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Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Open accessAbstract
As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. Here we describe a test based on massively parallel DNA sequencing to characterize base substitutions, short insertions and deletions (indels), copy number alterations and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens. We implemented a practical validation strategy with reference samples of pooled cell lines that model key determinants of accuracy, including mutant allele frequency, indel length and amplitude of copy change. Test sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%). We confirmed accuracy using 249 FFPE cancer specimens characterized by established assays. Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests.
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“Targeted multiplexed hotspot panels (e.g., Agena Oncocarta [Agena Bioscience, San Diego, CA], 47 SNaPshot [Applied Biosystems, Foster City, CA], 48 and next-generation sequencing [NGS] panels 49,50 ) have already been developed and are available in College of American Pathologists (CAP)-accredited academic and commercial laboratories.”
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“To identify drug-targetable mutations, CGP using nextgeneration sequencing using FoundationOne (Foundation Medicine, Cambridge, MA) was performed on the exons of 315 cancer-associated genes.(12) In addition, intronic regions of 28 genes that are known to be involved in somatic rearrangements were sequenced, and the mi…”
MethodPatil, T., Mushtaq, R. R., Marsh, S. A., Azelby, C. M., Pujara, M., Davies, K. D., Aisner, D. L., Purcell, W. T., Schenk, E. L., Pacheco, J. M., et al. (2019) · Clinical Lung Cancer · doi:10.1016/j.cllc.2019.11.008 · Cited by 39
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Twenty-First Century Precision Medicine in Oncology: Genomic Profiling in Patients With Cancer
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Park, Y., Lee, C. Y., Kang, S., Kim, H., Park, K. S., & Park, H. G. (2017) · Nanotechnology · doi:10.1088/1361-6528/aaa3a3 · Cited by 38
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“Base substitutions, indels, copy number alterations and rearrangements were called as previously described [12, 49].”
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“CGP was performed from FFPE tissue using the Clinical Laboratory Improvement Amendments-certified, College of American Pathologists-accredited, New York State-approved FoundationOne (DNA-seq) [8] or FoundationOne Heme (DNA/RNAseq) [9] assay.”
MethodJiao, X., He, X., Qin, B., Liu, K., Wu, Y., Liu, J., Hou, T., & Zang, Y. (2019) · Journal of Thoracic Disease · doi:10.21037/jtd.2019.11.04 · Cited by 38
“In addition to traditional targets such as EGFR, anaplastic lymphoma kinase (ALK), ROS proto-oncogene 1 (ROS1), MET, HER-2, BRAF, etc. Large test panels such as MSK-IMPACT (4), FMI (5) and Burning Rock (6) can provide more information, especially TMB, which Original Article The prognostic value of tumor mutation burde…”
On the Role of Artificial Intelligence in Genomics to Enhance Precision Medicine
Álvarez-Machancoses, Ó., deAndrés‐Galiana, E. J., Cernea, A., de la Viña, J. F. S., & Fernández‐Martínez, J. L. (2020) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s205082 · Cited by 53
Molecular characteristics and clinical features of multifocal glioblastoma
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Comprehensive molecular profiling broadens treatment options for breast cancer patients
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Clinical utility of comprehensive genomic profiling in Japan: Result of PROFILE-F study
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“The methods for this type of comprehensive genomic profiling have been previously published, and extensive methods can be found elsewhere [1, 2].”
MethodPredicting EGFR mutational status from pathology images using a real-world dataset
Pao, J. J., Biggs, M., Duncan, D., Lin, D. I., Davis, R., Huang, R. S. P., Ferguson, D., Janovitz, T., Hiemenz, M. C., Eddy, N. R., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-31284-6 · Cited by 40
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Molecular markers for breast cancer diagnosis, prognosis and targeted therapy
Lang, J. E., Wecsler, J. S., Press, M. F., & Tripathy, D. (2014) · Journal of Surgical Oncology · doi:10.1002/jso.23732 · Cited by 37
“Ross et al. used this approach to study metastatic CDH1 mutated invasive lobular carcinoma using FFPE specimens; the authors noted that 86% of such cases had one or more actionable mutation, including changes in PIK3CA, CCND1, ERBB2, FGFR1, MCL1, KRAS, NF1, AKT1, and BRCA2 [94].”
BackgroundInfluentialDetecting and targetting oncogenic fusion proteins in the genomic era
Davare, M. A., & Tognon, C. E. (2015) · Biology of the Cell · doi:10.1111/boc.201400096 · Cited by 37
“ROS1 CEP85L Angiosarcoma 23637631 Giacomini et al. (2013) GOPC Glioblastoma Multiforme 12661006 Charest et al.”
