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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Method
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Method
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BackgroundMethodResultInfluential
TP53 Alterations Correlate with Response to VEGF/VEGFR Inhibitors: Implications for Targeted Therapeutics
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HER2 Transmembrane Domain (TMD) Mutations (V659/G660) That Stabilize Homo- and Heterodimerization Are Rare Oncogenic Drivers in Lung Adenocarcinoma That Respond to Afatinib
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Identification of Targetable ALK Rearrangements in Pancreatic Ductal Adenocarcinoma
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“Genomic profiling of patient samples Hybrid capture-based next-generation sequencing was performed on formalin-fixed paraffin-embedded tissue sections or circulating tumor DNA isolated from blood samples in a Clinical Laboratory Improvement Amendments–certified, College of American Pathologists–accredited laboratory (…”
Method
NetSig: network-based discovery from cancer genomes
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Identification of NTRK fusions in pediatric mesenchymal tumors
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Clinical, pathological, and genomic features of EWSR1-PATZ1 fusion sarcoma
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Heterogeneity in Cancer
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RICTOR Amplification Defines a Novel Subset of Patients with Lung Cancer Who May Benefit from Treatment with mTORC1/2 Inhibitors
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“, Cambridge, MA) for genomic sequencing of their tumor samples [12].”
Background
Tumor Fraction Correlates With Detection of Actionable Variants Across > 23,000 Circulating Tumor DNA Samples
Husain, H., Pavlick, D. C., Fendler, B. J., Madison, R. W., Decker, B. J., Gjoerup, O. V., Parachoniak, C. A., McLaughlin-Drubin, M., Erlich, R., Schrock, A. B., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.22.00261 · Cited by 110
“Tissue biopsies were analyzed using FoundationOne CDx as previously described.(10,11) Briefly, the pathologic diagnosis of tissue biopsy was confirmed on routine hematoxylin and eosin–stained slides.”
Method
Comprehensive genomic profiling of anal squamous cell carcinoma reveals distinct genomically defined classes
Chung, J., Sanford, E. M., Johnson, A., Klempner, S. J., Schrock, A. B., Palma, N. A., Erlich, R., Frampton, G. M., Chalmers, Z. R., Vergilio, J., et al. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw152 · Cited by 104
“short insertions/deletions, focal gene amplifications, homozygous deletions, and rearrangements, were determined as described [11].”
Background
Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
Tsai, Y. S., Woodcock, M. G., Azam, S. H., Thorne, L. B., Kanchi, K. L., Parker, J. S., Vincent, B. G., & Pecot, C. V. (2022) · Journal of Clinical Investigation · doi:10.1172/jci155523 · Cited by 103
“When evaluating copy number changes among cancer-related gene loci (11), there were 15 genes with Figure 4.”
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“Patients with advanced NSCLC and available tissue specimens were subjected to hybrid capture– based comprehensive genomic profiling as previously described.(5) Appropriate patients were enrolled into the METex14–positive expansion cohort of a phase I clinical trial of crizotinib (NCT00585195).”
Method
Comprehensive Genomic Profiling of Upper-tract and Bladder Urothelial Carcinoma
Necchi, A., Madison, R. W., Pal, S. K., Ross, J. S., Agarwal, N., Sonpavde, G., Joshi, M., Yin, M., Miller, V. A., Grivas, P. D., et al. (2020) · European Urology Focus · doi:10.1016/j.euf.2020.08.001 · Cited by 106
Preclinical In Vivo Validation of the RAD51 Test for Identification of Homologous Recombination-Deficient Tumors and Patient Stratification
Pellegrino, B., Herencia-Ropero, A., Llop‐Guevara, A., Pedretti, F., Moles‐Fernández, A., Viaplana, C., Villacampa, G. J., Guzmán, M., Rodríguez, O., Grueso, J., et al. (2022) · Cancer Research · doi:10.1158/0008-5472.can-21-2409 · Cited by 102
Homologous Recombination Repair Deficiency: An Overview for Pathologists
Doig, K., FELLOWES, A. P., & Fox, S. B. (2023) · Modern Pathology · doi:10.1016/j.modpat.2022.100049 · Cited by 103
Comprehensive Genomic Profiling Facilitates Implementation of the National Comprehensive Cancer Network Guidelines for Lung Cancer Biomarker Testing and Identifies Patients Who May Benefit From Enrollment in Mechanism-Driven Clinical Trials
Suh, J. H., Johnson, A., Albacker, L. A., Wang, K., Chmielecki, J., Frampton, G. M., Gay, L. M., Elvin, J. A., Vergilio, J., Ali, S. M., et al. (2016) · The Oncologist · doi:10.1634/theoncologist.2016-0030 · Cited by 104
An Acquired HER2 T798I Gatekeeper Mutation Induces Resistance to Neratinib in a Patient with HER2 Mutant–Driven Breast Cancer
Hanker, A. B., Brewer, M. R., Sheehan, J. H., Koch, J. P., Sliwoski, G. R., Nagy, R. J., Lanman, R. B., Berger, M. F., Hyman, D. M., Solit, D. B., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-1431 · Cited by 99
“Results HER2 L869R exhibits a gain-of-function phenotype that is blocked by neratinib Targeted capture next-generation sequencing (NGS) (10) of DNA from a skin metastasis in a 54 year-old female with ER/PR+, HER2 non-amplified lobular breast carcinoma identified an ERBB2L869R (HER2L869R) somatic mutation (Supplementar…”
Influential
High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods
Su, D., Zhang, D., Chen, K., Lu, J. N., Wu, J., Cao, X., Ying, L., Jin, Q., Ye, Y., Xie, Z., et al. (2017) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-017-0591-4 · Cited by 103
“[5] Moreover, cancers are frequently caused by alterations on multiple genes, which collaborate to promote tumor development.”
