Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Targeted multiplexed hotspot panels are already developed and available in CAP-accredited academic and commercial laboratories.
“Targeted multiplexed hotspot panels (e.g., Agena Oncocarta [Agena Bioscience, San Diego, CA], 47 SNaPshot [Applied Biosystems, Foster City, CA], 48 and next-generation sequencing [NGS] panels 49,50 ) have already been developed and are available in College of American Pathologists (CAP)-accredited academic and commercial laboratories.”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063 · see citing works
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,216 · see citing works
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950 · see citing works
Self-citationdbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502 · see citing works
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017 · see citing works
Comprehensive genomic characterization of squamous cell lung cancers
The Cancer Genome Atlas Research Network (2012) · Nature · doi:10.1038/nature11404 · Cited by 3,994 · see citing works
Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,459 · see citing works
Systematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456 · see citing works
International network of cancer genome projects
The International Cancer Genome Consortium (2010) · Nature · doi:10.1038/nature08987 · Cited by 2,299 · see citing works
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
Forbes, S. A., Bindal, N., Bamford, S., Cole, C., Kok, C. Y., Beare, D., Jia, M., Shepherd, R., Leung, K., Menzies, A., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq929 · Cited by 2,278 · see citing works
The UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,269 · see citing works
Absolute quantification of somatic DNA alterations in human cancer
Carter, S. L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T. I., Laird, P. W., Onofrio, R. C., Winckler, W., Weir, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2203 · Cited by 2,003 · see citing works
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., et al. (2012) · Nature · doi:10.1038/nature10738 · Cited by 1,993 · see citing works
Mutational Processes Molding the Genomes of 21 Breast Cancers
Nik-Zainal, S., Alexandrov, L. B., Wedge, D. C., Van Loo, P., Greenman, C. D., Raine, K., Jones, D., Hinton, J., Marshall, J., Stebbings, L. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.024 · Cited by 1,909 · see citing works
The landscape of cancer genes and mutational processes in breast cancer
Stephens, P. J., Tarpey, P. S., Davies, H. R., Loo, P. V., Greenman, C., Wedge, D. C., Nik‐Zainal, S., Martin, S., Varela, I., Bignell, G. R., et al. (2012) · Nature · doi:10.1038/nature11017 · Cited by 1,686 · see citing works
The Life History of 21 Breast Cancers
Nik-Zainal, S., Van Loo, P., Wedge, D. C., Alexandrov, L. B., Greenman, C. D., Lau, K. W., Raine, K., Jones, D., Marshall, J., Ramakrishna, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.023 · Cited by 1,443 · see citing works
Self-citationGnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433 · see citing works
Allele-specific copy number analysis of tumors
Loo, P. V., Nord, S., Lingjærde, O. C., Russnes, H. G., Rye, I. H., Sun, W., Weigman, V., Marynen, P., Zetterberg, A., Naume, B., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009843107 · Cited by 1,231 · see citing works
High-throughput oncogene mutation profiling in human cancer
Thomas, R. K., Baker, A. C., Debiasi, R. M., Winckler, W., LaFramboise, T., Lin, W. M., Wang, M., Feng, W., Zander, T., MacConaill, L. E., et al. (2007) · Nature Genetics · doi:10.1038/ng1975 · Cited by 978 · see citing works
The BATTLE Trial: Personalizing Therapy for Lung Cancer
Kim, E. S., Herbst, R. S., Wistuba, I. I., Lee, J. J., Blumenschein, G. R., Tsao, A. S., Stewart, D. J., Hicks, M. E., Erasmus, J. J., Gupta, S. K., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8274.cd-10-0010 · Cited by 888 · see citing works
Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies
Lipson, D., Capelletti, M., Yelensky, R., Otto, G., Parker, A., Jarosz, M., Curran, J. A., Balasubramanian, S., Bloom, T., Brennan, K. W., et al. (2012) · Nature Medicine · doi:10.1038/nm.2673 · Cited by 869 · see citing works
Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer
Bose, R., Kavuri, S. M., Searleman, A. C., Shen, W., Shen, D., Koboldt, D. C., Monsey, J. D., Goel, N. J., Aronson, A. B., Li, S., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0349 · Cited by 869 · see citing works
Fisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 683 · see citing works
How to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673 · see citing works
Siva, N. (2008) · Nature Biotechnology · doi:10.1038/nbt0308-256b · Cited by 629 · see citing works
Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study
Roychowdhury, S., Iyer, M. K., Robinson, D. R., Lonigro, R. J., Wu, Y.-M., Cao, X., Sundaram, S. K., Sam, L. T., Balbin, O. A., Quist, M. J., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3003161 · Cited by 629 · see citing works
Wagle, N., Berger, M. F., Davis, M. J., Blumenstiel, B. S., DeFelice, M. T., Pochanard, P., Ducar, M. D., Hummelen, P. V., MacConaill, L. E., Hahn, W. C., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0184 · Cited by 526 · see citing works
Assuring the quality of next-generation sequencing in clinical laboratory practice
Gargis, A. S., Kalman, L. V., Berry, M. W., Bick, D. P., Dimmock, D., Hambuch, T. M., Lu, F., Lyon, E., Voelkerding, K. V., Zehnbauer, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2403 · Cited by 458 · see citing works
Beltran, H., Yelensky, R., Frampton, G. M., Park, K., Downing, S. R., MacDonald, T. Y., Jarosz, M. V., Lipson, D., Tagawa, S. T., Nanus, D. M., et al. (2012) · European Urology · doi:10.1016/j.eururo.2012.08.053 · Cited by 450 · see citing works
Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples
MacConaill, L. E., Campbell, C. D., Kehoe, S. M., Bass, A. J., Hatton, C., Niu, L., Davis, M., Yao, K., Hanna, M., Mondal, C., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007887 · Cited by 434 · see citing works