BackgroundLee, J., Kim, H. C., Hong, J. Y., Wang, K., Kim, S. Y., Jang, J., Kim, S. T., Park, J. O., Lim, H. Y., Kang, W. K., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.4462 · Cited by 37
“Sequencing data were processed using a customized analysis pipeline designed to detect all classes of genomic alterations, including base substitutions, short insertions and deletions, copy number alterations, and genomic rearrangements [13].”
MethodTumour heterogeneity: principles and practical consequences
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BRAF internal deletions and resistance to BRAF / MEK inhibitor therapy
Johnson, D. B., Childress, M. A., Chalmers, Z. R., Frampton, G. M., Ali, S. M., Rubinstein, S. M., Fabrizio, D. A., Ross, J. S., Balasubramanian, S., Miller, V. A., et al. (2017) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12674 · Cited by 37
“Both samples were evaluated by an extensively validated hybridcapturebased nextgeneration sequencing platform that sequences exons from 315 genes and introns from 28 genes (Frampton et al., 2013).”
MethodKaplan, H. G., Rostad, S. W., Ross, J. S., Ali, S. M., & Millis, S. Z. (2018) · Journal of the National Comprehensive Cancer Network · doi:10.6004/jnccn.2018.7033 · Cited by 36
Frequent ESR1 and CDK Pathway Copy-Number Alterations in Metastatic Breast Cancer
Basudan, A., Priedigkeit, N., Hartmaier, R. J., Sokol, E. S., Bahreini, A., Watters, R. J., Boisen, M. M., Bhargava, R., Weiss, K. R., Karsten, M. M., et al. (2018) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-18-0946 · Cited by 37
“Validation of ESR1CN amplifications enrichment in additional cohorts To validate our findings of ESR1 CN amplifications, we queried three additional data sets (AACR-GENIE, MSKCC, and FM) that used sequencing to characterize breast cancer metastases (35, 36, 43, 44).”
MethodComprehensive genetic alteration profiling in primary and recurrent glioblastoma
Neilsen, B. K., Sleightholm, R. L., McComb, R. D., Ramkissoon, S. H., Ross, J. S., Corona, R. J., Miller, V. A., Cooke, M. B., & Aizenberg, M. R. (2018) · Journal of Neuro-Oncology · doi:10.1007/s11060-018-03070-2 · Cited by 39
Unique mutation patterns in anaplastic thyroid cancer identified by comprehensive genomic profiling
Khan, S. A., Ci, B., Xie, Y., Gerber, D. E., Beg, M. S., Sherman, S. I., Cabanillas, M. E., Busaidy, N. L., Burtness, B. A., Heilmann, A. M. F., et al. (2019) · Head & Neck · doi:10.1002/hed.25634 · Cited by 38
“The methods employed for this analysis have been previously described.(15) In brief, formalin-fixed paraffin-embedded slides or blocks from tumor samples were subjected to CGP at the reference laboratory (Foundation Medicine, Inc.”
MethodLi, G., Pavlick, D. C., Chung, J., Bauer, T. M., Tan, B. A., Peguero, J., Ward, P. J., Kallab, A. M., Bufill, J. A., Hoffman, A. D., et al. (2019) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo.2019.05.05 · Cited by 37
Discovery through clinical sequencing in oncology
Donoghue, M. T. A., Schram, A. M., Hyman, D. M., & Taylor, B. S. (2020) · Nature Cancer · doi:10.1038/s43018-020-0100-0 · Cited by 38
Jardim, D. L. F., Millis, S. Z., Ross, J. S., Woo, M. S.-A., Ali, S. M., & Kurzrock, R. (2020) · The Oncologist · doi:10.1634/theoncologist.2020-0509 · Cited by 37
Shang, Y., Li, X., Liu, W., Shi, X., Yuan, S. H., Huo, R., Fang, G., Han, X., Zhang, J., Wang, K., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-76791-y · Cited by 36
Jiang, B., Mu, Q., Qiu, F., Li, X., Xu, W., Yu, J., Fu, W., Cao, Y. B., & Wang, J. (2021) · Nature Communications · doi:10.1038/s41467-021-27017-w · Cited by 39
Kim, K. B., Soroceanu, L., de Semir, D., Millis, S. Z., Ross, J. S., Vosoughi, E., Dar, A. A., Nosrati, M., Desprez, P., Ice, R. J., et al. (2021) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.01.024 · Cited by 38
Chiang, Y., Lin, P., & Cheng, W. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.675972 · Cited by 38
Ma, X., Guo, Z., Wei, X., Zhao, G., Han, D., Zhang, T., Chen, X., Cao, F., Dong, J., Zhao, L., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.786429 · Cited by 39
“High TMB tumors had the high possibility to produce more tumor neoantigens, thus elevating antigen presentation and inducing an A B DC FIGURE 8 | Spatial distribution of dendritic cells and macrophages associated with tumor mutation burden.”
