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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The Sequence Alignment/Map format and SAMtools
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Microsatellite-Stable Tumors with High Mutational Burden Benefit from Immunotherapy
Goodman, A. M., Sokol, E. S., Frampton, G. M., Lippman, S. M., & Kurzrock, R. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-19-0149 · Cited by 310
“The average sequencing depth of coverage was greater than 250 , with >100 at >99% of exons (12).”
Background
Open-Label, Multicenter, Phase II Study of Ceritinib in Patients With Non–Small-Cell Lung Cancer Harboring ROS1 Rearrangement
Lim, S. M., Kim, H. R., Lee, J.-S., Lee, K. H., Lee, Y., Min, Y. J., Cho, E. K., Lee, S. S., Kim, B.-S., Choi, M. Y., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2016.71.3701 · Cited by 315
Molecular classification and therapeutic targets in extrahepatic cholangiocarcinoma
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Patterns and functional implications of rare germline variants across 12 cancer types
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Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy
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“Genomic profiling of the resected tumor was performed by Foundation Medicine (Cambridge, MA)(16), and of the 315 genes assessed, 165 (52.”
Method
Candidate mechanisms of acquired resistance to first-line osimertinib in EGFR-mutated advanced non-small cell lung cancer
Chmielecki, J., Gray, J. E., Cheng, Y., Ohe, Y., Imamura, F., Cho, B. C., Lin, M., Majem, M., Shah, R. N. H., Rukazenkov, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35961-y · Cited by 298
RET Aberrations in Diverse Cancers: Next-Generation Sequencing of 4,871 Patients
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“Samples were required to have a surface area 25 mm(2), volume 1 mm(3), nucleated cellularity 80%, and tumor content 20% (28).”
BackgroundMethod
The Promises and Challenges of Tumor Mutation Burden as an Immunotherapy Biomarker: A Perspective from the International Association for the Study of Lung Cancer Pathology Committee
Sholl, L. M., Hirsch, F. R., Hwang, D. M., Botling, J., López‐Ríos, F., Bubendorf, L., Mino-Kenudson, M. A., Roden, A. C., Beasley, M. B., Borczuk, A., et al. (2020) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2020.05.019 · Cited by 286
Clinicogenomic Analysis of FGFR2 -Rearranged Cholangiocarcinoma Identifies Correlates of Response and Mechanisms of Resistance to Pemigatinib
Silverman, I. M., Hollebecque, A., Friboulet, L., Owens, S. L., Newton, R. C., Zhen, H., Féliz, L. R., Zecchetto, C., Melisi, D., & Burn, T. C. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0766 · Cited by 293
“), which uses hybrid capture–based DNA target enrichment to identify somatic GAs in the coding regions of 315 cancer-related genes and introns from 28 genes often rearranged in cancer (12).”
Background
Cell-free DNA next-generation sequencing in pancreatobiliary carcinomas
Zill, O. A., Greene, C., Sebisanovic, D., Siew, L. M., Leng, J., Vu, M., Hendifar, A. E., Wang, Z., Atreya, C. E., Kelley, R. K., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0274 · Cited by 282
“considerably higher than the average QNS rate reported by commercial vendors across multiple tumor types(24).”
BackgroundMethod
Patient-centric trials for therapeutic development in precision oncology
Biankin, A. V., Piantadosi, S., & Hollingsworth, S. J. (2015) · Nature · doi:10.1038/nature15819 · Cited by 286
Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion
Chakravarty, D., Johnson, A., Sklar, J., Lindeman, N. I., Moore, K. N., Ganesan, S., Lovly, C. M., Perlmutter, J., Gray, S. W., Hwang, J., et al. (2022) · Journal of Clinical Oncology · doi:10.1200/jco.21.02767 · Cited by 301
Upfront FOLFOXIRI plus Bevacizumab with or without Atezolizumab in the Treatment of Patients with Metastatic Colorectal Cancer (AtezoTRIBE): A Multicentre, Open-Label, Randomised, Controlled, Phase 2 Trial
Antoniotti, C., Rossini, D., Pietrantonio, F., Catteau, A., Salvatore, L., Lonardi, S., Boquet, I., Tamberi, S., Marmorino, F., Moretto, R., et al. (2022) · The Lancet Oncology · doi:10.1016/s1470-2045(22)00274-1 · Cited by 280
Broad, Hybrid Capture–Based Next-Generation Sequencing Identifies Actionable Genomic Alterations in Lung Adenocarcinomas Otherwise Negative for Such Alterations by Other Genomic Testing Approaches
Drilon, A., Wang, L., Arcila, M. E., Balasubramanian, S., Greenbowe, J. R., Ross, J. S., Stephens, P., Lipson, D., Miller, V. A., Kris, M. G., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2683 · Cited by 274
“The type ofNGS assay used in the present study offers the advantage of more comprehensive genomic characterization using as low as 50 ng of DNA, which can be obtained from lung cancer specimens with sufficient tumor content using core biopsy needles on average or a carefully prepared fine needle aspiration (32, 33).”