Dindel: Accurate indel calls from short-read dataPreprint
Albers, C. A., Lunter, G. A., MacArthur, D. G., McVean, G., Ouwehand, W. H., & Durbin, R. M. (2010) · Genome Research · doi:10.1101/gr.112326.110 · Cited by 407 · see citing works
Dias-Santagata, D. C., Akhavanfard, S., David, S. S., Vernovsky, K., Kuhlmann, G., Boisvert, S. L., Stubbs, H., McDermott, U., Settleman, J. E., Kwak, E. L., et al. (2010) · EMBO Molecular Medicine · doi:10.1002/emmm.201000070 · Cited by 392 · see citing works
Thomas, R. K., Nickerson, E., Simons, J. F., Janne, P. A., Tengs, T., Yuza, Y., Garraway, L. A., LaFramboise, T., Lee, J. C., Shah, K., et al. (2006) · Nature Medicine · doi:10.1038/nm1437 · Cited by 360 · see citing works
Hiatt, J. B., Pritchard, C. C., Salipante, S. J., O’Roak, B. J., & Shendure, J. (2013) · Genome Research · doi:10.1101/gr.147686.112 · Cited by 325 · see citing works
Translating insights from the cancer genome into clinical practice
Chin, L., & Gray, J. W. (2008) · Nature · doi:10.1038/nature06914 · Cited by 299 · see citing works
Clinical Implications of the Cancer Genome
MacConaill, L. E., & Garraway, L. A. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.27.4944 · Cited by 228 · see citing works
Craig, D. W., O'Shaughnessy, J. A., Kiefer, J. A., Aldrich, J., Sinari, S., Moses, T. M., Wong, S., Dinh, J., Christoforides, A., Blum, J. L., et al. (2013) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-12-0781 · Cited by 220 · see citing works
Targeted Cancer Therapies in the Twenty-First Century: Lessons From Imatinib
Stegmeier, F. P., Warmuth, M., Sellers, W. R., & Dorsch, M. (2010) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2009.297 · Cited by 192 · see citing works
Hadd, A. G., Houghton, J., Choudhary, A. K., Sah, S., Chen, L., Marko, A. C., Sanford, T., Buddavarapu, K., Krosting, J., Garmire, L. X., et al. (2013) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.11.006 · Cited by 184 · see citing works
Kerick, M., Isau, M., Timmermann, B., Sültmann, H., Herwig, R., Krobitsch, S., Schaefer, G., Verdorfer, I., Bartsch, G. H., Klocker, H., et al. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-68 · Cited by 181 · see citing works
Djordjevic, B., Hennessy, B. T., Li, J., Barkoh, B. A., Luthra, R., Mills, G. B., & Broaddus, R. R. (2012) · Modern Pathology · doi:10.1038/modpathol.2011.208 · Cited by 175 · see citing works
Reis-Filho, J. S., Savage, K., Lambros, M. B. K., James, M., Steele, D., Jones, R. L., & Dowsett, M. (2006) · Modern Pathology · doi:10.1038/modpathol.3800621 · Cited by 163 · see citing works
Yau, C., Mouradov, D., Jorissen, R. N., Colella, S., Mirza, G. K., Steers, G., Harris, A. L., Ragoussis, J., Sieber, O. M., & Holmes, C. C. (2010) · Genome biology · doi:10.1186/gb-2010-11-9-r92 · Cited by 129 · see citing works
Combining Highly Multiplexed PCR with Semiconductor-Based Sequencing for Rapid Cancer Genotyping
Beadling, C., Neff, T. L., Heinrich, M. C., Rhodes, K., Thornton, M., Leamon, J. H., Andersen, M., & Corless, C. L. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.09.003 · Cited by 119 · see citing works
Giulino-Roth, L. G., Wang, K., MacDonald, T. Y., Mathew, S., Tam, Y., Cronin, M. T., Palmer, G. A., Lucena‐Silva, N., Pedrosa, F. D. P. R., Pedrosa, M., et al. (2012) · Blood · doi:10.1182/blood-2012-06-437624 · Cited by 106 · see citing works
Genome-Wide Characterization of Pancreatic Adenocarcinoma Patients Using Next Generation Sequencing
Liang, W. S., Craig, D. W., Carpten, J. D., Borad, M. J., Demeure, M. J., Weiss, G. J., Izatt, T., Sinari, S. A., Christoforides, A., Aldrich, J., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043192 · Cited by 73 · see citing works
Mardis, E. R. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.03.005 · Cited by 69 · see citing works
Immunohistochemistry in the era of personalised medicine
McCourt, C., Boyle, D., James, J. A., & Salto‐Tellez, M. (2012) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2012-201140 · Cited by 45 · see citing works
My Cancer Genome: a unified genomics and clinical trial portal
Swanton, C. (2012) · The Lancet Oncology · doi:10.1016/s1470-2045(12)70312-1 · Cited by 34 · see citing works
Update on HER2 Testing for Breast and Upper Gastrointestinal Tract Cancers
Ross, J. S. (2011) · Biomarkers in Medicine · doi:10.2217/bmm.11.31 · Cited by 28 · see citing works
New Approaches to Targeted Therapy in Lung Cancer
Pao, W. J. (2012) · Proceedings of the American Thoracic Society · doi:10.1513/pats.201112-054ms · Cited by 23 · see citing works
Potentially actionable kinase fusions in inflammatory myofibroblastic tumors.
Lovly, C. M., Lipson, D., Otto, G. A., Brennan, T., Sankar, S., Stephens, P. J., Miller, V. A., & Coffin, C. M. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2013.31.15_suppl.10513 · Cited by 6 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden
Chalmers, Z. R., Connelly, C. F., Fabrizio, D., Gay, L., Ali, S. M., Ennis, R., Schrock, A., Campbell, B., Shlien, A., Chmielecki, J., et al. (2017) · Genome Medicine · doi:10.1186/s13073-017-0424-2 · Cited by 3,519 · see citing works
“CGP was performed using the FoundationOne assay (Cambridge, MA, USA), as previously described in detail [55, 56].”
BackgroundMethodRosenberg, J. E., Hoffman-Censits, J., Powles, T., van der Heijden, M. S., Balar, A. V., Necchi, A., Dawson, N., O'Donnell, P. H., Balmanoukian, A., Loriot, Y., et al. (2016) · The Lancet · doi:10.1016/s0140-6736(16)00561-4 · Cited by 3,669 · see citing works
Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S. M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4333 · Cited by 3,380 · see citing works
Self-citationNovello, S., Barlesi, F., Califano, R., Cufer, T., Ekman, S., Levra, M. G., Kerr, K., Popat, S., Reck, M., Senan, S., et al. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw326 · Cited by 2,631 · see citing works
Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers
Goodman, A. M., Kato, S., Bazhenova, L., Patel, S. P., Frampton, G. M., Miller, V., Stephens, P. J., Daniels, G. A., & Kurzrock, R. (2017) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-17-0386 · Cited by 2,264 · see citing works
“The methods have been previously described (20).”