Background
A machine learning approach for somatic mutation discovery
Wood, D. E., White, J. R., Georgiadis, A. P., Emburgh, B. V., Parpart-Li, S. T., Mitchell, J., Anagnostou, V., Niknafs, N., Karchin, R., Papp, E., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aar7939 · Cited by 101
Infigratinib in Patients with Recurrent Gliomas and FGFR Alterations: A Multicenter Phase II Study
Lassman, A. B., Sepúlveda-Sánchez, J. M., Cloughesy, T. F., Gil-Gil, M. J., Puduvalli, V. K., Raizer, J. J., Vos, F. D., Wen, P. Y., Butowski, N. A., Clément, P. M., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-2664 · Cited by 102
Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation
Rolfo, C. D., Madison, R. W., Pasquina, L. W., Brown, D. W., Huang, Y., Hughes, J. D., Graf, R. P., Oxnard, G. R., & Husain, H. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-3321 · Cited by 104
“F1LCDx also reports genomic signatures including ctDNA TF. TBx were analyzed using F1CDx as described previously (16, 17).”
Method
Impact of high tumor mutational burden in solid tumors and challenges for biomarker application
McNamara, M. G., Jacobs, T., Lamarca, Á., Hubner, R. A., Valle, J. W., & Amir, E. (2020) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2020.102084 · Cited by 102
Oncogenic Alterations in ERBB2/HER2 Represent Potential Therapeutic Targets Across Tumors From Diverse Anatomic Sites of Origin
Chmielecki, J., Ross, J. S., Wang, K., Frampton, G. M., Palmer, G. A., Ali, S. M., Palma, N. A., Morosini, D., Miller, V. A., Yelensky, R., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2014-0234 · Cited by 101
Sequencing Structural Variants in Cancer for Precision Therapeutics
Macintyre, G., Ylstra, B., & Brenton, J. D. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.07.002 · Cited by 97
Early onset sporadic colorectal cancer: Worrisome trends and oncogenic features
Cavestro, G. M., Mannucci, A., Zuppardo, R. A., Leo, M. D., Stoffel, E. M., & Tonon, G. (2018) · Digestive and Liver Disease · doi:10.1016/j.dld.2018.02.009 · Cited by 102
STUMP un“stumped”: anti-tumor response to anaplastic lymphoma kinase (ALK) inhibitor based targeted therapy in uterine inflammatory myofibroblastic tumor with myxoid features harboring DCTN1-ALK fusion
Subbiah, V., McMahon, C., PATEL, S. R., Zinner, R., Silva, E. G., Elvin, J. A., Subbiah, I. M., Ohaji, C., Ganeshan, D., Anand, D., et al. (2015) · Journal of Hematology & Oncology · doi:10.1186/s13045-015-0160-2 · Cited by 98
“At the same time, this specimen was submitted as an FFPE block for comprehensive genomic profiling [2].”
Background
Clinical Actionability Enhanced through Deep Targeted Sequencing of Solid Tumors
Chen, K., Meric‐Bernstam, F., Zhao, H., Zhang, Q. C., Ezzeddine, N., Tang, L.-Y., Qi, Y., Mao, Y., Chen, T., Chong, Z., et al. (2015) · Clinical Chemistry · doi:10.1373/clinchem.2014.231100 · Cited by 97
The Spectrum and Clinical Impact of Epigenetic Modifier Mutations in Myeloma
Pawlyn, C., Kaiser, M., Heuck, C. J., Melchor, L., Wardell, C. P., Murison, A., Chavan, S. S., Johnson, D. C., Begum, D. B., Dahir, N. M., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1790 · Cited by 101
“org Clin Cancer Res; 22(23) December 1, 2016 5789”
BackgroundMethodInfluential
Prognostic tumor sequencing panels frequently identify germ line variants associated with hereditary hematopoietic malignancies
Drazer, M. W., Kadri, S., SUKHANOVA, M. J., Patil, S., DePersia, A., Feurstein, S. K., Calderon, D. A., Jones, M. F., Weipert, C. M., Daugherty, C. K., et al. (2018) · Blood Advances · doi:10.1182/bloodadvances.2017013037 · Cited by 98
Clinical correlates of blood-derived circulating tumor DNA in pancreatic cancer
Patel, H., Okamura, R., Fanta, P. T., Patel, C., Lanman, R. B., Raymond, V. M., Kato, S., & Kurzrock, R. (2019) · Journal of Hematology & Oncology · doi:10.1186/s13045-019-0824-4 · Cited by 99
Prospective Clinical Study of Precision Oncology in Solid Tumors
Sohal, D. P. S., Rini, B. I., Khorana, A. A., Dreicer, R., Abraham, J., Procop, G. W., Saunthararajah, Y., Pennell, N. A., Stevenson, J. P., Pelley, R. J., et al. (2015) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djv332 · Cited by 97
“(Cambridge, MA), for sequencing using the FoundationOne platform (11); the test involves sequencing the entire coding region of up to 315 cancer-related genes and rearrangements in introns from 28 genes.”
