Cited by 2,157Cancer Genomics and DiagnosticsGenomics and Rare DiseasesBRCA gene mutations in cancer

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

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Frampton, Garrett M, Fichtenholtz, Alex, Otto, Geoff A, Wang, Kai, Downing, Sean R, He, Jie, Schnall-Levin, Michael, White, Jared, Sanford, Eric M, An, Peter, Sun, James, Juhn, Frank, Brennan, Kristina, Iwanik, Kiel, Maillet, Ashley, Buell, Jamie, White, Emily, Zhao, Mandy, Balasubramanian, Sohail, Terzic, Selmira, Richards, Tina, Banning, Vera, Garcia, Lazaro, Mahoney, Kristen, Zwirko, Zac, Donahue, Amy, Beltran, Himisha, Mosquera, Juan Miguel, Rubin, Mark A, Dogan, Snjezana, Hedvat, Cyrus V, Berger, Michael F, Pusztai, Lajos, Lechner, Matthias, Boshoff, Chris, Jarosz, Mirna, Vietz, Christine, Parker, Alex, Miller, Vincent A, Ross, Jeffrey S, Curran, John, Cronin, Maureen T, Stephens, Philip J, Lipson, Doron, Yelensky, Roman·2013·Nature Biotechnology

DOI 10.1038/nbt.2696PMC PMC5710001

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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.

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BackgroundMethod
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BackgroundMethod
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Background
Analysis ofMDM2Amplification: Next-Generation Sequencing of Patients With Diverse Malignancies
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Use of capture-based next-generation sequencing to detect ALK fusion in plasma cell-free DNA of patients with non-small-cell lung cancer
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“For low variant allele frequency (VAF) ranges (< 5%), BAM files were assessed in an Integrative Genomic Viewer and if the total read depth was > 500 with a mapping quality score > 25 for the alignment of various reads, the detected mutation was considered a true somatic event [13].”
Method
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Background
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“analysis using a more recent FoundationOne panel (Frampton et al., 2013) revealed the presence of the L858R mutation (c.”
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Method
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Method
A pilot study evaluating concordance between blood-based and patient-matched tumor molecular testing within pancreatic cancer patients participating in the Know Your Tumor (KYT) initiative
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Method
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Background
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Kao, H., Liao, B.-C., Huang, Y., Huang, H., Chen, C., Chen, T., Hong, Y.-J., Chan, C.-Y., Chia, J., & Hong, R. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-3025 · Cited by 70
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Method
Integrated Analysis of Multiple Biomarkers from Circulating Tumor Cells Enabled by Exclusion-Based Analyte Isolation
Sperger, J. M., Strotman, L. N., Welsh, A. W., Casavant, B. P., Chalmers, Z., Horn, S., Héninger, E., Thiede, S. M., Tokar, J. J., Gibbs, B. K., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-1021 · Cited by 69
“Comprehensive genomic profiling In samples passing primary quality metrics, amplified DNA (50–200 ng/sample) underwent whole-genome shotgun library construction and solution hybridization using methods previously developed and validated (35), to capture full exons from 315 cancer-related genes, as well as introns from…”
Comprehensive genomic profiling of head and neck squamous cell carcinoma reveals FGFR1 amplifications and tumour genomic alterations burden as prognostic biomarkers of survival
Dubot, C., Bernard, V., Sablin, M., Vacher, S., Chemlali, W., Schnitzler, A., Pierron, G., Raïs, K. A., Bessoltane, N., Jeannot, E., et al. (2018) · European Journal of Cancer · doi:10.1016/j.ejca.2017.12.016 · Cited by 69
Clinical impact of subclonal EGFR T790M mutations in advanced-stage EGFR-mutant non-small-cell lung cancers
Vaclová, T., Grazini, U., Ward, L. S. C., O’Neill, D. J., Markovets, A. A., Huang, X., Chmielecki, J., Hartmaier, R. J., Thress, K. S., Smith, P. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22057-8 · Cited by 69
A Novel SDHA-deficient Renal Cell Carcinoma Revealed by Comprehensive Genomic Profiling
Yakirevich, E., Ali, S. M., Mega, A. E., McMahon, C., Brodsky, A. S., Ross, J. S., Allen, J. M., Elvin, J. A., Safran, H. P., & Resnick, M. B. (2015) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000000403 · Cited by 68
The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer
Joseph, L. J., Cankovic, M., Caughron, S. K., Chandra, P., Emmadi, R., Hagenkord, J. M., Hallam, S., Jewell, K. E., Klein, R. D., Pratt, V. M., et al. (2016) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2016.05.007 · Cited by 68
Next‐generation sequencing: a change of paradigm in molecular diagnostic validation
Salto‐Tellez, M., & de Castro, D. G. (2014) · The Journal of Pathology · doi:10.1002/path.4365 · Cited by 67
“strategy (enriching for a specific sequence prior to NGS analysis by hybridization steps) is currently favoured [4,5], which opens new detection possibilities with the technology but could double the TAT up to 10 working days.”