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256 · see citing works
“Among the 299 genes we identified 59 novel genes that were not previously identified in 6 previous PanCancer publications (Frampton et al., 2013; Kandoth et al., 2013; Lawrence et al., 2014; Pritchard et al., 2014; Tamborero et al., 2013b; Vogelstein et al., 2013) or the cancer gene census list…”
BackgroundSelf-citationMemorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)
Cheng, D. T., Mitchell, T. N., Zehir, A., Shah, R. H., Benayed, R., Syed, A., Chandramohan, R., Liu, Z. Y., Won, H. H., Scott, S. N., et al. (2015) · The Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.12.006 · Cited by 2,119 · see citing works
Age-related mutations associated with clonal hematopoietic expansion and malignancies
Xie, M., Lu, C., Wang, J., McLellan, M. D., Johnson, K. J., Wendl, M. C., McMichael, J. F., Schmidt, H. K., Yellapantula, V., Miller, C. A., et al. (2014) · Nature Medicine · doi:10.1038/nm.3733 · Cited by 1,874 · see citing works
Using Multiplexed Assays of Oncogenic Drivers in Lung Cancers to Select Targeted Drugs
Kris, M. G., Johnson, B. E., Berry, L. D., Kwiatkowski, D. J., Iafrate, A. J., Wistuba, I. I., Varella-Garcia, M., Franklin, W. A., Aronson, S. L., Su, P.-F., et al. (2014) · JAMA · doi:10.1001/jama.2014.3741 · Cited by 1,724 · see citing works
<i>STK11/LKB1</i> Mutations and PD-1 Inhibitor Resistance in <i>KRAS</i> -Mutant Lung Adenocarcinoma
Skoulidis, F., Goldberg, M. E., Greenawalt, D. M., Hellmann, M. D., Awad, M. M., Gainor, J. F., Schrock, A. B., Hartmaier, R. J., Trabucco, S. E., Gay, L., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0099 · Cited by 1,641 · see citing works
“Samples submitted to Foundation Medicine were processed at a CLIA-certified laboratory as described previously (52).”
MethodSelf-citationAbou‐Alfa, G. K., Sahai, V., Hollebecque, A., Vaccaro, G. M., Melisi, D., Al-Rajabi, R. M. T., Paulson, A. S., Borad, M. J., Gallinson, D. H., Murphy, A. G., et al. (2020) · The Lancet Oncology · doi:10.1016/s1470-2045(20)30109-1 · Cited by 1,634 · see citing works
Powles, T., Durán, I., van der Heijden, M. S., Loriot, Y., Vogelzang, N. J., De Giorgi, U., Oudard, S., Retz, M. M., Castellano, D., Bamias, A., et al. (2018) · The Lancet · doi:10.1016/s0140-6736(17)33297-x · Cited by 1,408 · see citing works
Ledermann, J. A., Harter, P., Gourley, C., Friedlander, M. L., Vergote, I. B., Rustin, G. J. S., Scott, C. L., Meier, W., Shapira‐Frommer, R., Safra, T., et al. (2014) · The Lancet Oncology · doi:10.1016/s1470-2045(14)70228-1 · Cited by 1,437 · see citing works
The Challenges of Tumor Mutational Burden as an Immunotherapy Biomarker
Jardim, D. L., Goodman, A., de Melo Gagliato, D., & Kurzrock, R. (2021) · Cancer Cell · doi:10.1016/j.ccell.2020.10.001 · Cited by 1,192 · see citing works
Swisher, E. M., Lin, K. K., Oza, A. M., Scott, C. L., Giordano, H., Sun, J., Konecny, G. E., Coleman, R. L., Tinker, A. V., O'Malley, D. M., et al. (2017) · The Lancet Oncology · doi:10.1016/s1470-2045(16)30559-9 · Cited by 1,196 · see citing works
Hellmann, M. D., Nathanson, T., Rizvi, H., Creelan, B. C., Sanchez-Vega, F., Ahuja, A., Ni, A., Novik, J. B., Mangarin, L. M. B., Abu-Akeel, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.018 · Cited by 1,095 · see citing works
“…et al., 2017; Zehir et al., 2017), we found that limiting variants to the 468 genes represented in our institutional MSKIMPACT panel (Zehir et al., 2017) or the 315 genes in the FoundationOne panel (Frampton et al., 2013) maintained similar predictive fidelity for efficacy (Figures S3G–S3H).”
BackgroundMethodMosele, F., Remón, J., Mateo, J., Westphalen, C. B., Barlési, F., Lolkema, M. P., Normanno, N., Scarpa, A., Robson, M. E., Meric‐Bernstam, F., et al. (2020) · Annals of Oncology · doi:10.1016/j.annonc.2020.07.014 · Cited by 1,204 · see citing works
“Pioneering studies have shown that NGS presents a good analytical validity to detect clonally dominant alterations.(4) Based on this observation, several companies and academic centres have implemented NGS assays to guide treatment decisions.”
BackgroundGainor, J. F., Dardaei, L., Yoda, S., Friboulet, L., Leshchiner, I., Katayama, R., Dagogo‐Jack, I., Gadgeel, S. M., Schultz, K. R., Singh, M., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0596 · Cited by 1,158 · see citing works
Gandara, D. R., Paul, S. M., Kowanetz, M., Schleifman, E., Zou, W., Li, Y., Rittmeyer, A., Fehrenbacher, L., Otto, G. A., Malboeuf, C. M., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0134-3 · Cited by 1,156 · see citing works
Liquid biopsy enters the clinic — implementation issues and future challenges
Ignatiadis, M., Sledge, G. W., & Jeffrey, S. S. (2021) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-020-00457-x · Cited by 1,191 · see citing works
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research
Lai, Z., Markovets, A. A., Ahdesmaki, M. J., Chapman, B., Hofmann, O., McEwen, R. K., Johnson, J., Dougherty, B. A., Barrett, J. C., & Dry, J. R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw227 · Cited by 971 · see citing works
“As a platform for discovery NGS has revealed new genetic drivers of cancer leading to development of targeted cancer therapies (1), and in the clinic NGS provides a tool to detect mutations determining a patient therapy (2).”
BackgroundSkoulidis, F., Byers, L. A., Diao, L., Papadimitrakopoulou, V. A., Tong, P., Izzo, J., Behrens, C., Kadara, H., Parra, E. R., Canales, J. R., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-1236 · Cited by 936 · see citing works
“0 array profiling was performed by Foundation Medicine, as previously described (56).”