Method
Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing
Samorodnitsky, E., Jewell, B. M., Hagopian, R., Miya, J., Wing, M. R., Lyon, E., Damodaran, S., Bhatt, D., Reeser, J. W., Datta, J., et al. (2015) · Human Mutation · doi:10.1002/humu.22825 · Cited by 271
“We examined specifically high-level copy gains and losses [Frampton et al., 2013; Pritchard et al., 2014] and therefore removed bases whose sequencing log2–CNV ratio was between –0.”
Background
A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal
Sun, J., He, Y., Sanford, E. M., Montesion, M., Frampton, G. M., Vignot, S., Soria, J., Ross, J. S., Miller, V. A., Stephens, P. J., et al. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005965 · Cited by 273
“Further evidence of germline origin was that most variants had an entry in dbSNP, though few were classified as common SNPs.”
MethodInfluential
Nucleic Acid Tests for Clinical Translation
Li, M., Yin, F., Song, L., Mao, X., Li, F., Fan, C., Zuo, X., & Xia, Q. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00241 · Cited by 274
Molecular classification of breast cancer
Vuong, D., Simpson, P. T., Green, B., Cummings, M. C., & Lakhani, S. R. (2014) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-014-1593-7 · Cited by 299
STAT3 antisense oligonucleotide AZD9150 in a subset of patients with heavily pretreated lymphoma: results of a phase 1b trial
Reilley, M. J., McCoon, P., Cook, C., Lyne, P., Kurzrock, R., Kim, Y., Woessner, R., Younes, A., Nemunaitis, J., Fowler, N., et al. (2018) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-018-0436-5 · Cited by 245
Beyond ALK-RET, ROS1 and other oncogene fusions in lung cancer.
Kohno, T., Nakaoku, T., Tsuta, K., Tsuchihara, K., Matsumoto, S., Yoh, K., & Goto, K. (2015) · PubMed Central · doi:10.3978/j.issn.2218-6751.2014.11.11 · Cited by 263
“Some employ the method of target re-sequencing of tens to hundreds of genes using DNA or RNA extracted from tumor tissues (47,48), while others employ quantitative RT-PCR or RNA molecule counting (21,49,50).”
Method
Beyond microsatellite testing: assessment of tumor mutational burden identifies subsets of colorectal cancer who may respond to immune checkpoint inhibition
Fabrizio, D. A., George, T. J., Dunne, R. F., Frampton, G. M., Sun, J. X., Gowen, K. A., Kennedy, M., Greenbowe, J. R., Schrock, A. B., Hezel, A. F., et al. (2018) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo.2018.05.06 · Cited by 266
“Beyond TMB, it is important to note that MSI determination by NGS is not considered standard, however, mounting published data suggests excellent agreement with standard IHC and PCR methods (manuscript under review) (18).”
Method
Efficacy of BGJ398, a Fibroblast Growth Factor Receptor 1–3 Inhibitor, in Patients with Previously Treated Advanced Urothelial Carcinoma with FGFR3 Alterations
Pal, S. K., Rosenberg, J. E., Hoffman-Censits, J. H., Berger, R., Quinn, D. I., Galsky, M. D., Wolf, J., Dittrich, C., Keam, B., Delord, J., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0229 · Cited by 263
“16 methods.(24) FGFR3 mutations permitted in the study included mutations in exon 7 (R248C, S249C), exon 10 (G372C, A393E, Y375C), or exon 15 (K652M/T, K652E/Q).”
Background
RET fusions in solid tumors
Li, A. Y., McCusker, M. G., Russo, A., Scilla, K. A., Gittens, A., Arensmeyer, K. E., Mehra, R., Adamo, V., & Rolfo, C. D. (2019) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2019.101911 · Cited by 259
Next Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer
Morganti, S., Tarantino, P., Ferraro, E., D’Amico, P., Duso, B. A., & Curigliano, G. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-3-030-24100-1_2 · Cited by 246
Somatic HLA Class I Loss Is a Widespread Mechanism of Immune Evasion Which Refines the Use of Tumor Mutational Burden as a Biomarker of Checkpoint Inhibitor Response
Montesion, M., Murugesan, K., Jin, D. X., Sharaf, R., Sánchez, N., Guria, A., Minker, M., Li, G., Fisher, V. A., Sokol, E. S., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0672 · Cited by 253
“Analysis for genomic alterations, including short variant alterations (base substitutions, insertions, and deletions), copy-number alterations (amplifications and homozygous deletions), as well as gene rearrangements, was performed as previously described (22, 23).”
Method
Correlative Analysis of Genetic Alterations and Everolimus Benefit in Hormone Receptor–Positive, Human Epidermal Growth Factor Receptor 2–Negative Advanced Breast Cancer: Results From BOLERO-2
Hortobágyi, G. N., Chen, D. J., Piccart, M. J., Rugo, H. S., Burris, H. A., Pritchard, K. I., Campone, M., Noguchi, S., Perez, A., Deleu, I., et al. (2015) · Journal of Clinical Oncology · doi:10.1200/jco.2014.60.1971 · Cited by 256
“Tumor DNA preparation, library construction, hybrid capture, and sequencing were previously described.(10) Samples with a minimum unique coverage of 2503 were evaluated in the subsequent data analysis.”
