We confirmed accuracy using 249 FFPE cancer specimens characterized by established assays. Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests.

引用

页码：1023 / +

页数：11

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