Tumor Mutational Burden as a Predictive Biomarker in Solid Tumors
Sha, D., Jin, Z., Budczies, J., Kluck, K., Stenzinger, A., & Sinicrope, F. A. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0522 · Cited by 859 · see citing works
Hellmann, M. D., Callahan, M. K., Awad, M. M., Calvo, E., Ascierto, P. A., Atmaca, A., Rizvi, N. A., Hirsch, F. R., Selvaggi, G., Szustakowski, J. D., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.04.001 · Cited by 892 · see citing works
“Tumor mutational burden estimated byWES closely correlatedwith the estimate after in silico filtering to the 315 genes in the FoundationOne next-generation sequencing genomic profile (Frampton et al., 2013) (Figure S4).”
The FGFR Landscape in Cancer: Analysis of 4,853 Tumors by Next-Generation Sequencing
Helsten, T. L., Elkin, S. K., Arthur, E., Tomson, B. N., Carter, J., & Kurzrock, R. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-3212 · Cited by 818 · see citing works
“Samples were required to have a surface area 25 mm(2), volume 1mm(3), nucleated cellularity 80%, and tumor content 20% (10).”
BackgroundMethodFrampton, G. M., Ali, S. M., Rosenzweig, M., Chmielecki, J., Lu, X., Bauer, T. M., Akimov, M., Bufill, J. A., Lee, C., Jentz, D., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0285 · Cited by 796 · see citing works
Self-citationComprehensive Analysis of Hypermutation in Human Cancer
Campbell, B. B., Light, N. D., Fabrizio, D. A., Zatzman, M., Fuligni, F., de Borja, R., Davidson, S., Edwards, M., Elvin, J. A., Hodel, K. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.048 · Cited by 759 · see citing works
“Targeted regions of the genome were deeply sequenced using a validated cancer gene panel (Frampton et al., 2013).”
InfluentialNecchi, A., Anichini, A., Raggi, D., Briganti, A., Massa, S., Lucianò, R., Colecchia, M., Giannatempo, P., Mortarini, R., Bianchi, M., et al. (2018) · Journal of Clinical Oncology · doi:10.1200/jco.18.01148 · Cited by 741 · see citing works
“5 (15-24) Ileal conduit 13 (9-17) Median intraoperative blood loss, mL (IQR) 300 (150-500) 30-day readmission 11 (22) 30-day surgical reintervention 5 (10) Postoperative complications (Clavien Dindo) within 90 days 0 25 (50) II 10 (20) IIIa 9 (18) IIIb 5 (10) IV 1 (2) Type of postoperative complications Fever of unkno…”
BackgroundMolecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study
Sicklick, J. K., Kato, S., Okamura, R., Schwaederle, M. C., Hahn, M. E., Williams, C. B., De, P. K., Krie, A. K., Piccioni, D. E., Miller, V. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0407-5 · Cited by 713 · see citing works
Lanman, R. B., Mortimer, S. A., Zill, O. A., Sebisanovic, D., Lopez, R., Blau, S., Collisson, E. A., Divers, S. G., Hoon, D. S. B., Kopetz, E. S., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140712 · Cited by 695 · see citing works
“8% assay success rate for the Guardant360 panel starkly contrasts with tissue-based NGS assay failure rates of about 25% (20% because tissue is unavailable or QNS plus a 5% NGS assay failure rate), sparing repeat invasive biopsies [68].”
MethodMechanisms and therapeutic implications of hypermutation in gliomas
Touat, M., Li, Y. Y., Boynton, A. N., Spurr, L. F., Iorgulescu, J. B., Bohrson, C. L., Cortés‐Ciriano, I., Birzu, C., Geduldig, J. E., Pelton, K., et al. (2020) · Nature · doi:10.1038/s41586-020-2209-9 · Cited by 672 · see citing works
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
Zheng, G. X. Y., Lau, B. T., Schnall-Levin, M., Jarosz, M. V., Bell, J., Hindson, C. M., Kyriazopoulou-Panagiotopoulou, S., Masquelier, D. A., Merrill, L., Terry, J. M., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3432 · Cited by 678 · see citing works
“Exome sequencing does not detect gene fusions for which the breakpoint is more than a few hundred base pairs from an exon without custom targeting assays and extremely high sequencing coverage 22, 23 .”
Abida, W., Patnaik, A., Campbell, D., Shapiro, J., Bryce, A. H., McDermott, R., Sautois, B., Vogelzang, N. J., Bambury, R. M., Voog, E., et al. (2020) · Journal of Clinical Oncology · doi:10.1200/jco.20.01035 · Cited by 694 · see citing works
“Central testing was performed by Foundation Medicine.(12,13) Germline testing was performed by Color Genomics.”
MethodThe emerging clinical relevance of genomics in cancer medicine
Berger, M. F., & Mardis, E. R. (2018) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-018-0002-6 · Cited by 627 · see citing works
Schrock, A. B., Ouyang, C., Sandhu, J. S., Sokol, E. S., Jin, D. X., Ross, J. S., Miller, V. A., Lim, D. W., Amanam, I. U., Chao, J., et al. (2019) · Annals of Oncology · doi:10.1093/annonc/mdz134 · Cited by 620 · see citing works
Meric-Bernstam, F., Hurwitz, H., Raghav, K. P. S., McWilliams, R. R., Fakih, M., VanderWalde, A., Swanton, C., Kurzrock, R., Burris, H., Sweeney, C., et al. (2019) · The Lancet Oncology · doi:10.1016/s1470-2045(18)30904-5 · Cited by 573 · see citing works
Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial
Rodon, J. A., Soria, J., Berger, R., Miller, W. H., Rubin, E., Kugel, A., Tsimberidou, A. M., Saintigny, P., Ackerstein, A., Braña, I., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0424-4 · Cited by 579 · see citing works
Overcoming therapy resistance in EGFR-mutant lung cancer
Passaro, A., Jänne, P. A., Mok, T., & Peters, S. (2021) · Nature Cancer · doi:10.1038/s43018-021-00195-8 · Cited by 565 · see citing works
Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade
Motzer, R. J., Banchereau, R., Hamidi, H., Powles, T. B., McDermott, D. F., Atkins, M. B., Escudier, B. J., Liu, L.-F., Leng, N., Abbas, A. R., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.10.011 · Cited by 568 · see citing works
Goyal, L., Saha, S. K., Liu, L. Y., Siravegna, G., Leshchiner, I., Ahronian, L. G., Lennerz, J. K., Vu, P., Deshpande, V., Kambadakone, A. R., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-1000 · Cited by 562 · see citing works
Singal, G., Miller, P. G., Agarwala, V., Li, G., Kaushik, G. N., Backenroth, D., Gossai, A., Frampton, G. M., Torres, A. Z., Lehnert, E. M., et al. (2019) · JAMA · doi:10.1001/jama.2019.3241 · Cited by 551 · see citing works
“7% of all samples; eTable 1 in the Supplement).(8)Pointmutations, amplifications, deletions, duplications, insertions, splice site variants, and rearrangements werecategorizedaseitherknownpathogenic, likelypathogenic, variantsofunknownsignificance,orgermlinesingle-nucleotide polymorphisms.”