Background
Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing
Lokhandwala, P. M., Tseng, L., Rodriguez, E. F., Zheng, G., Pallavajjalla, A., Gocke, C. D., Eshleman, J. R., & Lin, M. (2019) · BMC Cancer · doi:10.1186/s12885-019-5864-1 · Cited by 70
“However, next generation sequencing (NGS) platforms have become popular in the clinical diagnostic setting for simultaneous mutational profiling of a panel of genes for melanomas and other cancers [16, 17].”
Background
Next-generation sequencing of adrenocortical carcinoma reveals new routes to targeted therapies
Ross, J. S., Wang, K., Rand, J. V., Gay, L. M., Presta, M., Sheehan, C. E., Ali, S. M., Elvin, J. A., LaBrecque, E., Hiemstra, C. N., et al. (2014) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2014-202514 · Cited by 67
Comprehensive Assessment of Immuno-oncology Biomarkers in Adenocarcinoma, Urothelial Carcinoma, and Squamous-cell Carcinoma of the Bladder
Necchi, A., Madison, R. W., Raggi, D., Jacob, J. M., Bratslavsky, G., Shapiro, O., Elvin, J. A., Vergilio, J., Killian, J. K., Ngo, N., et al. (2020) · European Urology · doi:10.1016/j.eururo.2020.01.003 · Cited by 70
Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias
Wang, K., Sánchez-Martín, M., Wang, X., Knapp, K. M., Koche, R. P., Vu, L., Nahas, M. K., He, J., Hadler, M., Stein, E. M., et al. (2016) · Leukemia · doi:10.1038/leu.2016.166 · Cited by 67
“…published as recurrent in leukemia from literature or public database COSMIC 17 , or were predicted to alter protein function on tumor suppressor genes were designated as somatic variant alleles (SVA); other genomic variants were designated as variants of unknown significance (VUS) 14, 18 .”
Influential
Structure–function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting
Du, Z., Brown, B. P., Kim, S., Ferguson, D. C., Pavlick, D. C., Jayakumaran, G., Benayed, R., Gallant, J., Zhang, Y., Yan, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21613-6 · Cited by 68
Real-World Genomic Profile of EGFR Second-Site Mutations and Other Osimertinib Resistance Mechanisms and Clinical Landscape of NSCLC Post-Osimertinib
Rotow, J. K., Lee, J., Madison, R. W., Oxnard, G. R., Janne, P. A., & Schrock, A. B. (2023) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2023.09.1453 · Cited by 69
Genomic Profiling of Parathyroid Carcinoma Reveals Genomic Alterations Suggesting Benefit from Therapy
Kang, H., Pettinga, D., Schubert, A. D., Ladenson, P. W., Ball, D. W., Chung, J., Schrock, A. B., Madison, R. W., Frampton, G. M., Stephens, P. J., et al. (2018) · The Oncologist · doi:10.1634/theoncologist.2018-0334 · Cited by 65
“To maximize mutation detection accuracy (sensitivity and specificity) in impure clinical specimens, the test was previously optimized and validated to detect base substitutions at a ≥ 5% mutant allele frequency (MAF), indels with a ≥ 10% MAF with ≥99% accuracy, and fusions occurring within baited introns/exons with >9…”
MethodInfluential
Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance
Casolino, R., Beer, P. A., Chakravarty, D., Davis, M. B., Malapelle, U., Mazzarella, L., Normanno, N., Pauli, C., Subbiah, V., Turnbull, C., et al. (2024) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21825 · Cited by 69
Analysis of Tissue and Circulating Tumor DNA by Next-Generation Sequencing of Hepatocellular Carcinoma: Implications for Targeted Therapeutics
Ikeda, S., Lim, J. S., & Kurzrock, R. (2018) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-17-0604 · Cited by 64
“Detailed methods for both liquid biopsy ctDNA and tissue NGS have been previously published (9, 10).”