Method
Prevalence ofPDL1Amplification and Preliminary Response to Immune Checkpoint Blockade in Solid Tumors
Goodman, A. M., Piccioni, D. E., Kato, S., Boichard, A., Wang, H., Frampton, G. M., Lippman, S. M., Connelly, C. F., Fabrizio, D. A., Miller, V. A., et al. (2018) · JAMA Oncology · doi:10.1001/jamaoncol.2018.1701 · Cited by 250
“Sequencingwasperformed fromOctober 1, 2012, to October 1, 2017.(24) PDL1 amplification was performed for 6 or more CNAs.”
Comprehensive Genomic Profiling of Carcinoma of Unknown Primary Site
Ross, J. S., Wang, K., Gay, L. M., Otto, G. A., White, E. T., Iwanik, K., Palmer, G. A., Yelensky, R., Lipson, D., Chmielecki, J., et al. (2015) · JAMA Oncology · doi:10.1001/jamaoncol.2014.216 · Cited by 248
Lung Master Protocol (Lung-MAP)—A Biomarker-Driven Protocol for Accelerating Development of Therapies for Squamous Cell Lung Cancer: SWOG S1400
Herbst, R. S., Gandara, D. R., Hirsch, F. R., Redman, M. W., LeBlanc, M. L., Mack, P. C., Schwartz, L. H., Vokes, E. E., Ramalingam, S. S., Bradley, J. D., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-3473 · Cited by 247
“…are defined by specific genomic alterations (mutations, amplifications, rearrangements) detected by NGS using the FMI FoundationOne platform (28), supplemented with immunohistochemistry assays (to detect over-expression of the actionable target) or other methodologies as appropriate,…”
Extended follow-up and impact of high-risk prognostic factors from the phase 3 RESONATE study in patients with previously treated CLL/SLL
Brown, J. R., Hillmen, P., O’Brien, S. J., Barrientos, J. C., Reddy, N. M., Coutre, S. E., Tam, C. S. L., Mulligan, S. P., Jaeger, U., Barr, P. M., et al. (2017) · Leukemia · doi:10.1038/leu.2017.175 · Cited by 244
Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group
Mandelker, D. L., Donoghue, M. T. A., Talukdar, S., Bandlamudi, C., Srinivasan, P., Vivek, M., Jezdic, S., Hanson, H., Snape, K. M. G., Kulkarni, A., et al. (2019) · Annals of Oncology · doi:10.1093/annonc/mdz136 · Cited by 242
Diverse EGFR Exon 20 Insertions and Co-Occurring Molecular Alterations Identified by Comprehensive Genomic Profiling of NSCLC
Riess, J. W., Gandara, D. R., Frampton, G. M., Madison, R., Peled, N., Bufill, J. A., Dy, G. K., Ou, S.-H. I., Stephens, P. J., McPherson, J. D., et al. (2018) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2018.06.019 · Cited by 240
“TMB intermediate high (10-20) 3325 (26) 82 (6.”
Self-citation
Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions
Stenzinger, A., Allen, J. D., Maas, J., Stewart, M. D., Merino, D. M., Wempe, M. M., & Dietel, M. (2019) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22733 · Cited by 245
Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study
Wheler, J. J., Jankú, F., Naing, A., Li, Y., Stephen, B., Zinner, R., Subbiah, V., Fu, S., Karp, D. D., Falchook, G. S., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-3043 · Cited by 241
Multi‑layered prevention and treatment of chronic inflammation, organ fibrosis and cancer associated with canonical WNT/β‑catenin signaling activation (Review)
Katoh, M. (2018) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2018.3689 · Cited by 251
“Genomics-based testing platforms, including MSK-IMPAcT (43), FoundationOne (163) and Oncomine comprehensive Panel (164), and organoid-or PdX-based drug screening (165-167) are useful tools for the prescription of targeted therapeutics; however, there remain unmet medical needs for patients with refractory cancer drive…”
FGFR1 and NTRK3 actionable alterations in “Wild-Type” gastrointestinal stromal tumors
Shi, E., Chmielecki, J., Tang, C., Wang, K., Heinrich, M. C., Kang, G., Corless, C. L., Hong, D. S., Fero, K. E., Murphy, J. D., et al. (2016) · Journal of Translational Medicine · doi:10.1186/s12967-016-1075-6 · Cited by 236
First-in-Human Dose Study of the Novel Transforming Growth Factor-β Receptor I Kinase Inhibitor LY2157299 Monohydrate in Patients with Advanced Cancer and Glioma
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) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-1380 · Cited by 239
“8 Where sufficient tumor tissue was available, 287 cancer-related genes were assessed for somatic variants using massive parallel sequencing methods to identify base substitutions, short insertions and deletions, and copy number changes (Foundation Medicine, NY) (23, 24).”