BackgroundPD-L1 expression and tumor mutational burden are independent biomarkers in most cancers
Yarchoan, M. M., Albacker, L. A., Hopkins, A. C., Montesion, M., Murugesan, K., Vithayathil, T., Zaidi, N., Azad, N. S., Laheru, D. A., Frampton, G. M., et al. (2019) · JCI Insight · doi:10.1172/jci.insight.126908 · Cited by 554 · see citing works
“TMB was assessed using a targeted comprehensive genomic profiling assay (FoundationOne) as previously described (28, 29).”
Genetic Analysis of 779 Advanced Differentiated and Anaplastic Thyroid Cancers
Pozdeyev, N. V., Gay, L. M., Sokol, E. S., Hartmaier, R. J., Deaver, K. E., Davis, S., French, J. D., Borre, P. V., LaBarbera, D. V., Tan, A. C., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-0373 · Cited by 538 · see citing works
“Targeted next-generation sequencing (NGS) assays, such as MSK-IMPACT (7) and FoundationOne (8), are commonly used for cancer genotyping in clinical practice.”
BackgroundMethodDiverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms
Diamond, E. L., Durham, B. H., Haroche, J., Yao, Z., Ma, J., Parikh, S. A., Wang, Z., Choi, J. K., Kim, E. H., Aubart, F. C., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0913 · Cited by 538 · see citing works
“Targeted DNA Sequencing We sequenced the regions of known mutations in MAP2K1, NRAS, KRAS, and PIK3CA, as well as all coding exons of ARAF using Sanger sequencing (primer sequences listed in Supplementary Table S5) and/or hybrid-capture, next generation sequencing using the MSKCC IMPACT assay as previously described (…”
Имянитов, Е. Н., Iyevleva, A. G., & Levchenko, E. (2020) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2020.103194 · Cited by 528 · see citing works
Garcia, E. P., Minkovsky, A., Jia, Y., Ducar, M. D., Shivdasani, P., Gong, X., Ligon, A. H., Sholl, L. M., Kuo, F. C., MacConaill, L. E., et al. (2017) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2016-0527-oa · Cited by 521 · see citing works
Merino, D. M., McShane, L. M., Fabrizio, D. A., Funari, V. A., Chen, S., White, J. R., Wenz, P., Baden, J. F., Barrett, J. C., Chaudhary, R., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2019-000147 · Cited by 517 · see citing works
Implementing Genome-Driven Oncology
Hyman, D. M., Taylor, B. S., & Baselga, J. M. (2017) · Cell · doi:10.1016/j.cell.2016.12.015 · Cited by 505 · see citing works
Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade
Johnson, D. B., Frampton, G. M., Rioth, M. J., Yusko, E., Xu, Y., Guo, X., Ennis, R. C., Fabrizio, D., Chalmers, Z. R., Greenbowe, J., et al. (2016) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-16-0143 · Cited by 481 · see citing works
“Methods for DNA extraction and sequencing have been extensively validated and published (16).”
BackgroundSelf-citationStructure-based classification predicts drug response in EGFR-mutant NSCLC
Robichaux, J. P., Le, X., Vijayan, R. S. K., Hicks, J. K., Heeke, S., Elamin, Y. Y., Lin, H. Y., Udagawa, H., Skoulidis, F., Tran, H., et al. (2021) · Nature · doi:10.1038/s41586-021-03898-1 · Cited by 490 · see citing works
Camidge, D. R., Dziadziuszko, R., Peters, S., Mok, T. S. K., Noé, J., Nowicka, M., Gadgeel, S. M., Cheema, P. K., Pavlakis, N., de Marinis, F., et al. (2019) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2019.03.007 · Cited by 492 · see citing works
Miller, R. E., Leary, A. F., Scott, C. L., Serra, V., Lord, C. J., Bowtell, D. D. L., Chang, D. K.-F., Garsed, D. W., Jonkers, J., Ledermann, J. A., et al. (2020) · Annals of Oncology · doi:10.1016/j.annonc.2020.08.2102 · Cited by 485 · see citing works
Kim, S., Dent, R. A., Im, S., Espié, M., Blau, S. H., Tan, A. R., Isakoff, S. J., Oliveira, M., Saura, C., Wongchenko, M. J., et al. (2017) · The Lancet Oncology · doi:10.1016/s1470-2045(17)30450-3 · Cited by 478 · see citing works
Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines
Roy, S., Coldren, C. D., Karunamurthy, A. D., Kip, N. S., Klee, E. W., Lincoln, S. E., Leon, A., Pullambhatla, M., Temple‐Smolkin, R., Voelkerding, K. V., et al. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2017.11.003 · Cited by 469 · see citing works
Institutional implementation of clinical tumor profiling on an unselected cancer population
Sholl, L. M., Do, K., Shivdasani, P., Cerami, E., Dubuc, A. M., Kuo, F. C., Garcia, E. P., Jia, Y., Davineni, P., Abo, R. P., et al. (2016) · JCI Insight · doi:10.1172/jci.insight.87062 · Cited by 450 · see citing works
“Discussion In recent years, a number of academic cancer centers, hospitals, and commercial entities have established genomic profiling programs (11, 12, 16, 17, 20, 24, 26, 40) that differ in terms of technology and gene panel content (varying from tens to hundreds or thousands of genes) as well as target patient popu…”
BackgroundPiotrowska, Z., Niederst, M. J., Karlovich, C., Wakelee, H. A., Neal, J. W., Mino-Kenudson, M. A., Fulton, L. E., Hata, A. N., Lockerman, E. L., Kalsy, A., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0399 · Cited by 459 · see citing works
Ross, J. S., Wang, K., Gay, L. M., Al-Rohil, R. N., Rand, J. V., Jones, D., Lee, H. J., Sheehan, C. E., Otto, G. A., Palmer, G. A., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2013-0352 · Cited by 453 · see citing works
Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification
Kamps, R., Brandão, R. D., van den Bosch, B. J. C., Paulussen, A. D. C., Xanthoulea, S., Blok, M. J., & Romano, A. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18020308 · Cited by 454 · see citing works
Piotrowska, Z., Isozaki, H., Lennerz, J. K., Gainor, J. F., Lennes, I. T., Zhu, V. W., Marcoux, N., Banwait, M. K., Digumarthy, S. R., Su, W., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-1022 · Cited by 447 · see citing works
“All osimertinib-resistant tissue biopsies were analyzed by Clinical Laboratory Improvement Amendments–certified assays performed in the MGH Center for Integrated Diagnostics or Foundation Medicine using methods which have been described previously, including the MGH SNaPshot NGS panel, MGH SFA, FoundationOne NGS panel…”
MethodLin, K., Harrell, M. I., Oza, A. M., Oaknin, A., Ray-Coquard, I. L., Tinker, A. V., Helman, E., Radke, M. R., Say, C., Vo, L.-T., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0715 · Cited by 441 · see citing works
“Sequencing of formalin-fixed paraffin-embedded tumor specimens was performed using the Foundation Medicine T5 NGS-based assay (29), which sequences the exons of 287 cancer-related genes, including BRCA1, BRCA2, and TP53.”
