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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“7 sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%)(25).”
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Method
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“Common approaches include the use of oncology patient samples previously tested in CLIA laboratories via smaller, highly targeted assays (eg, Sanger sequencing and SNAPSHOT) or the use of wellcharacterized cell lines previously sequenced at one or many research institutions.(1,2) The first option controls for sample t…”
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“A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-IdU / anti-BrdU clone B44 BD Biosciences Cat# B44; RRID: AB_2313824 Rat monoclonoal anti-CldU / anti-BrdU (BU1/75 ICR1) Santa Cruz Biotechnology Cat# sc-56258, RRID: AB_781696 Goa…”
MethodInfluential
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Self-citation
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Method
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Retracted
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Background
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Background
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Background
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Method
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Background
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Method
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“Each sample was sequenced using the Foundation Medicine NGS FoundationOneCDx assay 68 .”
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Background
Prognosis and Clinicopathologic Features of Patients With Advanced Stage Isocitrate Dehydrogenase (IDH) Mutant and IDH Wild-Type Intrahepatic Cholangiocarcinoma
Goyal, L., Govindan, A., Sheth, R. A., Nardi, V., Blaszkowsky, L. S., Faris, J. E., Clark, J. W., Ryan, D. P., Kwak, E. L., Allen, J. N., et al. (2015) · The Oncologist · doi:10.1634/theoncologist.2015-0210 · Cited by 134
Genomic Characterization of Renal Cell Carcinoma with Sarcomatoid Dedifferentiation Pinpoints Recurrent Genomic Alterations
Malouf, G. G., Ali, S. M., Wang, K., Balasubramanian, S., Ross, J. S., Miller, V. A., Stephens, P. J., Khayat, D., Pal, S. K., Su, X., et al. (2016) · European Urology · doi:10.1016/j.eururo.2016.01.051 · Cited by 133
ALKFusions in a Wide Variety of Tumor Types Respond to Anti-ALK Targeted Therapy
Ross, J. S., Ali, S. M., Fasan, O. O., Block, J. G., Pal, S. K., Elvin, J. A., Schrock, A. B., Suh, J. H., Nozad, S., Kim, S., et al. (2017) · The Oncologist · doi:10.1634/theoncologist.2016-0488 · Cited by 134
“All three versions of the CGP assay used in this study detect ALK rearrangements (rALK) through DNA sequencing [30, 31].”
Method
Tracking the Evolution of Resistance to ALK Tyrosine Kinase Inhibitors Through Longitudinal Analysis of Circulating Tumor DNA
Dagogo‐Jack, I., Brannon, A. R., Ferris, L. A., Campbell, C. D., Lin, J. J., Schultz, K. R., Ackil, J., Stevens, S. E., Dardaei, L., Yoda, S., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00160 · Cited by 133
Analysis of Circulating Tumor DNA and Clinical Correlates in Patients with Esophageal, Gastroesophageal Junction, and Gastric Adenocarcinoma
Kato, S., Okamura, R., Baumgartner, J. M., Patel, H., Leichman, L., Kelly, K. J., Sicklick, J. K., Fanta, P. T., Lippman, S. M., & Kurzrock, R. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1128 · Cited by 129
“All tissue DNA analyses were performed by Foundation Medicine as described previously (21, 22).”
Method
Metastatic basal cell carcinoma with amplification of PD-L1: exceptional response to anti-PD1 therapy
Ikeda, S., Goodman, A. M., Cohen, P. R., Jensen, T. J., Ellison, C. K., Frampton, G. M., Miller, V. A., Patel, S. P., & Kurzrock, R. (2016) · npj Genomic Medicine · doi:10.1038/npjgenmed.2016.37 · Cited by 130
Overall Survival and Clinical Characteristics of BRCA-Associated Cholangiocarcinoma: A Multicenter Retrospective Study
Golan, T., Raitses‐Gurevich, M., Kelley, R. K., Bocobo, A. G., Borgida, A., Shroff, R. T., Holter, S., Gallinger, S., Ahn, D. H., Aderka, D., et al. (2017) · The Oncologist · doi:10.1634/theoncologist.2016-0415 · Cited by 130
“Samples collected at Mount Sinai Hospital were analyzed in a clinical Advanced Molecular Diagnostics lab [28]; samples collected at MD Anderson, The Ohio State University Medical Center, and University of California, San Francisco Medical Center were analyzed at Foundation Medicine [29].”