Comprehensive Genomic Landscapes in Early and Later Onset Colorectal Cancer
Lieu, C. H., Golemis, E. A., Serebriiskii, I. G., Newberg, J. Y., Hemmerich, A. C., Connelly, C. F., Messersmith, W. A., Eng, C., Eckhardt, S. G., Frampton, G. M., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-0899 · Cited by 234
“Statistical analysis Sequence data were evaluated for GAs including point mutations, insertions and deletions, copy number alterations, and select gene fusions/rearrangements, as described previously (18).”
Method
Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer
Rothé, F., Laes, J., Lambrechts, D., Smeets, D., Vincent, D., Maetens, M., Fumagalli, D., Michiels, S., Drisis, S., Moerman, C., et al. (2014) · Annals of Oncology · doi:10.1093/annonc/mdu288 · Cited by 235
“In contrast, molecular screening using tumor tissue often analyzes a much higher number of genes [13].”
Background
Candidate biomarkers of PARP inhibitor sensitivity in ovarian cancer beyond the BRCA genes
Hodgson, D., Dougherty, B. A., Lai, Z., Fielding, A., Grinsted, L. M., Spencer, S., O’Connor, M. J., Ho, T. W., Robertson, J. D., Lanchbury, J. S. S., et al. (2018) · British Journal of Cancer · doi:10.1038/s41416-018-0274-8 · Cited by 233
“Specifically, analysis was not performed with the commercially available Foundation Focus diagnostic test but with the Foundation Medicine T5 panel (entire coding sequence of 287 cancerrelated genes plus select introns from 27 genes and other genetic alterations, deletions and functional rearrangements) at Foundation…”
Method
Frequency of Germline Mutations in Cancer Susceptibility Genes in Malignant Mesothelioma
Panou, V., Gadiraju, M., Wolin, A. R., Weipert, C. M., Skarda, E., Husain, A. N., Patel, J. D., Rose, B., Zhang, S. R., Weatherly, M., et al. (2018) · Journal of Clinical Oncology · doi:10.1200/jco.2018.78.5204 · Cited by 228
Biomarker-Guided Development of DNA Repair Inhibitors
Cleary, J. M., Aguirre, A. J., Shapiro, G. I., & D’Andrea, A. D. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.035 · Cited by 239
Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors
Chen, F., Zou, Z., Du, J., Su, S., Shao, J., Meng, F., Yang, J. D., Xu, Q., Ding, N., Yang, Y., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci99538 · Cited by 233
“Mutations identified in targeted sequencing panels that query a subset of cancer-related genes have been widely implicated in cancer biology or clinical management (21, 31–34).”
Background
Clinicopathological features, treatment approaches, and outcomes in Rosai-Dorfman disease
Goyal, G., Ravindran, A., Young, J. R., Shah, M. V., Bennani, N. N., Patnaik, M. M., Nowakowski, G. S., Thanarajasingam, G., Habermann, T. M., Vassallo, R., et al. (2019) · Haematologica · doi:10.3324/haematol.2019.219626 · Cited by 229
Dynamic variations in epithelial-to-mesenchymal transition (EMT), ATM, and SLFN11 govern response to PARP inhibitors and cisplatin in small cell lung cancer
Stewart, C. A., Tong, P., Cardnell, R. J., Sen, T., Li, L., Gay, C. M., Masrorpour, F., Fan, Y. H., Bara, R. O., Feng, Y., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.15338 · Cited by 232
Genomic Profiling of Small-Bowel Adenocarcinoma
Schrock, A. B., Devoe, C., McWilliams, R. R., Sun, J. X., Aparicio, T., Stephens, P. J., Ross, J. S., Wilson, R. H., Miller, V. A., Ali, S. M., et al. (2017) · JAMA Oncology · doi:10.1001/jamaoncol.2017.1051 · Cited by 232
“Age, median (range), y 60 (18-86) 56 (13-101) 58 (12-88)”
Genomic and Epigenomic Alterations in Cancer
Chakravarthi, B. V. S. K., Nepal, S., & Varambally, S. (2016) · American Journal Of Pathology · doi:10.1016/j.ajpath.2016.02.023 · Cited by 232
A Novel Next-Generation Sequencing Approach to Detecting Microsatellite Instability and Pan-Tumor Characterization of 1000 Microsatellite Instability–High Cases in 67,000 Patient Samples
Trabucco, S. E., Gowen, K. A., Maund, S. L., Sanford, E. M., Fabrizio, D. A., Hall, M. J., Yakirevich, E., Gregg, J. P., Stephens, P. J., Frampton, G. M., et al. (2019) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2019.06.011 · Cited by 229
“, Cambridge, MA) for hybrid capture, followed by nextgeneration sequencing.(22) For samples submitted for FoundationOne testing (n Z 61,731), 395 cancer genes, 315 of which are reported clinically, were sequenced on DNA, covering 2.”
Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors
Hovelson, D. H., McDaniel, A. S., Cani, A. K., Johnson, B., Rhodes, K., Williams, P. D., Bandla, S., Bien, G., Choppa, P., Hyland, F., et al. (2015) · Neoplasia · doi:10.1016/j.neo.2015.03.004 · Cited by 224
“Large companies have also been established with the goal of providing comprehensive NGS-based precision oncology services [18]; however, interpretation of results and prioritizing treatment strategiesmay still be outsourced.”
BackgroundInfluential
Circulating Tumor DNA Mutation Profiling by Targeted Next Generation Sequencing Provides Guidance for Personalized Treatments in Multiple Cancer Types
Shu, Y., Wu, X., Tong, X., Wang, X., Chang, Z., Mao, Y., Chen, X., Sun, J., Wang, Z., Hong, Z., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-00520-1 · Cited by 226
Clinicopathologic Features of Non–Small-Cell Lung Cancer Harboring an NTRK Gene Fusion
Farago, A. F., Taylor, M. S., Doebele, R. C., Zhu, V. W., Kummar, S., Spira, A. I., Boyle, T. A., Haura, E. B., Arcila, M. E., Benayed, R., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.18.00037 · Cited by 234
Comprehensive characterization of RAS mutations in colon and rectal cancers in old and young patients
Serebriiskii, I. G., Connelly, C., Frampton, G., Newberg, J., Cooke, M., Miller, V., Ali, S., Ross, J. S., Handorf, E., Arora, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11530-0 · Cited by 215
BRAF Mutant Lung Cancer: Programmed Death Ligand 1 Expression, Tumor Mutational Burden, Microsatellite Instability Status, and Response to Immune Check-Point Inhibitors
Dudnik, E., Peled, N., Nechushtan, H., Wollner, M., Onn, A., Agbarya, A., Moskovitz, M. T., Keren, S., Popovits‐Hadari, N., Urban, D., et al. (2018) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2018.04.024 · Cited by 221
Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome
Rusch, M., Nakitandwe, J., Shurtleff, S. A., Newman, S., Zhang, Z., Edmonson, M. N., Parker, M. D., Jiao, Y., Ma, X., Liu, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06485-7 · Cited by 219
Application of Next Generation Sequencing in Laboratory Medicine
Zhong, Y., Xu, F., Wu, J., Schubert, J. A., & Li, M. M. (2020) · Annals of Laboratory Medicine · doi:10.3343/alm.2021.41.1.25 · Cited by 231
“The US FDA approved Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) panel, developed by the Memorial Sloan Kettering Cancer Center, and the FoundationOne CDx (F1CDx), developed by Foundation Medicine, for in vitro diagnosis via detection of genetic variants in November…”
Method
Implementing tumor mutational burden (TMB) analysis in routine diagnostics—a primer for molecular pathologists and clinicians
Allgäuer, M., Budczies, J., Christopoulos, P., Endris, V., Lier, A., Rempel, E., Volckmar, A., Kirchner, M., von Winterfeld, M., Leichsenring, J., et al. (2018) · Translational Lung Cancer Research · doi:10.21037/tlcr.2018.08.14 · Cited by 212
Genetic hallmarks of recurrent/metastatic adenoid cystic carcinoma
Ho, A. S., Ochoa, A., Jayakumaran, G., Zehir, A., Valero, C., Tepe, J., Makarov, V., Dalin, M. G., He, J., Bailey, M., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci128227 · Cited by 212
High-throughput phenotyping of lung cancer somatic mutations
Berger, A. H., Brooks, A. N., Wu, X., Shrestha, Y., Chouinard, C., Piccioni, F., Bagul, M., Kamburov, A., Imielinski, M., Hogstrom, L., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.06.022 · Cited by 192
Targeting HER2 in colorectal cancer: The landscape of amplification and short variant mutations in ERBB2 and ERBB3
Ross, J. S., Fakih, M., Ali, S. M., Elvin, J. A., Schrock, A. B., Suh, J. H., Vergilio, J., Ramkissoon, S. H., Severson, E. A., Daniel, S., et al. (2018) · Cancer · doi:10.1002/cncr.31125 · Cited by 218
“Median age (range), y 56 (8-96) 54 (22-88) 59 (31-79) 57 (29-87) 54 (14-83) 53 (46-80)”
Molecular and clinical determinants of response and resistance to rucaparib for recurrent ovarian cancer treatment in ARIEL2 (Parts 1 and 2)
Swisher, E. M., Kwan, T. T., Oza, A. M., Tinker, A. V., Ray-Coquard, I. L., Oaknin, A., Coleman, R. L., Aghajanian, C. A., Konecny, G. E., O’Malley, D. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22582-6 · Cited by 209
“BRCAwt/LOH-high resistant/refractory 73 (0) 8 (62) 3 (67) 0 (70) BRCAwt/LOH-high sensitive 83 (0) 26 (50) 10 (66) 2 (74) 2 (74) 2 (74) 0 (74) BRCAwt/LOH-high resistant/refractory (n=73) 1.”