MethodMeric-Bernstam, F., Brusco, L., Shaw, K., Horombe, C., Kopetz, S., Davies, M. A., Routbort, M., Piha-Paul, S. A., Janku, F., Ueno, N., et al. (2015) · Journal of Clinical Oncology · doi:10.1200/jco.2014.60.4165 · Cited by 424 · see citing works
“Such larger panels may demonstrate potentially actionable alterations in many more patients.(3-6) We noted several challenges in linking genomic testing to genomically matched trials.”
BackgroundJavle, M. M., Borad, M. J., Azad, N. S., Kurzrock, R., Abou‐Alfa, G. K., George, B., Hainsworth, J. D., Meric‐Bernstam, F., Swanton, C., Sweeney, C. J., et al. (2021) · The Lancet Oncology · doi:10.1016/s1470-2045(21)00336-3 · Cited by 431 · see citing works
Sholl, L. M., Aisner, D. L., Varella-Garcia, M., Berry, L. D., Dias-Santagata, D., Wistuba, I. I., Chen, H., Fujimoto, J., Kugler, K., Franklin, W. A., et al. (2015) · Journal of Thoracic Oncology · doi:10.1097/jto.0000000000000516 · Cited by 430 · see citing works
Biliary cancer: Utility of next‐generation sequencing for clinical management
Javle, M. M., Bekaii‐Saab, T., Jain, A., Wang, Y., Kelley, R. K., Wang, K., Kang, H. C., Catenacci, D. V. T., Ali, S. M., Krishnan, S., et al. (2016) · Cancer · doi:10.1002/cncr.30254 · Cited by 420 · see citing works
“The sequence analysis methods and validation of the CGP platform included extensive comparisons with orthogonal methodologies.(28) Base substitution detection was performed with a Bayesian methodology, which detected novel somatic mutations at a low mutant allele frequency (MAF) and with increased sensitivity for muta…”
MethodInfluentialPersonalized genomic analyses for cancer mutation discovery and interpretation
Jones, S., Anagnostou, V., Lytle, K., Parpart-Li, S. T., Nesselbush, M. C., Riley, D. R. J., Shukla, M., Chesnick, B., Kadan, M., Papp, E., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa7161 · Cited by 413 · see citing works
Schoenfeld, A. J., Chan, J. M., Kubota, D., Sato, H., Rizvi, H., Daneshbod, Y., Chang, J. C., Paik, P. K., Offin, M., Arcila, M. E., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-3563 · Cited by 411 · see citing works
“The primary NGS platform was MSK-IMPACT (27), but other NGS platforms, such as MSK-Ampliseq (Supplementary Materials and Methods) and Foundation Medicine NGS (28), were occasionally utilized.”
MethodAccelerating Discovery of Functional Mutant Alleles in Cancer
Chang, M. T., Shrestha-Bhattarai, T., Schram, A. M., Bielski, C. M., Donoghue, M. T. A., Jonsson, P., Chakravarty, D., Phillips, S. M., Kandoth, C., Penson, A. V., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0321 · Cited by 402 · see citing works
“Retrospective mutational data were obtained from three publicly available sources: (1) The Cancer Genome Atlas (TCGA), (2) the International Cancer Genome Consortium, and (3) independent published sequencing projects (10).”
MethodKondrashova, O., Nguyen, M., Shield‐Artin, K., Tinker, A. V., Teng, N. N. H., Harrell, M. I., Kuiper, M. J., Ho, G., Barker, H. E., Jasin, M., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0419 · Cited by 410 · see citing works
“5 are being increasingly identified in the clinic due to use of germline multiplex genetic testing and tumor sequencing (16,19).”
BackgroundMethodPeters, S., Gettinger, S. N., Johnson, M. L., Janne, P. A., Garassino, M. C., Christoph, D. C., Toh, C., Rizvi, N. A., Chaft, J. E., Carcereny, E., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2016.71.9476 · Cited by 400 · see citing works
“(%) EGFR*† 13/117 (11) 18/219 (8) 14/207 (7) 45/543 (8) KRAS* 33/100 (33) 50/200 (25) 54/188 (29) 137/488 (28) ALK* 3/79 (4) 2/151 (1) 4/146 (3) 9/376 (2) TC3 or IC3 status, % 47 46 46 46”
Klempner, S. J., Fabrizio, D. A., Bane, S., Reinhart, M. L., Peoples, T., Ali, S. M., Sokol, E. S., Frampton, G. M., Schrock, A. B., Anhorn, R., et al. (2019) · The Oncologist · doi:10.1634/theoncologist.2019-0244 · Cited by 398 · see citing works
“The two quality control metrics that should be considered when evaluating samples for TMB are median depth of sequencing coverage and coverage uniformity, as coverage is directly related to the sensitivity of calling both single nucleotide variants and indels, the two components that contribute to the TMB calculation…”
BackgroundTargeting MET in Lung Cancer: Will Expectations Finally Be MET?