Method
Genomic profiling of BCOR-rearranged uterine sarcomas reveals novel gene fusion partners, frequent CDK4 amplification and CDKN2A loss
Lin, D. I., Hemmerich, A. C., Edgerly, C. I., Duncan, D. L., Severson, E. A., Huang, R. S. P., Ramkissoon, S. H., Connor, Y., Shea, M., Hecht, J. L., et al. (2020) · Gynecologic Oncology · doi:10.1016/j.ygyno.2020.02.024 · Cited by 66
Molecular Markers Guiding Thyroid Cancer Management
Nylén, C., Mechera, R., Maréchal-Ross, I., Tsang, V., Chou, A. S. Y., Gill, A. J., Clifton-Bligh, R. J., Robinson, B. G., Sywak, M. S., Sidhu, S. B., et al. (2020) · Cancers · doi:10.3390/cancers12082164 · Cited by 67
Emergence of FGFR3-TACC3 fusions as a potential by-pass resistance mechanism to EGFR tyrosine kinase inhibitors in EGFR mutated NSCLC patients
Ou, S. I., Horn, L., Cruz, M. R., Vafai, D., Lovly, C. M., Spradlin, A., Williamson, M. J., Dagogo‐Jack, I., Johnson, A., Miller, V. A., et al. (2017) · Lung Cancer · doi:10.1016/j.lungcan.2017.07.006 · Cited by 64
“1A), a plasma-based circulating tumor DNA (ctDNA) assay was performed as previously described [10] and revealed the original EGFR ex19del as well as an acquired FGFR3-TACC3 fusion (F18; T10) (Fig.”
Method
Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer
Huang, C., Du, M., & Wang, L. (2019) · Cancers · doi:10.3390/cancers11060805 · Cited by 67
“This provides a sound methodology for identifying somatic mutations from solid tumor biopsies [41].”
Method
Characterization of Clinical Cases of Malignant PEComa via Comprehensive Genomic Profiling of DNA and RNA
Akumalla, S., Madison, R. W., Lin, D. I., Schrock, A. B., Yakirevich, E., Rosenzweig, M. R., Balar, A. V., Frampton, G. M., Edgerly, C. I., Erlich, R., et al. (2020) · Oncology · doi:10.1159/000510241 · Cited by 65
Randomized Phase II Study of Axitinib Versus Observation in Patients with Recurred or Metastatic Adenoid Cystic Carcinoma
Kang, E. J., Ahn, M., Ock, C.-Y., Lee, K., Kwon, J. H., Yang, Y., Choi, Y. H., Kim, M. K., Ji, J. H., Yun, T., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-1061 · Cited by 69
Positive Association Between Location of Melanoma, Ultraviolet Signature, Tumor Mutational Burden, and Response to Anti–PD-1 Therapy
Dousset, L., Poizeau, F., Robert, C., Mansard, S., Mortier, L., Caumont, C., Routier, É., Dupuy, A., Rouanet, J., Battistella, M., et al. (2021) · JCO Precision Oncology · doi:10.1200/po.21.00084 · Cited by 71
“DNA was extracted from formalin-fixed, paraffin-embedded tissue sections to perform comprehensive genomic profiling with FoundationOne Assay in a Clinical Laboratory Improvement Amendments–certified, College of American Pathologists–accredited, New York State–approved laboratory (Foundation Medicine).(14) TMB was calc…”
Method
Liquid versus tissue biopsy for detecting actionable alterations according to the ESMO Scale for Clinical Actionability of molecular Targets in patients with advanced cancer: a study from the French National Center for Precision Medicine (PRISM)
Bayle, A., Peyraud, F., Belcaid, L., Brunet, M., Aldea, M. D., Clodion, R., Dubos, P., Vasseur, D., Nicotra, C., Géraud, A., et al. (2022) · Annals of Oncology · doi:10.1016/j.annonc.2022.08.089 · Cited by 65
Genomic landscape of 891 RET fusions detected across diverse solid tumor types
Parimi, V., Tolba, K. A., Danziger, N. A., Kuang, Z., Sun, D., Lin, D. I., Hiemenz, M., Schrock, A. B., Ross, J. S., Oxnard, G. R., et al. (2023) · npj Precision Oncology · doi:10.1038/s41698-023-00347-2 · Cited by 68
RICTOR amplification identifies a subgroup in small cell lung cancer and predicts response to drugs targeting mTOR
Sakre, N., Wildey, G. M., Behtaj, M., Kresak, A. M., Yang, M., Fu, P., & Dowlati, A. (2016) · Oncotarget · doi:10.18632/oncotarget.13362 · Cited by 64