Method
Biological and clinical evidence for somatic mutations in BRCA1 and BRCA2 as predictive markers for olaparib response in high-grade serous ovarian cancers in the maintenance setting
Dougherty, B. A., Lai, Z., Hodgson, D., Orr, M. C. M., Hawryluk, M. J., Sun, J. X., Yelensky, R., Spencer, S., Robertson, J. D., Ho, T. W., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.17613 · Cited by 96
“The Foundation Medicine FoundationOneTM (T5 panel) NGS assay [23] was used to perform a pre-specified retrospective genetic analysis of tumor samples.”
Multicenter Study Using Desorption-Electrospray-Ionization-Mass-Spectrometry Imaging for Breast-Cancer Diagnosis
Porcari, A. M., Zhang, J., Garza, K. Y., Peres, R. M. R., Lin, J. Q., Young, J. H., Tibshirani, R. J., Nagi, C. S., Silva, G. R. D. P., Carter, S. A., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01961 · Cited by 97
Clinical applications of next generation sequencing in cancer: from panels, to exomes, to genomes
Shen, T. S., der Stadt, S. P.-V., Yeat, N. C., & Lin, J. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00215 · Cited by 97
“…ALK, BRAF, RAS, AKT1, DDR2, HER2, MEK1, NRAS, PIK3CA, PTEN RET, ROS1, ALK, EML4, NTRK1 EGFR, FHIT, FRA3B, FGFR1, HER2 EGFR, BRAF, RAS, KRAS, TP53 Brose et al., 2002; Kosaka et al., 2004; Vogelstein and Kinzler, 2004; Soda et al., 2007; Lipson et al., 2012; Vogelstein et al., 2013 Liver…”
MethodInfluential
Comprehensive Genomic Profiling of Advanced Esophageal Squamous Cell Carcinomas and Esophageal Adenocarcinomas Reveals Similarities and Differences
Wang, K., Johnson, A., Ali, S. M., Klempner, S. J., Bekaii‐Saab, T., Vacirca, J. L., Khaira, D., Yelensky, R., Chmielecki, J., Elvin, J. A., et al. (2015) · The Oncologist · doi:10.1634/theoncologist.2015-0156 · Cited by 96
Real-time genomic profiling of histiocytoses identifies early-kinase domain BRAF alterations while improving treatment outcomes
Lee, L. H., Gasilina, A., Roychoudhury, J., Clark, J. P., McCormack, F. X., Pressey, J. G., Grimley, M. S., Lorsbach, R. B., Ali, S. M., Bailey, M., et al. (2017) · JCI Insight · doi:10.1172/jci.insight.89473 · Cited by 98
Detection of Known and Novel FGFR Fusions in Non–Small Cell Lung Cancer by Comprehensive Genomic Profiling
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Olaparib as maintenance treatment for patients with platinum-sensitive relapsed ovarian cancer
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Comprehensive genomic profiling of inflammatory breast cancer cases reveals a high frequency of clinically relevant genomic alterations
Ross, J. S., Ali, S. M., Wang, K., Khaira, D., Palma, N. A., Chmielecki, J., Palmer, G. A., Morosini, D., Elvin, J. A., Fernandez, S. V., et al. (2015) · Breast Cancer Research and Treatment · doi:10.1007/s10549-015-3592-z · Cited by 96
“Captured libraries were sequenced to a median exon coverage depth of[8009, and resultant sequences were analyzed for base substitutions, short insertions and deletions (INDELs), copy number alterations (focal amplifications and homozygous deletions), and gene fusions, as previously described [21].”
BackgroundMethodInfluential
Evaluation of a Congenital Infantile Fibrosarcoma by Comprehensive Genomic Profiling Reveals an LMNA-NTRK1 Gene Fusion Responsive to Crizotinib
Wong, V., Pavlick, D. C., Brennan, T. J., Yelensky, R., Crawford, J. R., Ross, J. S., Miller, V. A., Malicki, D. M., Stephens, P. J., Ali, S. M., et al. (2015) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djv307 · Cited by 95
“Captured libraries were sequenced by DNA- and RNA-seq, with 100% of related genomic regions sequenced to be greater than 100X coverage and 477X median coverage (5).”
