Title | Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. |
Publication Type | Journal Article |
Year of Publication | 2013 |
Authors | Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A, Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JMiguel, Rubin MA, Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D, Yelensky R |
Journal | Nat Biotechnol |
Volume | 31 |
Issue | 11 |
Pagination | 1023-31 |
Date Published | 2013 Nov |
ISSN | 1546-1696 |
Keywords | DNA Copy Number Variations, DNA Mutational Analysis, Gene Frequency, Humans, Molecular Diagnostic Techniques, Neoplasms, Reproducibility of Results, Sensitivity and Specificity, Sequence Analysis, DNA |
Abstract | 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. |
DOI | 10.1038/nbt.2696 |
Alternate Journal | Nat. Biotechnol. |
PubMed ID | 24142049 |
Grant List | WT093855MA / / Wellcome Trust / United Kingdom |