Immune Activation and Benefit From Avelumab in EBV-Positive Gastric Cancer
Panda, A., Mehnert, J. M., Hirshfield, K. M., Riedlinger, G., Damare, S., Saunders, T., Kane, M., Sokol, L. O., Stein, M. N., Poplin, E. A., et al. (2017) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djx213 · Cited by 209
Genomic context of NTRK1/2/3 fusion-positive tumours from a large real-world population
Westphalen, C. B., Krebs, M., Tourneau, C. L., Sokol, E. S., Maund, S. L., Wilson, T. R., Jin, D. X., Newberg, J. Y., Fabrizio, D. A., Véronèse, L., et al. (2021) · npj Precision Oncology · doi:10.1038/s41698-021-00206-y · Cited by 210
Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma
Gounder, M. M., Agaram, N. P., Trabucco, S. E., Robinson, V. L., Ferraro, R., Millis, S. Z., Krishnan, A., Lee, J., Attia, S., Abida, W. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30496-0 · Cited by 221
MET Alterations Are a Recurring and Actionable Resistance Mechanism in ALK-Positive Lung Cancer
Dagogo‐Jack, I., Yoda, S., Lennerz, J. K., Langenbucher, A., Lin, J. J., Rooney, M. M., Prutisto-Chang, K., Oh, A., Adams, N. A., Yeap, B. Y., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-3906 · Cited by 207
“MET rearrangements andmutations andALKmutations were detected in tissue using either FoundationOne or the MGH SNaPshot/Solid Fusion Assays (19, 22).”
MethodInfluential
Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing
Chung, C. H., Guthrie, V. B., Masica, D. L., Tokheim, C. J., Kang, H., Richmon, J. D., Agrawal, N., Fakhry, C., Quon, H., Subramaniam, R. M., et al. (2015) · Annals of Oncology · doi:10.1093/annonc/mdv109 · Cited by 211
“Methods for the NGS-based clinical cancer gene assay used in this project have been previously published and assay performance has been rigorously validated [12].”
Method
Prevalence and detection of low-allele-fraction variants in clinical cancer samples
Shin, H., Choi, Y., Yun, J. W., Kim, N. K. D., Kim, S., Jeon, H. J., Nam, J., Lee, C., Ryu, D., Kim, S. C., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01470-y · Cited by 204
Validation of biomarkers to predict response to immunotherapy in cancer: Volume I — pre-analytical and analytical validation
Masucci, G. V., Cesano, A., Hawtin, R. E., Janetzki, S., Zhang, J., Kirsch, I. R., Dobbin, K. K., Alvarez, J. D., Robbins, P. B., Selvan, S. R., et al. (2016) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-016-0178-1 · Cited by 200
“Each platform has specific parameters relevant to the laboratory and test requirements including instrument size, instrument cost, run time, read length, and cost per sample [116, 139, 140].”
Background
Whole-tissue biopsy phenotyping of three-dimensional tumours reveals patterns of cancer heterogeneity
Tanaka, N., Kanatani, S., Tomer, R., Sahlgren, C., Kronqvist, P., Kaczyńska, D., Louhivuori, L. M., Kis, L. L., Lindh, C., Mitura, P., et al. (2017) · Nature Biomedical Engineering · doi:10.1038/s41551-017-0139-0 · Cited by 202
Biomarkers Associated With Response to Regorafenib in Patients With Hepatocellular Carcinoma
Teufel, M., Seidel, H., Köchert, K., Meinhardt, G., Finn, R. S., Llovet, J. M., & Bruix, J. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.01.261 · Cited by 204
Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA
Clark, T. A., Chung, J. H., Kennedy, M., Hughes, J. D., Chennagiri, N., Lieber, D. S., Fendler, B., Young, L., Zhao, M., Coyne, M., et al. (2018) · The Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2018.05.004 · Cited by 200
“Filters were applied to ensure highquality alignments, and a minimum number of reads supporting the re-arrangement were required, as described.(1)”
MethodInfluential
The International Association for the Study of Lung Cancer Consensus Statement on Optimizing Management of EGFR Mutation–Positive Non–Small Cell Lung Cancer: Status in 2016
Tan, D. S. W., Yom, S. S., Tsao, M. S., Pass, H. I., Kelly, K., Peled, N., Yung, R. C., Wistuba, I. I., Yatabe, Y., Unger, M., et al. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.05.008 · Cited by 201
Genomic Alterations Observed in Colitis-Associated Cancers Are Distinct From Those Found in Sporadic Colorectal Cancers and Vary by Type of Inflammatory Bowel Disease
Yaeger, R. D., Shah, M. A., Miller, V. A., Kelsen, J. R., Wang, K., Heins, Z. J., Ross, J. S., He, Y., Sanford, E. M., Yantiss, R. K., et al. (2016) · Gastroenterology · doi:10.1053/j.gastro.2016.04.001 · Cited by 200
Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers
Goldstein, L. D., Lee, J., Gnad, F., Klijn, C. N., Schaub, A., Reeder, J., Daemen, A., Bakalarski, C. E., Holcomb, T., Shames, D. S., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.08.010 · Cited by 205
Library preparation for next generation sequencing: A review of automation strategies
Hess, J. F., Kohl, T. A., Kotrová, M., Rönsch, K., Paprotka, T., Mohr, V., Hutzenlaub, T., Brüggemann, M., Zengerle, R., Niemann, S., et al. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107537 · Cited by 207
Using patient-derived organoids to predict locally advanced or metastatic lung cancer tumor response: A real-world study
Wang, H.-M., Zhang, C.-Y., Peng, K., Chen, Z.-X., Su, J., Li, Y., Li, W., Gao, Q.-Y., Zhang, S., Chen, Y., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100911 · Cited by 221
“In the context of modern precision medicine, NGS presents good analytical validity to detect clonally dominant alterations.(53) It has recently been applied in clinics with the aim of identifying targetable alterations.”