Method
Mutational profiling of colorectal cancers with microsatellite instability
Lin, E. I., Tseng, L., Gocke, C. D., Reil, S., Le, D. T., Azad, N. S., & Eshleman, J. R. (2015) · Oncotarget · doi:10.18632/oncotarget.5997 · Cited by 95
“NGS assays have shown both a high analytic sensitivity and a broad reportable range in the clinical diagnostic setting [28, 29].”
BackgroundMethod
Loss of function of NF1 is a mechanism of acquired resistance to endocrine therapy in lobular breast cancer
Sokol, E. S., Feng, Y., Jin, D. X., Basudan, A., Lee, A. V., Atkinson, J. M., Chen, J., Stephens, P. J., Frampton, G. M., Gupta, P. B., et al. (2018) · Annals of Oncology · doi:10.1093/annonc/mdy497 · Cited by 100
“We assessed all classes of genomic alterations (GA) including short variant, copy number, and rearrangement alterations, as described previously [9].”
Method
Tumor mutational burden in lung cancer: a systematic literature review
Willis, C., Fiander, M., Tran, D., Korytowsky, B., Thomas, J.-M., Calderon, F., Zyczynski, T. M., Brixner, D. I., & Stenehjem, D. D. (2019) · Oncotarget · doi:10.18632/oncotarget.27287 · Cited by 95
“Recent advances in comprehensive genomic profiling (CGP), using targeted NGS, which measures the number of mutations on a portion of the coding region while simultaneously providing data on specific DNA alterations, have been validated [19] and shown to reflect measurements obtained by WES [20].”
Background
Current views on tumor mutational burden in patients with non-small cell lung cancer treated by immune checkpoint inhibitors
Berland, L., Heeke, S., Humbert, O., Macocco, A., Long-Mira, E., Lassalle, S., Lespinet-Fabre, V., Lalvée, S., Bordone, O., Cohen, C., et al. (2019) · Journal of Thoracic Disease · doi:10.21037/jtd.2018.11.102 · Cited by 95
“For example, the FoundationOne assay, one FFPE block or 10 unstained tumor slides cut at 4–5 μm thickness with a minimum of 25 mm(2) surface area and at least 20% of tumor, are required (35).”
Method
Genomic Profiling of a Large Set of Diverse Pediatric Cancers Identifies Known and Novel Mutations across Tumor Spectra
Chmielecki, J., Bailey, M., He, J., Elvin, J. A., Vergilio, J., Ramkissoon, S. H., Suh, J. H., Frampton, G. M., Sun, J., Morley, S., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-1106 · Cited by 98
“Captured libraries were sequenced to a median exon coverage depth of >600 using Illumina sequencing, and resultant sequences were analyzed for base substitutions, insertions, deletions, copy number alterations (focal amplifications and homozygous deletions) and select gene fusions, as previously described (16, 17).”
Method
Clinical utility of tumor mutational burden in patients with non-small cell lung cancer treated with immunotherapy
Hendriks, L. E. L., Rouleau, É., & Besse, B. (2018) · Translational Lung Cancer Research · doi:10.21037/tlcr.2018.09.22 · Cited by 96
“In 2018, turnaround time is approximately two weeks, and cost is between 2,500 and 5,000 US dollars although it is expected that price will decrease with time (18,19,60).”
BackgroundMethod
CDK12 -Mutated Prostate Cancer: Clinical Outcomes With Standard Therapies and Immune Checkpoint Blockade
Schweizer, M. T., Ha, G., Gulati, R., Brown, L. C., McKay, R. R., Dorff, T. B., Hoge, A. C. H., Reichel, J. B., Vats, P., Kilari, D., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00383 · Cited by 98
Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material
de Leng, W. W. J., Hooijdonk, C. G. G., Barendregt-Smouter, F. A. S., Koudijs, M. J., Nijman, I., Hinrichs, J. W. J., Cuppen, E. P. J. G., van Lieshout, S., Loberg, R. D., de Jonge, M. J. A., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0149405 · Cited by 99
“[10] Variant calling of FFPE samples in a clinical setting relies on variant allele frequencies (VAF) of 5–15%, [7, 11, 12] detection of VAF<5% require further validation, and TAT is typically one to two weeks for FFPE samples.[8, 13, 14] The Ion Torrent platform in combination with Ion AmpliSeq multiplex PCR can use…”
Method
Molecular Analysis of Plasma From Patients With ROS1-Positive NSCLC
Dagogo‐Jack, I., Rooney, M. M., Nagy, R. J., Lin, J. J., Chin, E. N., Ferris, L. A., Ackil, J., Lennerz, J. K., Lanman, R. B., Gainor, J. F., et al. (2019) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2019.01.009 · Cited by 93
High Tumor Mutational Burden Correlates with Longer Survival in Immunotherapy-Naïve Patients with Diverse Cancers
Riviere, P. J., Goodman, A. M., Okamura, R., Barkauskas, D. A., Whitchurch, T. J., Lee, S., Khalid, N. K., Collier, R., Mareboina, M., Frampton, G. M., et al. (2020) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-20-0161 · Cited by 96
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads
Moncunill, V., González, S., Beà, S., Andrieux, L. O., Salaverría, I., Royo, C., Martinez, L., Puiggròs, M., Segura‐Wang, M., Stütz, A. M., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.3027 · Cited by 93
Clinical genomic profiling to identify actionable alterations for investigational therapies in patients with diverse sarcomas
Groisberg, R., Hong, D. S., Holla, V. R., Jankú, F., Piha-Paul, S. A., Ravi, V., Benjamin, R. S., Patel, S., Somaiah, N., Conley, A. P., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.16845 · Cited by 93
“com), a clinical grade CLIA-approved NGS test analyzing 236 or 315 cancer-related genes in at least 50ng of DNA from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens [42].”