Genomic and clinical characterization of B/T mixed phenotype acute leukemia reveals recurrent features and T‐ALL like mutations
Mi, X., Griffin, G. K., Lee, W., Patel, S. S., Ohgami, R. S., Ok, C. Y., Wang, S., Geyer, J. T., Xiao, W., Roshal, M., et al. (2018) · American Journal of Hematology · doi:10.1002/ajh.25256 · Cited by 64
Genomic Profiling of Metastatic Uveal Melanoma and Clinical Results of a Phase I Study of the Protein Kinase C Inhibitor AEB071
Piperno-Neumann, S., Larkin, J., Carvajal, R. D., Luke, J. J., Schwartz, G. K., Hodi, F. S., Sablin, M., Shoushtari, A. N., Szpakowski, S., Chowdhury, N. R., et al. (2020) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-19-0098 · Cited by 65
“Targeted sequencingwas performed at high depth (median 625 ) to characterize mutations (substitutions, excluding synonymous mutations, and insertions/deletions), amplifications (≥6 copies), homozygous deletions, and gene fusions/rearrangements, as described previously (27).”
Background
PARP inhibitors in platinum-sensitive high-grade serous ovarian cancer
Morgan, R. D., Clamp, A. R., Evans, D. G., Edmondson, R. J., & Jayson, G. C. (2018) · Cancer Chemotherapy and Pharmacology · doi:10.1007/s00280-018-3532-9 · Cited by 66
“This assay was used to detect mutations in 30 HR repair genes and to quantify genomewide LOH (as a percentage) by sequencing over 3500 evenly distributed SNPs in DNA extracted from archival ovarian tumour tissue [96].”
Method
Histiocytic and Dendritic Cell Sarcomas of Hematopoietic Origin Share Targetable Genomic Alterations Distinct from Follicular Dendritic Cell Sarcoma
Massoth, L. R., Hung, Y. P., Ferry, J. A., Hasserjian, R. P., Nardi, V., Nielsen, G. P., Sadigh, S., Venkataraman, V., Selig, M. K., Friedmann, A. M., et al. (2021) · The Oncologist · doi:10.1002/onco.13801 · Cited by 67
Clinical Tumor Sequencing: Opportunities and Challenges for Precision Cancer Medicine
Damodaran, S., Berger, M. F., & Roychowdhury, S. (2015) · American Society of Clinical Oncology Educational Book · doi:10.14694/edbook_am.2015.35.e175 · Cited by 64
Comprehensive Genomic Profiling of Clinically Advanced Medullary Thyroid Carcinoma
Heilmann, A. M. F., Subbiah, V., Wang, K., Sun, J., Elvin, J. A., Chmielecki, J., Sherman, S. I., Murthy, R., Busaidy, N. L., Subbiah, I. M., et al. (2016) · Oncology · doi:10.1159/000445978 · Cited by 63
Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker
Chavan, S. S., He, J., Tytarenko, R. G., Deshpande, S., Patel, P., Bailey, M., Epstein, J., Stephens, O., Weinhold, N., Petty, N. M., et al. (2017) · Blood Cancer Journal · doi:10.1038/bcj.2017.12 · Cited by 62
PARP inhibitors as potential therapeutic agents for various cancers: focus on niraparib and its first global approval for maintenance therapy of gynecologic cancers
Sisay, M., & Edessa, D. (2017) · Gynecologic Oncology Research and Practice · doi:10.1186/s40661-017-0055-8 · Cited by 63
Identifying a Clinically Applicable Mutational Burden Threshold as a Potential Biomarker of Response to Immune Checkpoint Therapy in Solid Tumors
Panda, A., Betigeri, A. M., Subramanian, K., Ross, J. S., Pavlick, D. C., Ali, S. M., Markowski, P. A., Silk, A. W., Kaufman, H. L., Lattime, E. C., et al. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00146 · Cited by 64
Clinical validation of the Tempus xO assay
Beaubier, N. T., Tell, R. W., Huether, R., Bontrager, M., Bush, S., Parsons, J., Shah, K. P., Baker, T., Selkov, G., Taxter, T., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.25381 · Cited by 63
“Comprehensive genomic profiling using deep, high-quality, clinically certified (CAP/CLIA) laboratory sequencing has emerged as a key tool in clinical decision support [1, 2].”