Background
A Phase I Study of the CDK4/6 Inhibitor Ribociclib (LEE011) in Pediatric Patients with Malignant Rhabdoid Tumors, Neuroblastoma, and Other Solid Tumors
Geoerger, B., Bourdeaut, F., DuBois, S. G., Fischer, M., Geller, J. I., Gottardo, N. G., Marabelle, A., Pearson, A. D. J., Modak, S. I., Cash, T., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-2898 · Cited by 189
“Vomiting 1 (20) 0 6 (40) 0 5 (42) 0 12 (38) 0”
MethodInfluential
Comprehensive Genomic Profiling of Pancreatic Acinar Cell Carcinomas Identifies Recurrent RAF Fusions and Frequent Inactivation of DNA Repair Genes
Chmielecki, J., Hutchinson, K. E., Frampton, G. M., Chalmers, Z. R., Johnson, A., Shi, C., Elvin, J. A., Ali, S. M., Ross, J. S., Baştürk, O., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-0617 · Cited by 188
“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) and indels with a ≥10% MAF with ≥99% accuracy (9).”
MethodInfluential
Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations
Oberg, J. A., Bender, J. G., Sulis, M. L., Pendrick, D., Sireci, A. N., Hsiao, S. J., Turk, A. T., Cruz, F. S. D., Hibshoosh, H. H., Remotti, H. E., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0389-6 · Cited by 188
Comprehensive pan-cancer genomic landscape of KRAS altered cancers and real-world outcomes in solid tumors
Lee, J. K., Sivakumar, S., Schrock, A. B., Madison, R., Fabrizio, D., Gjoerup, O., Ross, J. S., Frampton, G. M., Napalkov, P., Montesion, M., et al. (2022) · npj Precision Oncology · doi:10.1038/s41698-022-00334-z · Cited by 187
CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors
Skoulidis, F., Araujo, H. A., Do, M. T., Qian, Y., Sun, X., Galan-Cobo, A., Le, J. T., Montesion, M., Palmer, R., Jahchan, N., et al. (2024) · Nature · doi:10.1038/s41586-024-07943-7 · Cited by 194
Precision medicine treatment in acute myeloid leukemia using prospective genomic profiling: feasibility and preliminary efficacy of the Beat AML Master Trial
Burd, A. L., Levine, R. L., Ruppert, A. S., Mims, A. S., Borate, U., Stein, E. M., Patel, P. A., Baer, M. R., Stock, W., Deininger, M. W., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1089-8 · Cited by 195
Nanotherapy for Cancer: Targeting and Multifunctionality in the Future of Cancer Therapies
Ediriwickrema, A., & Saltzman, W. M. (2015) · ACS Biomaterials Science & Engineering · doi:10.1021/ab500084g · Cited by 193
ARID1A alterations function as a biomarker for longer progression-free survival after anti-PD-1/PD-L1 immunotherapy
Okamura, R., Kato, S., Lee, S., Jimenez, R. E., Sicklick, J. K., & Kurzrock, R. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2019-000438 · Cited by 189
Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies
Du, W., & Elemento, O. (2014) · Oncogene · doi:10.1038/onc.2014.291 · Cited by 185
The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non–Small-Cell Lung Cancer
Papadimitrakopoulou, V. A., Lee, J. J., Wistuba, I. I., Tsao, A. S., Fossella, F. V., Kalhor, N., Gupta, S. K., Byers, L. A., Izzo, J. G., Gettinger, S. N., et al. (2016) · Journal of Clinical Oncology · doi:10.1200/jco.2015.66.0084 · Cited by 182
Orthogonal Comparison of Four Plasma NGS Tests With Tumor Suggests Technical Factors are a Major Source of Assay Discordance
Stetson, D., Ahmed, A., Xu, X., Nuttall, B. R. B., Lubinski, T. J., Johnson, J. H., Barrett, J. C., & Dougherty, B. A. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00191 · Cited by 182
Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA)
Chin, R.-I., Chen, K., Usmani, A., Chua, C., Harris, P. K., Binkley, M. S., Azad, T. D., Dudley, J. C., & Chaudhuri, A. A. (2019) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-019-00390-5 · Cited by 191
Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project
Vega, D. M., Yee, L. M., McShane, L. M., Williams, P. M., Chen, L., Vilimas, T., Fabrizio, D. A., Funari, V. A., Newberg, J. Y., Bruce, L. K., et al. (2021) · Annals of Oncology · doi:10.1016/j.annonc.2021.09.016 · Cited by 192
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine
Garofalo, A., Sholl, L. M., Reardon, B. M., Taylor-Weiner, A. N., Amin‐Mansour, A., Miao, D., Liu, D., Oliver, N. M., MacConaill, L. E., Ducar, M. D., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0333-9 · Cited by 184
“Moreover, although sequencing of paired normal blood or tissue samples is standard practice for research-oriented WES applications, many targeted panel approaches do not include matched normal samples [2, 3, 9, 21, 22].”