Background
Consensus on precision medicine for metastatic cancers: a report from the MAP conference
Swanton, C., Soria, J., Bardelli, A., Biankin, A. V., Caldas, C., Chandarlapaty, S., de Koning, L., Dive, C., Feunteun, J., Leung, S.-Y., et al. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw192 · Cited by 94
“[4] reported the analytical validity of a panel of 287 cancer-related genes.”
Background
SMARCA4 inactivation defines a subset of undifferentiated uterine sarcomas with rhabdoid and small cell features and germline mutation association
Lin, D. I., Allen, J. M., Hecht, J. L., Killian, J. K., Ngo, N., Edgerly, C. I., Severson, E. A., Ali, S. M., Erlich, R., Ramkissoon, S. H., et al. (2019) · Modern Pathology · doi:10.1038/s41379-019-0303-z · Cited by 92
Biomarker discovery studies for patient stratification using machine learning analysis of omics data: a scoping review
Glaab, E., Rauschenberger, A., Banzi, R., Gerardi, C., Garcia, P., & Demotes‐Mainard, J. (2021) · BMJ Open · doi:10.1136/bmjopen-2021-053674 · Cited by 96
Second-line dovitinib (TKI258) in patients with FGFR2-mutated or FGFR2-non-mutated advanced or metastatic endometrial cancer: a non-randomised, open-label, two-group, two-stage, phase 2 study
Konecny, G. E., Finkler, N. J., García, A. A., Lorusso, D., Lee, P. S., Rocconi, R. P., Fong, P. C. C., Squires, M. S., Mishra, K., Upalawanna, A., et al. (2015) · The Lancet Oncology · doi:10.1016/s1470-2045(15)70159-2 · Cited by 91
BRAF V600E-mutated lung adenocarcinoma with metastases to the brain responding to treatment with vemurafenib
Robinson, S. D., O’Shaughnessy, J., Cowey, C. L., & Konduri, K. (2014) · Lung Cancer · doi:10.1016/j.lungcan.2014.05.009 · Cited by 93
BRAF V600E Mutations in High-Grade Colorectal Neuroendocrine Tumors May Predict Responsiveness to BRAF–MEK Combination Therapy
Klempner, S. J., Gershenhorn, B. G., Tran, P. N., Lee, T. K. M., Erlander, M. G., Gowen, K. A., Schrock, A. B., Morosini, D., Ross, J. S., Miller, V. A., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-1192 · Cited by 91
ERBB2 -Mutated Metastatic Non–Small Cell Lung Cancer: Response and Resistance to Targeted Therapies
Chuang, J. C., Stehr, H., Liang, Y., Das, M. S., Huang, J. Q., Diehn, M., Wakelee, H. A., & Neal, J. W. (2017) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2017.01.023 · Cited by 91
“ERBB2 mutations in tissue were identified using a Stanford PCR-based ERBB2 sizing assay, the NGS based methods Stanford Solid Tumor Actionable Mutation Panel (STAMP) assay [10], NGS-based Foundation One assay [11], or Geneseeq assay Technology Inc [12].”
Analysis of DNA Damage Response Gene Alterations and Tumor Mutational Burden Across 17,486 Tubular Gastrointestinal Carcinomas: Implications for Therapy
Parikh, A. R., He, Y., Hong, T. S., Corcoran, R. B., Clark, J. W., Ryan, D. P., Zou, L., Ting, D. T., Catenacci, D. V. T., Chao, J., et al. (2019) · The Oncologist · doi:10.1634/theoncologist.2019-0034 · Cited by 92
“Next-generation sequencing (NGS) was performed on hybridization-captured, adaptor ligation-based libraries to high, uniform coverage (>500×) for all coding exons of 236 (version 1) or 315 (version 2) cancer-related genes plus 19 (version 1) or 28 (version 2) genes frequently rearranged in cancer [33].”