Method
A Phase 2 Study of Capmatinib in Patients With MET-Altered Lung Cancer Previously Treated With a MET Inhibitor
Dagogo‐Jack, I., Moonsamy, P., Gainor, J. F., Lennerz, J. K., Piotrowska, Z., Lin, J. J., Lennes, I. T., Sequist, L. V. D., Shaw, A. T., Goodwin, K., et al. (2021) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2021.01.1605 · Cited by 63
A targeted next-generation sequencing method for identifying clinically relevant mutation profiles in lung adenocarcinoma
Шао, Д., Lin, Y., Liu, J., Wan, L., Zu, L., Cheng, S., Fei, L., Deng, R., Wang, J. Z., Chen, X., et al. (2016) · Scientific Reports · doi:10.1038/srep22338 · Cited by 63
A Targeted Next-Generation Sequencing Assay Detects a High Frequency of Therapeutically Targetable Alterations in Primary and Metastatic Breast Cancers: Implications for Clinical Practice
Vasan, N., Yelensky, R., Wang, K., Moulder, S., Dzimitrowicz, H. E., Avritscher, R., Wang, B., Wu, Y., Cronin, M. T., Palmer, G. A., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2013-0377 · Cited by 62
ETV3-NCOA2 in indeterminate cell histiocytosis: clonal translocation supports sui generis
Brown, R. A., Kwong, B. Y., McCalmont, T. H., Ragsdale, B. D., Ma, L., Cheung, C., Rieger, K. E., Arber, D. A., & Kim, J. (2015) · Blood · doi:10.1182/blood-2015-07-655530 · Cited by 62
Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis
Ascierto, P. A., Bifulco, C. B., Palmieri, G., Peters, S., & Sidiropoulos, N. (2019) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2019.05.004 · Cited by 65
Real-world outcomes treating patients with advanced cutaneous squamous cell carcinoma with immune checkpoint inhibitors (CPI)
Hanna, G. J., Ruiz, E. S., LeBoeuf, N. R., Thakuria, M., Schmults, C. D., DeCaprio, J. A., & Silk, A. W. (2020) · British Journal of Cancer · doi:10.1038/s41416-020-01044-8 · Cited by 62
Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection
Gray, P. N., Dunlop, C. L. M., & Elliott, A. M. (2015) · Cancers · doi:10.3390/cancers7030837 · Cited by 62
“A stage 4 prostate cancer specimen from a 43 year old individual (FFPE DNA) was sent to Foundation Medicine for analysis on FoundationOner, a CLIA validated probe-based target enrichment tumor profiling test [18].”