Method
EGFR Kinase Domain Duplication ( EGFR -KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib
Gallant, J., Sheehan, J. H., Shaver, T. M., Bailey, M., Lipson, D., Chandramohan, R., Brewer, M. R., York, S. J., Kris, M. G., Pietenpol, J. A., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0654 · Cited by 128
Precision Oncology Medicine: The Clinical Relevance of Patient‐Specific Biomarkers Used to Optimize Cancer Treatment
Schmidt, K. T., Chau, C. H., Price, D. K., & Figg, W. D. (2016) · The Journal of Clinical Pharmacology · doi:10.1002/jcph.765 · Cited by 129
RET rearrangements are actionable alterations in breast cancer
Paratala, B., Chung, J., Williams, C. B., Yilmazel, B., Petrosky, W., Williams, K. A., Schrock, A. B., Gay, L. M., Lee, E. C., Dolfi, S. C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07341-4 · Cited by 124
Integration of cell of origin into the clinical CNS International Prognostic Index improves CNS relapse prediction in DLBCL
Klánová, M., Sehn, L. H., Bence‐Bruckler, I., Cavallo, F., Jin, J., Martelli, M., Stewart, D. A., Vitolo, U., Zaja, F. F., Zhang, Q., et al. (2019) · Blood · doi:10.1182/blood-2018-07-862862 · Cited by 134
Loss of function JAK1 mutations occur at high frequency in cancers with microsatellite instability and are suggestive of immune evasion
Albacker, L. A., Wu, J., Smith, P. G., Warmuth, M., Stephens, P. J., Zhu, P., Yu, L., & Chmielecki, J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176181 · Cited by 128
Successful Treatment of HIV-Associated Kaposi Sarcoma with Immune Checkpoint Blockade
Galanina, N., Goodman, A. M., Cohen, P. R., Frampton, G. M., & Kurzrock, R. (2018) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0121 · Cited by 126
“Average sequencing depth of coverage was greater than 250 , with >100 at >99% of exons (16).”
BackgroundMethod
Biomarker-driven therapies for previously treated squamous non-small-cell lung cancer (Lung-MAP SWOG S1400): a biomarker-driven master protocol
Redman, M. W., Papadimitrakopoulou, V. A., Minichiello, K., Hirsch, F. R., Mack, P. C., Schwartz, L. H., Vokes, E. E., Ramalingam, S. S., Leighl, N. B., Bradley, J. D., et al. (2020) · The Lancet Oncology · doi:10.1016/s1470-2045(20)30475-7 · Cited by 129
Defining actionable mutations for oncology therapeutic development
Carr, T. H., McEwen, R. K., Dougherty, B. A., Johnson, J. H., Dry, J. R., Lai, Z., Ghazoui, Z. F., Laing, N. M., Hodgson, D., Cruzalegui, F. H., et al. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2016.35 · Cited by 128
Genomic profiling of ER + breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance
Giltnane, J. M., Hutchinson, K. E., Stricker, T. P., Formisano, L., Young, C. D., Estrada, M. V., Nixon, M. J., Du, L., Sanchez, V. M., Ericsson, P. I. G., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aai7993 · Cited by 126
Targeted Therapies for Targeted Populations: Anti-EGFR Treatment for EGFR -Amplified Gastroesophageal Adenocarcinoma
Maron, S. B., Alpert, L., Kwak, H. A., Lomnicki, S., Chase, L. M., Xu, D., O’Day, E., Nagy, R. J., Lanman, R. B., Cecchi, F., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1260 · Cited by 128
“Number of patients (%) 8 (6) 132 (94) < 2.”