Background
Clinical sequencing using a next‐generation sequencing‐based multiplex gene assay in patients with advanced solid tumors
Kou, T., Kanai, M., Yamamoto, Y., Kamada, M., Nakatsui, M., Sakuma, T., Mochizuki, H., Hiroshima, A., Sugiyama, A., Nakamura, E., et al. (2017) · Cancer Science · doi:10.1111/cas.13265 · Cited by 90
CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer
Zhao, Z.-M., Yost, S. E., Hutchinson, K. E., Li, S. M., Yuan, Y., Noorbakhsh, J., Liu, Z., Warden, C., Johnson, R. M., Wu, X., et al. (2019) · BMC Cancer · doi:10.1186/s12885-019-5290-4 · Cited by 88
“The FoundationOneTM sequencing panel version used herein included the entire coding regions of 395 cancerrelated genes, and select introns of 31 genes that are rearranged or altered in cancer, capable of achieving a median sequencing depth greater than 500X [27, 28].”
Method
An Accurate and Comprehensive Clinical Sequencing Assay for Cancer Targeted and Immunotherapies
Cao, J., Chen, L., Li, H., Chen, H., Yao, J., Mu, S., Liu, W., Zhang, P., Cheng, Y., Liu, B., et al. (2019) · The Oncologist · doi:10.1634/theoncologist.2019-0236 · Cited by 89
“These performance specifications for SNV and short indels were also comparable to those of the Foundation-One assay.”
MethodInfluential
Precision therapy for lymphoma—current state and future directions
Intlekofer, A. M., & Younes, A. (2014) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2014.137 · Cited by 91
Therapeutic Targeting of DNA Damage Response in Cancer
Choi, W., & Lee, E. S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031701 · Cited by 97
“Consequently, commercial tests, validated in clinical trials, are available for the estimation of BRCAness; these include myChoice CDx (Myriad Genetics), which combines tumor BRCA gene mutation analysis and the genomic instability score (unweighted sum of LOH, LST, and TAI) [132], and FoundationOne CDx (Foundation Med…”
Method
Next-generation sequencing (NGS) of cell-free circulating tumor DNA and tumor tissue in patients with advanced urothelial cancer: a pilot assessment of concordance
Barata, P. C., Koshkin, V. S., Funchain, P., Sohal, D. P. S., Pritchard, A. L., Klek, S., Adamowicz, T., Gopalakrishnan, D., García, J., Rini, B. I., et al. (2017) · Annals of Oncology · doi:10.1093/annonc/mdx405 · Cited by 89
“The FoundationOne (F1; Foundation Medicine) test used formalin-fixed, paraffin-embedded (FFPE) tumors to sequence exons from 315 cancerassociated genes and introns from 28 genes involved in rearrangements [8].”
Method
APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy
Boichard, A., Pham, T. V., Yeerna, H., Goodman, A. M., Tamayo, P., Lippman, S. M., Frampton, G. M., Tsigelny, I. F., & Kurzrock, R. (2018) · OncoImmunology · doi:10.1080/2162402x.2018.1550341 · Cited by 90
“The methods have been previously described in.(38) Average sequencing depth of coverage was greater than 250X, with more than 100X for more than 99% of the exons covered.”
Method
Genomic Landscape of Malignant Mesotheliomas
Kato, S., Tomson, B. N., Buys, T. P. H., Elkin, S. K., Carter, J. L., & Kurzrock, R. (2016) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-16-0229 · Cited by 88
“Samples required surface area 25 mm(2), volume 1 mm(3),nucleated cellularity 80%, and tumor content 20%(26).”
BackgroundMethod
Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
Tsai, Y., Woodcock, M. G., Azam, S. H., Thorne, L. B., Kanchi, K., Parker, J. S., Vincent, B. G., & Pecot, C. V. (2022) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 87
Comparative Effectiveness of Immune Checkpoint Inhibitors vs Chemotherapy by Tumor Mutational Burden in Metastatic Castration-Resistant Prostate Cancer
Graf, R. P., Fisher, V. A., Weberpals, J. G., Gjoerup, O. V., Tierno, M. B., Huang, R. S. P., Sayegh, N., Lin, D. I., Raskina, K., Schrock, A. B., et al. (2022) · JAMA Network Open · doi:10.1001/jamanetworkopen.2022.5394 · Cited by 90
PARP Inhibitors Resistance: Mechanisms and Perspectives
Giudice, E., Gentile, M., Salutari, V., Ricci, C., Musacchio, L., Carbone, M. V., Ghizzoni, V., Camarda, F., Tronconi, F., Nero, C., et al. (2022) · Cancers · doi:10.3390/cancers14061420 · Cited by 95
“Meanwhile, the instability score derives from genomic signatures assessment, including microsatellite instability (MSI) and tumor mutational burden (TMB), in the FoundationOne CDx test [12,13].”
Background
AKT1 E17K mutation profiling in breast cancer: prevalence, concurrent oncogenic alterations, and blood-based detection
Rudolph, M., Anzeneder, T., Schulz, A., Beckmann, G., Byrne, A. T., Jeffers, M., Peña, C. E., Politz, O., Köchert, K., Vonk, R., et al. (2016) · BMC Cancer · doi:10.1186/s12885-016-2626-1 · Cited by 85
“assay The Foundation Medicine solid-tumor assay (FoundationOne® T5a panel) is a validated next-generation sequencing-based cancer genome profiling test that interrogates 4557 exons of 287 cancer-related genes with established performance benchmarks supporting direct clinical use [20].”
