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


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

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@article{Frampton2013DevelopmentAV, title={Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.}, author={Garrett M. Frampton and Alex M. Fichtenholtz and Geoff A. Otto and Kai Wang and Sean R. Downing and Jie He and Michael Schnall-Levin and Jared White and Eric M Sanford and Peter An and James Sun and Frank S. Juhn and Kristina W Brennan and Kiel Iwanik and Ashley Maillet and Jamie K Buell and Emily White and Mandy Zhao and Sohail Balasubramanian and Selmira Terzic and Tina Richards and Vera Banning and L{\'a}zaro Hern{\'a}ndez Garc{\'i}a and Kristen Mahoney and Zac Zwirko and Amy L Donahue and Himisha Beltran and Juan Miguel Mosquera and Mark A. Rubin and Snjezana Dogan and Cyrus V. Hedvat and Michael F. Berger and Lajos Pusztai and Matthias Lechner and Chris Boshoff and M. E. Jarosz and Christine M Vietz and Alex N. Parker and V. A. Miller and Jeffrey S Ross and John A. Curran and Maureen T. Cronin and P. Stephens and Doron Lipson and R. Yelensky}, journal={Nature biotechnology}, year={2013}, volume={31 11}, pages={1023-31} }