ABRA: improved coding indel detection via assembly-based realignment
Mose, L. E., Wilkerson, M. D., Hayes, D. N., Perou, C. M., & Parker, J. S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu376 · Cited by 178
Pan-Cancer Analysis of BRCA1 and BRCA2 Genomic Alterations and Their Association With Genomic Instability as Measured by Genome-Wide Loss of Heterozygosity
Sokol, E. S., Pavlick, D. C., Khiabanian, H., Frampton, G. M., Ross, J. S., Gregg, J. P., Lara, P. N., Oesterreich, S., Agarwal, N., Necchi, A., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00345 · Cited by 182
Biomarker-Based Phase II Trial of Savolitinib in Patients With Advanced Papillary Renal Cell Cancer
Choueiri, T. K., Plimack, E. R., Arkenau, H., Jonasch, E., Heng, D. Y. C., Powles, T. B., Frigault, M. M., Clark, E. A., Handzel, A. A., Gardner, H., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2017.72.2967 · Cited by 177
“Any AE 57 (52) 51 (47) 108 (99) Any treatment-related AE† 75 (69) 21 (19) 96 (88) Any SAE (including death) 23 (21) Death Related to PRCC or disease progression 32 (29) Considered treatment related 1 (, 1) Treatment discontinuation Due to any AE 9 (8) Due to any SAE 3 (3) AEs considered treatment-related occurring in…”
Cholangiocarcinoma With FGFR Genetic Aberrations: A Unique Clinical Phenotype
Jain, A., Borad, M. J., Kelley, R. K., Wáng, Y., Abdel‐Wahab, R., Meric‐Bernstam, F., Baggerly, K., Kaseb, A. O., Al-Shamsi, H. O., Ahn, D. H., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00080 · Cited by 174
Pulmonary Sarcomatoid Carcinomas Commonly Harbor Either Potentially Targetable Genomic Alterations or High Tumor Mutational Burden as Observed by Comprehensive Genomic Profiling
Schrock, A. B., Li, S. D., Frampton, G. M., Suh, J. H., Braun, E., Mehra, R., Buck, S. C., Bufill, J. A., Peled, N., Karim, N. A., et al. (2017) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2017.03.005 · Cited by 176
“DNA was extracted from 40 mM formalin-fixed paraffinembedded sections, and CGP was performed on hybridization-captured, adaptor ligation–based libraries to a mean coverage depth of 650 for 236 or 315 cancerrelated genes plus select introns from 19 or 28 genes frequently rearranged in cancer.(19) All classes of GAs wer…”
Method
PureCN: copy number calling and SNV classification using targeted short read sequencing
Riester, M., Singh, A., Brannon, A. R., Yu, K., Campbell, C. D., Chiang, D. Y., & Morrissey, M. (2016) · Source Code for Biology and Medicine · doi:10.1186/s13029-016-0060-z · Cited by 169
“8), which were obtained from a commercial vendor using a targeted panel with copy number tiling probes [26] and internally using whole exome sequencing on remnant DNA.”
Method
Comparison of 2 Commercially Available Next-Generation Sequencing Platforms in Oncology
Kuderer, N. M., Burton, K. A., Blau, S. H., Rose, A. L., Parker, S., Lyman, G. H., & Blau, C. A. (2016) · JAMA Oncology · doi:10.1001/jamaoncol.2016.4983 · Cited by 170
Crizotinib in Patients With MET-Amplified NSCLC
Camidge, D. R., Otterson, G. A., Clark, J. W., Ou, S. I., Weiss, J. M., Ades, S., Shapiro, G. I., Socinski, M. A., Murphy, D. A., Conte, U., et al. (2021) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2021.02.010 · Cited by 177
Translating cancer genomes and transcriptomes for precision oncology
Roychowdhury, S., & Chinnaiyan, A. M. (2015) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21329 · Cited by 168
The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy
Knepper, T. C., Montesion, M., Russell, J. S., Sokol, E. S., Frampton, G. M., Miller, V. A., Albacker, L. A., McLeod, H. L., Eroglu, Z., Khushalani, N. I., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-4159 · Cited by 172

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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