Method
Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel NGS panel testing
Guo, Q., Wang, J., Xiao, J., Wang, L., Hu, X., Yu, W., Song, G., Lou, J., & Chen, J. (2018) · Molecular Cancer · doi:10.1186/s12943-018-0875-0 · Cited by 61
Revisiting Epidermal Growth Factor Receptor (EGFR) Amplification as a Target for Anti-EGFR Therapy: Analysis of Cell-Free Circulating Tumor DNA in Patients With Advanced Malignancies
Kato, S., Okamura, R., Mareboina, M., Lee, S., Goodman, A. M., Patel, S. P., Fanta, P. T., Schwab, R. B., Vu, P., Raymond, V. M., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00180 · Cited by 64
Retinoblastoma mutation predicts poor outcomes in advanced non small cell lung cancer
Bhateja, P., Chiu, M., Wildey, G. M., Lipka, M. B., Fu, P., Yang, M., Ardeshir‐Larijani, F., Sharma, N., & Dowlati, A. (2019) · Cancer Medicine · doi:10.1002/cam4.2023 · Cited by 61
Fit‐for‐Purpose Biometric Monitoring Technologies: Leveraging the Laboratory Biomarker Experience
Godfrey, A., Vandendriessche, B., Bakker, J. P., Fitzer‐Attas, C., Gujar, N., Hobbs, M., Liu, Q., Northcott, C. A., Parks, V., Wood, W. A., et al. (2021) · Clinical and Translational Science · doi:10.1111/cts.12865 · Cited by 60
“Yet, this work took several years, whereas prior to these approvals, a comprehensive validation study was performed to provide an example of assay performance characteristics and acceptance criteria.(66) Platform validation performance characteristics were established using DNA derived from a wide range of tissue type…”
EWSR1-PATZ1-rearranged sarcoma: a report of nine cases of spindle and round cell neoplasms with predilection for thoracoabdominal soft tissues and frequent expression of neural and skeletal muscle markers
Michal, M., Rubin, B. P., Agaimy, A., Kösemehmetoğlu, K., Rudzinski, E. R., Linos, K. D., John, I., Gatalica, Z., Davis, J. L., Liu, Y. J., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-00684-8 · Cited by 60
“Cases 3 and 7 were tested by a commercial NGS platform (Foundation Medicine, Cambridge, MA, USA) as reported elsewhere [15].”
Method
Correlation of genomic alterations assessed by next-generation sequencing (NGS) of tumor tissue DNA and circulating tumor DNA (ctDNA) in metastatic renal cell carcinoma (mRCC): potential clinical implications
Hahn, A. W., Gill, D. M., Maughan, B. L., Agarwal, A. M., Arjyal, L., Gupta, S. V., Streeter, J., Bailey, E. B., Pal, S. K., & Agarwal, N. (2017) · Oncotarget · doi:10.18632/oncotarget.16833 · Cited by 60
“FoundationOne is a NGS platform that analyzes tumor tissue and characterizes 315 somatic and germline cancer-associated genes (supplementary document 1) [7].”
Background
Malignant Melanoma: Diagnostic and Management Update
Knackstedt, T., Knackstedt, R. W., Couto, R. A., & Gastman, B. (2018) · Plastic & Reconstructive Surgery · doi:10.1097/prs.0000000000004571 · Cited by 62
Tumor Mutational Burden From Tumor-Only Sequencing Compared With Germline Subtraction From Paired Tumor and Normal Specimens
Parikh, K., Huether, R., White, K. P., Hoskinson, D. C., Beaubier, N. T., Dong, H., Adjei, A. A., & Mansfield, A. S. (2020) · JAMA Network Open · doi:10.1001/jamanetworkopen.2020.0202 · Cited by 58
“(%) Brain 4 (8) Breast 4 (8) Colorectal 6 (12) Endometrial 3 (6) Lung 3 (6) Ovarian 6 (12) Pancreatic 4 (8) Prostate 5 (10) Other rare tumors 6 (12) Unknown 9 (18)”
Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer
Lindquist, K. E., Karlsson, A., Levéen, P., Brunnström, H., Reuterswärd, C., Holm, K., Jönsson, M., Annersten, K., Rosengren, F., Jirström, K., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.16276 · Cited by 60
Implementation of individualized medicine for cancer patients by multiomics-based analyses—the Project HOPE—
Yamaguchi, K., Urakami, K., Ohshima, K., Mochizuki, T., Akiyama, Y., Uesaka, K., Nakajima, T., Takahashi, M., Tamai, S., & Kusuhara, M. (2014) · Biomedical Research · doi:10.2220/biomedres.35.407 · Cited by 59

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: Frampton, Garrett M
He, Jie
Sanford, Eric M
Sun, James
Zhao, Mandy
Beltran, Himisha
Mosquera, Juan Miguel
Rubin, Mark A
Hedvat, Cyrus V
Berger, Michael F
Pusztai, Lajos
Lechner, Matthias
Parker, Alex
Miller, Vincent A
Ross, Jeffrey S
Curran, John
Cronin, Maureen T
Lipson, Doron
Yelensky, Roman
Venue: Nature Biotechnology
Publisher: Springer Science and Business Media LLC
Published: 2013-11
Volume: 31
Issue: 11
Pages: 1023-1031
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/nbt.2696
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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

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