Drilon, A. E. D. C., Cappuzzo, F., Ou, S. I., & Camidge, D. R. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.10.014 · Cited by 393 · see citing works
“tested positive for amplification of other genes such as ERBB2 by FISH.(50,51) As with FISH, copy number gains detected by NGS are reported as continuous variables,”
MethodKopetz, S., Guthrie, K. A., Morris, V. K., Lenz, H., Magliocco, A. M., Maru, D. M., Yan, Y., Lanman, R. B., Manyam, G. C., Hong, D. S., et al. (2020) · Journal of Clinical Oncology · doi:10.1200/jco.20.01994 · Cited by 390 · see citing works
Characterization of 298 Patients with Lung Cancer Harboring MET Exon 14 Skipping Alterations
Schrock, A. B., Frampton, G. M., Suh, J. H., Chalmers, Z. R., Rosenzweig, M. R., Erlich, R., Halmos, B., Goldman, J. W., Forde, P. M., Leuenberger, K., et al. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.06.004 · Cited by 386 · see citing works
“Unknown 62 (24) 8 (18) METex14 alterations, n (%) 0.”
Best practices for variant calling in clinical sequencing
Koboldt, D. C. (2020) · Genome Medicine · doi:10.1186/s13073-020-00791-w · Cited by 387 · see citing works
Abida, W. M., Campbell, D. C., Patnaik, A., Shapiro, J. D., Sautois, B. R., Vogelzang, N. J., Voog, É., Bryce, A. H., McDermott, R., Ricci, F., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-0394 · Cited by 384 · see citing works
“Central testing was performed by Foundation Medicine, Inc (19, 20).”
MethodMilbury, C. A., Creeden, J., Yip, W., Smith, D. L., Pattani, V. P., Maxwell, K., Sawchyn, B., Gjoerup, O. V., Meng, W., Skoletsky, J., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0264138 · Cited by 384 · see citing works
“F1CDx is the result of the evolution of Foundation Medicine’s original FoundationOne(1) assay [64].”
BackgroundDelivering precision oncology to patients with cancer
Mateo, J., Steuten, L., Aftimos, P. G., André, F., Davies, D. M., Garralda, E., Geißler, J., Husereau, D., Martínez‐López, I., Normanno, N., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01717-2 · Cited by 380 · see citing works
Sunami, K., Ichikawa, H., Kubo, T., Kato, M., Fujiwara, Y., Shimomura, A., Koyama, T., Kakishima, H., Kitami, M., Matsushita, H., et al. (2019) · Cancer Science · doi:10.1111/cas.13969 · Cited by 379 · see citing works
Turner, N. C., Kingston, B., Kilburn, L., Kernaghan, S., Wardley, A. M., Macpherson, I. R., Baird, R. D., Roylance, R. R., Stephens, P., Oikonomidou, O., et al. (2020) · The Lancet Oncology · doi:10.1016/s1470-2045(20)30444-7 · Cited by 376 · see citing works
“Sensitivity (or percent-positive agreement reflecting the absence of gold standard) for digital PCR was 93% (95% CI 83–98) overall and 98% (87–100) in patients with contemporaneous biopsies (appendix pp 17, 20).”
InfluentialCopy number alteration burden predicts prostate cancer relapse
Hieronymus, H., Schultz, N. D., Gopalan, A., Carver, B. S., Chang, M. T., Xiao, Y., Heguy, A., Huberman, K. H., Bernstein, M. L., Assel, M. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1411446111 · Cited by 364 · see citing works
“As we have shown that CNA burden can be successfully determined in formalin-fixed needle biopsies, future work may explore CNA burden within large biopsy cohorts to determine its prognostic power (29, 30).”
BackgroundYoshizato, T., Nannya, Y., Atsuta, Y., Shiozawa, Y., Iijima‐Yamashita, Y., Yoshida, K., Shiraishi, Y., Suzuki, H., Nagata, Y., Sato, Y., et al. (2017) · Blood · doi:10.1182/blood-2016-12-754796 · Cited by 351 · see citing works
“0) Age at diagnosis (n 5 796), y 51 (12-65) Age at transplantation (n 5 797), y 53 (16-66) Time from diagnosis to transplantation (n 5 793), mo 9.”
BackgroundThe distribution of BRAF gene fusions in solid tumors and response to targeted therapy
Ross, J. S., Wang, K., Chmielecki, J., Gay, L. M., Johnson, A., Chudnovsky, J., Yelensky, R., Lipson, D., Ali, S. M., Elvin, J. A., et al. (2015) · International Journal of Cancer · doi:10.1002/ijc.29825 · Cited by 354 · see citing works
“Base substitution detection is performed using a Bayesian methodology, which allows detection of novel somatic mutations at low mutant allele frequency (MAF) and increased sensitivity for mutations at hotspot sites through the incorporation of tissue-specific prior expectations.(15) Reads with mapping quality <25 are…”
BackgroundMethodInfluentialPD-1 Blockade in Anaplastic Thyroid Carcinoma
Capdevila, J., Wirth, L. J., Ernst, T., Ponce-Aix, S., Lin, C., Ramlau, R., Butler, M. O., Delord, J., Gelderblom, H. A. J., Ascierto, P. A., et al. (2020) · Journal of Clinical Oncology · doi:10.1200/jco.19.02727 · Cited by 355 · see citing works
“…were also analyzed by next-generation sequencing (Foundation Medicine, Cambridge, Massachusetts) to assess mutations affecting cancer-related genes and tumor mutation burden, 17 and by RNA sequencing (RNAseq) to evaluate gene expression patterns, including interferon gamma (IFN γ ) signature.”
Singhi, A. D., George, B., Greenbowe, J. R., Chung, J., Suh, J., Maitra, A., Klempner, S. J., Hendifar, A., Milind, J. M., Golan, T., et al. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.02.037 · Cited by 348 · see citing works
Self-citationLin, J. J., Zhu, V. W., Yoda, S., Yeap, B. Y., Schrock, A. B., Dagogo‐Jack, I., Jessop, N. A., Jiang, G. Y., Le, L. P., Gowen, K. A., et al. (2018) · Journal of Clinical Oncology · doi:10.1200/jco.2017.76.2294 · Cited by 347 · see citing works
“of patients 129 55 51 Median age, years (range) 52 (22-78) 55 (22-78) 51 (31-76) .”