Method
Ultrasensitive Detection of Prostate‐Specific Antigen and Thrombin Based on Gold‐Upconversion Nanoparticle Assembled Pyramids
Hao, T., Wu, X., Xu, L., Liu, L., Ma, W., Kuang, H., & Xu, C. (2017) · Small · doi:10.1002/smll.201603944 · Cited by 85
PD-L1 and tumor-associated macrophages in de novo DLBCL
McCord, R., Bolen, C. R., Koeppen, H., Kadel, E. E., Oestergaard, M. Z., Nielsen, T. G., Sehn, L. H., & Venstrom, J. M. (2019) · Blood Advances · doi:10.1182/bloodadvances.2018020602 · Cited by 84
“1 amplification was determined among 443 GOYA samples using the FoundationOne Heme platform (Foundation Medicine Incorporated, Cambridge, MA) as previously described.(24) Next-generation sequencing data are publically available at accession #GSE125966.”
Method
Pharmacodynamics and molecular correlates of response to glofitamab in relapsed/refractory non-Hodgkin lymphoma
Bröske, A.-M. E., Korfi, K., Belousov, A., Wilson, S., Ooi, C.-H., Bolen, C. R., Cañamero, M., Alcaide, E. G., James, I., Piccione, E. C., et al. (2021) · Blood Advances · doi:10.1182/bloodadvances.2021005954 · Cited by 84
“9 homozygous deletions), and gene fusions/rearrangements, as previously described.(15) Only mutations known or likely to be pathogenic were included in the analysis, and alterations were summarized as presence/absence calls for each gene.”
Nonamplification ERBB2 genomic alterations in 5605 cases of recurrent and metastatic breast cancer: An emerging opportunity for anti‐HER2 targeted therapies
Ross, J. S., Gay, L. M., Wang, K., Ali, S. M., Chumsri, S., Elvin, J. A., Bose, R., Vergilio, J., Suh, J. H., Yelensky, R., et al. (2016) · Cancer · doi:10.1002/cncr.30102 · Cited by 84
“The samples were sequenced to high, uniform coverage, with a mean sequencing depth of 5643, as previously described.(17) GAs, including base substitutions, small insertions or deletions (indels), rearrangements, and copy number alterations, were determined and reported for these samples.”
Background
Real-Time Genomic Characterization Utilizing Circulating Cell-Free DNA in Patients with Anaplastic Thyroid Carcinoma
Sandulache, V. C., Williams, M. D., Lai, S. Y., Lu, C., William, W. N., Busaidy, N. L., Cote, G. J., Singh, R. R., Luthra, R., & Cabanillas, M. E. (2016) · Thyroid · doi:10.1089/thy.2016.0076 · Cited by 84
“One particular interesting aspect of the TP53 data summarized above is the partial discordance identified with respect to the specific TP53 mutations between the two platforms.”
MethodInfluential
Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS)
Al‐Kateb, H., Nguyen, T. T., Steger-May, K., & Pfeifer, J. D. (2015) · Molecular Oncology · doi:10.1016/j.molonc.2015.05.004 · Cited by 84
“…et al., 2014; Frederick et al., 2014; Sehn et al., 2014), identification of therapeutic targets in different types of cancer (Cottrell et al., 2014; Frampton et al., 2013; Hagemann et al., 2015; Kris et al., 2014; Pritchard et al., 2014; Tsimberidou et al., 2012), improvement of…”
Background
Development and clinical application of an integrative genomic approach to personalized cancer therapy
Uzilov, A. V., Ding, W., Fink, M. Y., Antipin, Y., Brohl, A. S., Davis, C., Lau, C. Y., Pandya, C., Shah, H., Kasai, Y., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0313-0 · Cited by 83
“Retrospective analyses of archived tumor samples using targeted gene panels or WES have been reported [6–9].”
Method
Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer
Bennett, C. W., Berchem, G., Kim, Y. J., & El‐Khoury, V. (2016) · Oncotarget · doi:10.18632/oncotarget.11717 · Cited by 83
“found that MET exon 14 splicing alterations, but not MET amplification, were often concomitant with the presence of MDM2/CDK4 amplifications in solid tumor samples [122, 123].”
Background
Preclinical Therapeutic Synergy of MEK1/2 and CDK4/6 Inhibition in Neuroblastoma
Hart, L. S., Rader, J., Raman, P., Batra, V., Russell, M. R., Tsang, M., Gagliardi, M. E., Chen, L. L., Martínez, D., Li, Y., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-1131 · Cited by 83
“To associate the activity of the inhibitors to relevant genomics variables, including gene mutations and copy number alterations, we used a validated cancerspecific gene panel approach (21) in 22 human neuroblastoma cell lines (Table 1 and Supplementary Tables S1 and S2).”