MethodInfluential
Profiling of 149 Salivary Duct Carcinomas, Carcinoma Ex Pleomorphic Adenomas, and Adenocarcinomas, Not Otherwise Specified Reveals Actionable Genomic Alterations
Wang, K., Russell, J. S., McDermott, J. D., Elvin, J. A., Khaira, D., Johnson, A., Jennings, T. A., Ali, S. M., Murray, M., Marshall, C. B., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2568 · Cited by 123
“Captured libraries were sequenced to amedian exon coverage depthof 600 for up to 315 genes, and resultant sequences were analyzed for base substitutions, short insertions/deletions, copy number alterations (focal amplifications and homozygous deletions), and gene fusions/ rearrangements, as described previously (14).”
Background
Oncogenic ALK Fusion in Rare and Aggressive Subtype of Colorectal Adenocarcinoma as a Potential Therapeutic Target
Yakirevich, E., Resnick, M. B., Mangray, S., Wheeler, M., Jackson, C. L., Lombardo, K. A., Lee, J., Kim, K., Gill, A. J., Wang, K., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-3000 · Cited by 124
“Sequence reads were mapped to the reference human genome (hg19) and analyzed for genomic alterations including base substitutions, small insertions and deletions (indels), copy number alterations (amplifications and homozygous deletions), and select gene fusions/rearrangements as previously described (20).”
MethodResult
Computational analysis of cancer genome sequencing data
Cortés‐Ciriano, I., Gulhan, D., Lee, J. J.-K., Melloni, G. E. M., & Park, P. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00431-y · Cited by 118
“For FFPE samples, specialized experimental protocols and algorithms must be used for variant detection 118–121 .”
Method
Truncated FGFR2 is a clinically actionable oncogene in multiple cancers
Zingg, D., Bhin, J., Yemelyanenko, J., Kas, S. M., Rolfs, F., Lutz, C., Lee, J., Klarenbeek, S., Silverman, I. M., Annunziato, S., et al. (2022) · Nature · doi:10.1038/s41586-022-05066-5 · Cited by 124
Open source machine-learning algorithms for the prediction of optimal cancer drug therapies
Huang, C., Mezencev, R., McDonald, J. F., & Vannberg, F. O. (2017) · PLoS ONE · doi:10.1371/journal.pone.0186906 · Cited by 119
Molecular pathology of lung cancer: current status and perspectives
Oberndorfer, F., & Müllauer, L. (2017) · Current Opinion in Oncology · doi:10.1097/cco.0000000000000429 · Cited by 122
Salivary Secretory Carcinoma With a Novel ETV6-MET Fusion
Rooper, L. M., Karantanos, T., Ning, Y., Bishop, J. A., Gordon, S. W., & Kang, H. (2018) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001065 · Cited by 120
A phase 1 study of veliparib, a PARP-1/2 inhibitor, with gemcitabine and radiotherapy in locally advanced pancreatic cancer
Tuli, R., Shiao, S. L., Nissen, N. N., Tighiouart, M., Kim, S., Osipov, A., Bryant, M., Ristow, L., Placencio-Hickok, V., Hoffman, D., et al. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2018.12.060 · Cited by 120
“NGS was available for 26 of 30 patients (87%; Table 5) [13].”
Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes
Zhao, T., & Schranz, M. E. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1801757116 · Cited by 120
Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling
Pal, S. K., Choueiri, T. K., Wang, K., Khaira, D., Karam, J. A., Allen, E. M. V., Palma, N. A., Stein, M. N., Johnson, A., Squillace, R. M., et al. (2015) · European Urology · doi:10.1016/j.eururo.2015.06.019 · Cited by 120
Targeting FGFR for cancer therapy
Zhang, P., Yue, L., Leng, Q., Chen, C., Gan, C., Ye, T., & Cao, D. (2024) · Journal of Hematology & Oncology · doi:10.1186/s13045-024-01558-1 · Cited by 130
“Targeted NGS panels, focusing on specific genes or gene regions, have been developed for comprehensive FGFR profiling [85].”