Implementing TMB measurement in clinical practice: considerations on assay requirements
Büttner, R., Longshore, J. W., López‐Ríos, F., Merkelbach‐Bruse, S., Normanno, N., Rouleau, É., & Penault-Llorca, F. M. (2019) · ESMO Open · doi:10.1136/esmoopen-2018-000442 · Cited by 342 · see citing works
Jones, J. C., Renfro, L. A., Al-Shamsi, H. O., Schrock, A. B., Rankin, A., Zhang, B. Y., Kasi, P. M., Voss, J. S., Leal, A. D., Sun, J. X., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2016.71.4394 · Cited by 342 · see citing works
Individualized Medicine from Prewomb to Tomb
Topol, E. J. (2014) · Cell · doi:10.1016/j.cell.2014.02.012 · Cited by 340 · see citing works
“Using predominantly fixed-formalin, paraffin-embedded samples, mutation cell concordance was established compared with mass spectrometric methodology (Sequenom), and the typical driver mutations were identified in a cohort of more than 2,000 individuals, such as TP53, KRAS, CDKN2A, and PIK3CA (Frampton et al., 2013).”
Kris, M. G., Camidge, D. R., Giaccone, G., Hida, T., Li, B. T., O'Connell, J., Taylor, I., Zhang, H., Arcila, M. E., Goldberg, Z., et al. (2015) · Annals of Oncology · doi:10.1093/annonc/mdv186 · Cited by 334 · see citing works
“The growing use of multiplexed genomic assays that can detect both mutations and amplifications has led to the identification of an increasing number of individuals with HER2-driven lung cancers [12].”
BackgroundFusions in solid tumours: diagnostic strategies, targeted therapy, and acquired resistance
Schram, A. M., Chang, M. T., Jonsson, P., & Drilon, A. E. D. C. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.127 · Cited by 328 · see citing works
MET-dependent solid tumours — molecular diagnosis and targeted therapy
Guo, R., Luo, J., Chang, J. C., Rekhtman, N., Arcila, M. E., & Drilon, A. E. D. C. (2020) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-020-0377-z · Cited by 329 · see citing works
Necchi, A., Raggi, D., Andrea Gallina, A., Madison, R. W., Colecchia, M., Lucianò, R., Montironi, R., Giannatempo, P., Farè, E., Pederzoli, F., et al. (2019) · European Urology · doi:10.1016/j.eururo.2019.10.026 · Cited by 326 · see citing works
Ivosidenib in Isocitrate Dehydrogenase 1–Mutated Advanced Glioma
Mellinghoff, I. K., Ellingson, B. M., Touat, M., Maher, E. A., de la Fuente, M. I., Holdhoff, M., Cote, G. M., Burris, H. A., Jankú, F., Young, R. J., et al. (2020) · Journal of Clinical Oncology · doi:10.1200/jco.19.03327 · Cited by 322 · see citing works
Evaluating eligibility criteria of oncology trials using real-world data and AI
Liu, R., Rizzo, S., Whipple, S., Pal, N., Pineda, A. L., Lu, M. W., Arnieri, B., Lü, Y., Capra, W. B., Copping, R., et al. (2021) · Nature · doi:10.1038/s41586-021-03430-5 · Cited by 326 · see citing works
Castellanos, E. H., Feld, E., & Horn, L. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.12.014 · Cited by 319 · see citing works
“For example, FoundationOne utilizes massively parallel DNA sequencing to characterize clinically actionable mutations across a wide array of cancer-related genes from routine formalin-fixed and paraffin-embedded tissue specimens.(82) This information is provided in conjunction with an interpretive report”
Detecting the mutational signature of homologous recombination deficiency in clinical samples
Gulhan, D., Lee, J. J.-K., Melloni, G. E. M., Cortés‐Ciriano, I., & Park, P. J. (2019) · Nature Genetics · doi:10.1038/s41588-019-0390-2 · Cited by 316 · see citing works
AKT Inhibition in Solid Tumors With AKT1 Mutations
Hyman, D. M., Smyth, L. M., Donoghue, M. T. A., Westin, S. N., Bedard, P. L., Dean, E. J., Bando, H., El-Khoueiry, A. B., Fidalgo, J. A. P., Mita, A. C., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2017.73.0143 · Cited by 309 · see citing works
“Next-generation sequencing was performed utilizing both targeted and whole-exome sequencing on pre-treatment DNA from formalin-fixed paraffin embedded tumor and matched blood specimens (Table S3).(20,21) Droplet digital polymerase-chainreaction analysis (ddPCR) using an allele-specific assay was performed on cfDNA fro…”
MethodImmunotherapeutic approaches for small-cell lung cancer
Iams, W. T., Porter, J., & Horn, L. (2020) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-019-0316-z · Cited by 312 · see citing works
Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting
He, J., Abdel-Wahab, O. I., Nahas, M. K., Wang, K., Rampal, R. K., Intlekofer, A. M., Patel, J. L., Krivstov, A. V., Frampton, G. M., Young, L. E., et al. (2016) · Blood · doi:10.1182/blood-2015-08-664649 · Cited by 307 · see citing works
“Additional details of the methods were described previously.(7)”
BackgroundMethodInfluential
- Authors
- Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., 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, J. M., Rubin, M. A., Dogan, S., Hedvat, C. V., Berger, M. F., Pusztai, L., Lechner, M., Boshoff, C., Jarosz, M., Vietz, C., Parker, A., Miller, V. A., Ross, J. S., Curran, J., Cronin, M. T., Stephens, P. J., Lipson, D., & Yelensky, R.
- Affiliations
- Foundation Medicine (United States) (US)
- NewYork–Presbyterian Hospital (US)
- Memorial Sloan Kettering Cancer Center (US)
- Yale Cancer Center (US)
- University College London (GB)
- Corresponding author
- Lipson, Doron
- Yelensky, Roman
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2013-11
- Volume
- 31
- Issue
- 11
- Pages
- 1023-1031
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC5710001
- OpenAlex
- W2160981405
- Cited by
- 2,157
- References
- 54
- Citations by year
- 2026: 91 · 2025: 122 · 2024: 139 · 2023: 215 · 2022: 208 · 2021: 188 · 2020: 213 · 2019: 185 · 2018: 195 · 2017: 180 · 2016: 182 · 2015: 159 · 2014: 76 · 2013: 2
- FWCI
- 49.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust (WT093855MA)
- National Cancer Institute (P30CA008748)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Keywords
- tumor genomic profiling, analytical method validation, formalin-fixed paraffin-embedded tissue, copy number alterations, indels, gene fusion, actionable mutations, mutant allele frequency, sensitivity and specificity, precision oncology
- MeSH terms
- DNA Mutational Analysis, Gene Frequency, Humans, Neoplasms, Sensitivity and Specificity, Reproducibility of Results, Sequence Analysis, DNA, Molecular Diagnostic Techniques, DNA Copy Number Variations
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