First-in-Human Phase I Study of the Tamoxifen Metabolite Z-Endoxifen in Women With Endocrine-Refractory Metastatic Breast Cancer
Goetz, M. P., Suman, V. J., Reid, J. M., Northfelt, D., Mahr, M. A., Ralya, A. T., Kuffel, M. J., Buhrow, S. A., Safgren, S. L., McGovern, R. M., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2017.73.3246 · Cited by 82
A clinico-genomic analysis of soft tissue sarcoma patients reveals CDKN2A deletion as a biomarker for poor prognosis
Bui, N. Q., Przybył, J., Trabucco, S. E., Frampton, G. M., Hastie, T. J., van de Rijn, M., & Ganjoo, K. N. (2019) · Clinical Sarcoma Research · doi:10.1186/s13569-019-0122-5 · Cited by 82
Colorectal cancer in the young, many questions, few answers
Deen, K. I., Silva, H., Deen, R., & Chandrasinghe, P. C. (2016) · World Journal of Gastrointestinal Oncology · doi:10.4251/wjgo.v8.i6.481 · Cited by 82
Deep Learning Artificial Intelligence Predicts Homologous Recombination Deficiency and Platinum Response From Histologic Slides
Bergstrom, E. N., Abbasi, A., Díaz-Gay, M., Galland, L., Ladoire, S., Lippman, S. M., & Alexandrov, L. B. (2024) · Journal of Clinical Oncology · doi:10.1200/jco.23.02641 · Cited by 83
Adavosertib with Chemotherapy in Patients with Primary Platinum-Resistant Ovarian, Fallopian Tube, or Peritoneal Cancer: An Open-Label, Four-Arm, Phase II Study
Moore, K. N., Chambers, S. K., Hamilton, E. P., Chen, L.-M., Oza, A. M., Ghamande, S. A., Konecny, G. E., Plaxe, S. C., Spitz, D. L., Geenen, J. J. J., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-0158 · Cited by 81
“FoundationOne assay and analyzed using Foundation Medicine, Inc’s F1 classification rules (31).”
Method
Stem cell architecture drives myelodysplastic syndrome progression and predicts response to venetoclax-based therapy
Gañán‐Gómez, I., Yang, H., Ma, F., Bravo, G. M., Thongon, N., Marchica, V., Richard‐Carpentier, G., Chien, K. S., Manyam, G. C., Wang, F., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01696-4 · Cited by 82
Emergence of EGFR G724S mutation in EGFR-mutant lung adenocarcinoma post progression on osimertinib
Oztan, A., Fischer, S., Schrock, A. B., Erlich, R. L., Lovly, C. M., Stephens, P. J., Ross, J. S., Miller, V., Ali, S. M., Ou, S.-H. I., et al. (2017) · Lung Cancer · doi:10.1016/j.lungcan.2017.07.002 · Cited by 80
Responses to the multitargeted MET/ALK/ROS1 inhibitor crizotinib and co-occurring mutations in lung adenocarcinomas with MET amplification or MET exon 14 skipping mutation
Jorge, S. E., Schulman, S., Freed, J. A., VanderLaan, P. A., Rangachari, D., Kobayashi, S. S., Huberman, M. S., & Costa, D. B. (2015) · Lung Cancer · doi:10.1016/j.lungcan.2015.10.028 · Cited by 82
Clinical Impact of Hybrid Capture–Based Next-Generation Sequencing on Changes in Treatment Decisions in Lung Cancer
Rozenblum, A. B., Ilouze, M., Dudnik, E., Dvir, A., Soussan‐Gutman, L., Geva, S., & Peled, N. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.10.021 · Cited by 80
Safety, Clinical Activity, and Biological Correlates of Response in Patients with Metastatic Melanoma: Results from a Phase I Trial of Atezolizumab
Hamid, O., Molinero, L. L., Bolen, C. R., Sosman, J. A., Muñoz‐Couselo, E., Kluger, H. M., McDermott, D. F., Powderly, J. D., Sarkar, I., Ballinger, M. D., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-3488 · Cited by 82
Phase I Study of Ceralasertib (AZD6738), a Novel DNA Damage Repair Agent, in Combination with Weekly Paclitaxel in Refractory Cancer
Kim, S. T., Smith, S. A., Mortimer, P. G. S., Loembé, A., Cho, H., Kim, K., Smith, C. L., Willis, S. E., Irurzun‐Arana, I., Berges, A., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-0251 · Cited by 83
“The methods for DNA/RNA extraction and for sequencing/reporting/validation of the assay were carried out according to previously published reports (23).”
Method
Pan-cancer Analysis of Homologous Recombination Repair–associated Gene Alterations and Genome-wide Loss-of-Heterozygosity Score
Westphalen, C. B., Fine, A. D., André, F., Ganesan, S., Heinemann, V., Rouleau, É., Turnbull, C., Palacios, L. G., López, J. A., Sokol, E. S., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-2096 · Cited by 78
“…MRE11 ), was performed in a pan-cancer cohort of 160,790 tumor samples for multiple classes of alterations (short variants, insertions, deletions, copy-number events, and rearrangements), using the Foun-dationOne, FoundationOne Heme, and FoundationOne CDx assays (Foundation Medicine, Inc.; 26, 27).”

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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