Background
Systematic discovery of complex insertions and deletions in human cancers
Ye, K., Wang, J., Jayasinghe, R. G., Lameijer, E.-W., McMichael, J. F., Ning, J., McLellan, M. D., Xie, M., Cao, S., Yellapantula, V. D., et al. (2015) · Nature Medicine · doi:10.1038/nm.4002 · Cited by 118
“A subset of 518 genes originated from recent publications, including 294 genes from Frampton et al. 24 , 125 genes from Kandoth et al. 26 , 212 genes from Lawrence et al. 27 , 194 genes from Pritchard et al. 28 , 124 genes from Vogelstein et al. 31 , 48 genes from Rahman et al., 29 and 48 from Kanchi et al. 25 .”
Characterization of Clinical Cases of Advanced Papillary Renal Cell Carcinoma via Comprehensive Genomic Profiling
Pal, S. K., Ali, S. M., Yakirevich, E., Geynisman, D. M., Karam, J. A., Elvin, J. A., Frampton, G. M., Huang, X., Lin, D. I., Rosenzweig, M. R., et al. (2017) · European Urology · doi:10.1016/j.eururo.2017.05.033 · Cited by 119
Avelumab maintenance in advanced urothelial carcinoma: biomarker analysis of the phase 3 JAVELIN Bladder 100 trial
Powles, T. B., Sridhar, S. S., Loriot, Y., Joaquim Bellmunt, B., Mu, X. J., Ching, K. A., Pu, J., Sternberg, C. N., Petrylak, D. P., Tambaro, R., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01579-0 · Cited by 116
Comprehensive Genomic Profiling Identifies a Subset of Crizotinib-Responsive ALK -Rearranged Non-Small Cell Lung Cancer Not Detected by Fluorescence In Situ Hybridization
Ali, S. M., Hensing, T. A., Schrock, A. B., Allen, J. M., Sanford, E. M., Gowen, K. A., Kulkarni, A., He, J., Suh, J. H., Lipson, D., et al. (2016) · The Oncologist · doi:10.1634/theoncologist.2015-0497 · Cited by 119
“, base-pair substitutions, insertions/deletions, copy number alterations and rearrangements), and then matches all clinically relevant alterations to potential targeted treatment options [8].”
Background
Image-Guided Biopsy in the Era of Personalized Cancer Care: Proceedings from the Society of Interventional Radiology Research Consensus Panel
Tam, A. L., Lim, H. J., Wistuba, I. I., Tamrazi, A., Kuo, M. D., Ziv, E., Wong, S. T. C., Shih, A. J., Webster, R. J., III, Fischer, G. S., et al. (2015) · Journal of Vascular and Interventional Radiology · doi:10.1016/j.jvir.2015.10.019 · Cited by 120
Development of genome-derived tumor type prediction to inform clinical cancer care
Penson, A., Camacho, N., Zheng, Y., Varghese, A. M., Al-Ahmadie, H., Razavi, P., Chandarlapaty, S., Vallejo, C. E., Vakiani, E., Gilewski, T., et al. (2020) · JAMA Oncology · doi:10.1001/jamaoncol.2019.3985 · Cited by 115
Self-citation
Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non–Small-Cell Lung Cancer
Vokes, N. I., Liu, D., Ricciuti, B., Jimenez-Aguilar, E., Rizvi, H. A., Dietlein, F., He, M., Margolis, C. A., Elmarakeby, H., Girshman, J., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.19.00171 · Cited by 112
“Med age at diagnosis (range) 65 (24-90) Med age at diagnosis (range) 66 (22-92)”
Background
Genomic landscape of pleural and peritoneal mesothelioma tumours
Hiltbrunner, S., Fleischmann, Z., Sokol, E. S., Zoche, M., Felley‐Bosco, E., & Fontecedro, A. C. (2022) · British Journal of Cancer · doi:10.1038/s41416-022-01979-0 · Cited by 125
A Blood-based Assay for Assessment of Tumor Mutational Burden in First-line Metastatic NSCLC Treatment: Results from the MYSTIC Study
Si, H., Kuziora, M. A., Quinn, K., Helman, E., Ye, J., Liu, F., Scheuring, U. J., Peters, S., Rizvi, N. A., Brohawn, P. Z., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3771 · Cited by 113
Liquid biopsy for therapy monitoring in early-stage non-small cell lung cancer
Nagasaka, M., Uddin, M. H., Hallak, M. N. A., Rahman, S. B., Balasubramanian, S. K., Sukari, A. W., & Azmi, A. S. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01371-1 · Cited by 116
Rucaparib for the Treatment of Metastatic Castration-resistant Prostate Cancer Associated with a DNA Damage Repair Gene Alteration: Final Results from the Phase 2 TRITON2 Study
Abida, W. M., Campbell, D. C., Patnaik, A., Bryce, A. H., Shapiro, J. D., Bambury, R. M., Zhang, J., Burke, J. M., Castellano, D., Pous, A. F., et al. (2023) · European Urology · doi:10.1016/j.eururo.2023.05.021 · Cited by 119
Concordance between genomic alterations assessed by next-generation sequencing in tumor tissue or circulating cell-free DNA
Chae, Y. K., Davis, A. A., Carneiro, B. A., Chandra, S., Mohindra, N., Kalyan, A., Kaplan, J., Matsangou, M., Pai, S., Costa, R., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.11692 · Cited by 110
“Of these, 29 patients had comprehensive tissue NGS testing (FoundationOne) commercially performed by Foundation Medicine (Cambridge, MA) [26].”
Method
A pan-cancer analysis of PD-L1 immunohistochemistry and gene amplification, tumor mutation burden and microsatellite instability in 48,782 cases
Huang, R. S. P., Haberberger, J., Severson, E. A., Duncan, D. L., Hemmerich, A. C., Edgerly, C. I., Ferguson, N. L., Williams, E. A., Elvin, J. A., Vergilio, J., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-00664-y · Cited by 114
Pan-cancer proteogenomics connects oncogenic drivers to functional states
Li, Y., Porta‐Pardo, E., Tokheim, C. J., Bailey, M. H., Yaron, T. M., Stathias, V., Geffen, Y., Imbach, K. J., Cao, S., Anand, S. K., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.014 · Cited by 124
“Subsequently, the FDA has approved the testing of broad gene panels to reveal clinically actionable variants,(70) where specific alterations are matched with targeted therapies.(71,72) These developments have spurred analyses of molecular underpinnings of pan-cancer drivers.”
Clinical benefit of a precision medicine based approach for guiding treatment of refractory cancers
Radovich, M., Kiel, P. J., Nance, S. M., Niland, E. E., Parsley, M. E., Ferguson, M. E., Jiang, G., Ammakkanavar, N. R., Einhorn, L. H., Cheng, L., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.10606 · Cited by 111
“Of note, one patient in our study received testing using the FoundationOne test, whose methods are described elsewhere [26].”
Method
SMARCA4-deficient Uterine Sarcoma and Undifferentiated Endometrial Carcinoma Are Distinct Clinicopathologic Entities
Kolin, D. L., Quick, C. M., Dong, F., Fletcher, C. D. �., Stewart, C. J. R., Soma, A., Hornick, J. L., Nucci, M. R., & Howitt, B. E. (2019) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001375 · Cited by 111
Distinct genomic subclasses of high-grade/progressive meningiomas: NF2-associated, NF2-exclusive, and NF2-agnostic
Williams, E. A., Santagata, S., Wakimoto, H., Shankar, G. M., Barker, F. G., Sharaf, R. R., Reddy, A. K., Spear, P., Alexander, B. M., Ross, J. S., et al. (2020) · Acta Neuropathologica Communications · doi:10.1186/s40478-020-01040-2 · Cited by 111
Addition of camrelizumab to docetaxel, cisplatin, and radiation therapy in patients with locally advanced esophageal squamous cell carcinoma: a phase 1b study
Zhang, W., Yan, C., Zhang, T., Chen, X., Dong, J., Zhao, J., Han, D., Wang, J., Zhao, G., Cao, F., et al. (2021) · OncoImmunology · doi:10.1080/2162402x.2021.1971418 · Cited by 111
A First-in-Human Phase 1 Study of LY3023414, an Oral PI3K/mTOR Dual Inhibitor, in Patients with Advanced Cancer
Bendell, J. C., Varghese, A. M., Hyman, D. M., Bauer, T. M., Pant, S., Callies, S., Lin, J., Martínez, R., Wickremsinhe, E. R., Fink, A. A., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-3421 · Cited by 110
“2 (13) 245 (22) 36 (2) 1; 2 807; 810 3708; 2640 3.”
Method
Tumor Mutational Burden, Toxicity, and Response of Immune Checkpoint Inhibitors Targeting PD(L)1, CTLA-4, and Combination: A Meta-regression Analysis
Osipov, A., Lim, S. J., Popović, A., Azad, N. S., Laheru, D. A., Zheng, L., Jaffee, E. M., Wang, H., & Yarchoan, M. M. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-0458 · Cited by 115
“Details of the assay have been previously reported, which estimates the total number of somatic, coding mutations (including synonymous and nonsynonymous mutations and short indels) per megabase of tumor genome (23).”
Background
Comprehensive genomic profiles of metastatic and relapsed salivary gland carcinomas are associated with tumor type and reveal new routes to targeted therapies
Ross, J. S., Gay, L. M., Wang, K., Vergilio, J., Suh, J. H., Ramkissoon, S. H., Somerset, H., Johnson, J. M., Russell, J. S., Ali, S. M., et al. (2017) · Annals of Oncology · doi:10.1093/annonc/mdx399 · Cited by 109
“Full methods can be found in the supplementary Methods, available at Annals of Oncology online, and have been described previously [9].”
Method
Identification of somatic genetic alterations in ovarian clear cell carcinoma with next generation sequencing
Shibuya, Y., Tokunaga, H., Saito, S., Shimokawa, K., Katsuoka, F., Li, B., Kojima, K., Nagasaki, M., Yamamoto, M. P., Yaegashi, N., et al. (2017) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22507 · Cited by 112
MHC-I genotype and tumor mutational burden predict response to immunotherapy
Goodman, A. M., Castro, A., Pyke, R. M., Okamura, R., Kato, S., Riviere, P. J., Frampton, G. M., Sokol, E. S., Zhang, X., Ball, E. D., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00743-4 · Cited by 112
Pharmacokinetic, pharmacodynamic and biomarker evaluation of transforming growth factor-β receptor I kinase inhibitor, galunisertib, in phase 1 study in patients with advanced cancer
Rodon, J. A., Carducci, M. A., Sepúlveda-Sánchez, J. M., Azaro, A., Calvo, E., Seoane, J., Braña, I., Sicart, E., Gueorguieva, I., Cleverly, A., et al. (2014) · Investigational New Drugs · doi:10.1007/s10637-014-0192-4 · Cited by 108
“As previously described, an MAIP was used [13] to determine plasma protein levels at baseline.”
Method
Enabling a Genetically Informed Approach to Cancer Medicine: A Retrospective Evaluation of the Impact of Comprehensive Tumor Profiling Using a Targeted Next-Generation Sequencing Panel
Johnson, D. B., Dahlman, K. H., Knol, J., Gilbert, J., Puzanov, I. J., Means-Powell, J. A., Balko, J. M., Lovly, C. M., Murphy, B. A., Goff, L. W., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2014-0011 · Cited by 109

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

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