MethodInfluentialDagogo‐Jack, I., Madison, R. W., Lennerz, J. K., Chen, K., Hopkins, J. F., Schrock, A. B., Ritterhouse, L. L., Lester, A., Wharton, K. A., Mino-Kenudson, M. A., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.21.00422 · Cited by 37
HRAS Mutations Define a Distinct Subgroup in Head and Neck Squamous Cell Carcinoma
Coleman, N., Marcelo, K. L., Hopkins, J. F., Khan, N., Du, R. R., Hong, L., Park, E., Balsara, B., Leoni, M., Pickering, C. R., et al. (2023) · JCO Precision Oncology · doi:10.1200/po.22.00211 · Cited by 36
Bauer, T. M., Moore, K. N., Rader, J. S., Simpkins, F. A., Mita, A. C., Beck, J. T., Hart, L. L., Chu, Q. S.-C., Oza, A. M., Tinker, A. V., et al. (2023) · Targeted Oncology · doi:10.1007/s11523-023-00965-7 · Cited by 38
“Profiling of somatic genetic alterations in the archival tumors of patients responding to adavosertib treatment was performed using the FoundationOne® assay (F1) and analyzed using FMI’s F1 classification rules; targeted genomic profiling was presented using an in-house bioinformatics platform (Oncoprofile tool) and c…”
MethodPtashkin, R. N., Ewalt, M. D., Jayakumaran, G., Kiecka, I. J., Bowman, A. S., Yao, J., Casanova, J., Lin, Y.-T. D., Petrova‐Drus, K., Mohanty, A. S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42585-9 · Cited by 39
Bhatia, A., Moreno, R., Reiner, A. S., Nandakumar, S., Walch, H. S., Thomas, T. M., Nicklin, P. J., Choi, Y., Skakodub, A., Malani, R., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-1180 · Cited by 40
Orechia, J. A., Pathak, A., Shi, Y., Nawani, A., Belozerov, A., Fontes, C., Lakhiani, C., Jawale, C. V., Patel, C., Quinn, D., et al. (2015) · Applied & Translational Genomics · doi:10.1016/j.atg.2015.08.005 · Cited by 37
RET Fusion Lung Carcinoma: Response to Therapy and Clinical Features in a Case Series of 14 Patients
Sarfaty, M., Moore, A., Neiman, V., Dudnik, E., Ilouze, M., Gottfried, M., Katznelson, R., Nechushtan, H., Sorotsky, H. G., Paz, K., et al. (2016) · Clinical Lung Cancer · doi:10.1016/j.cllc.2016.09.003 · Cited by 36
Clinical mutational profiling of 1006 lung cancers by next generation sequencing
Illei, P. B., Belchis, D., Tseng, L., Nguyen, D. N., Marchi, F. D., Haley, L. M., Riel, S. L., Beierl, K. F., Zheng, G., Brahmer, J. R., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.18042 · Cited by 36
“Analysis of VAF may yield important information regarding mutant allelespecific imbalance (such as gene amplification or loss of heterozygosity), tumor heterogeneity, and germline mutations [7, 34, 35].”
BackgroundInfluentialRucaparib: a novel PARP inhibitor for BRCA advanced ovarian cancer
Colombo, I., Lheureux, S., & Oza, A. M. (2018) · Drug Design Development and Therapy · doi:10.2147/dddt.s130809 · Cited by 36
Calculating the Tumor Nuclei Content for Comprehensive Cancer Panel Testing
Mikubo, M., Seto, K., Kitamura, A., Nakaguro, M., Hattori, Y., Maeda, N., Miyazaki, T., Watanabe, K., Murakami, H., Tsukamoto, T., et al. (2019) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2019.09.081 · Cited by 36
Massoth, L. R., Hung, Y. P., Dias-Santagata, D. C., Onozato, M. L., Shah, N., Severson, E. A., Duncan, D. L., Gillespie, B. J., Williams, N. F., Ross, J. S., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00288 · Cited by 36
The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study
Conley, B. A., Staudt, L., Takebe, N., Wheeler, D. A., Wang, L., Cardenas, M., Korchina, V., Zenklusen, J. C., McShane, L. M., Tricoli, J. V., et al. (2020) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djaa061 · Cited by 36
“pdf) (17), which sequences the coding region of more than 300 cancer-related genes plus introns from 28 genes often”
BackgroundGobbini, É., Swalduz, A., Levra, M. G., Ortiz‐Cuaran, S., Toffart, A., Pérol, M., Moro‐Sibilot, D., & Saintigny, P. (2020) · Cancers · doi:10.3390/cancers12113112 · Cited by 36
“TMB status can be assessed on tissue using whole-exome sequencing (WES) or targeted NGS of a more focused panel of genes [99,100].”
BackgroundGraf, R. P., Fisher, V. A., Mateo, J., Gjoerup, O. V., Madison, R. W., Raskina, K., Tukachinsky, H., Creeden, J., Cunningham, R., Huang, R. S. P., et al. (2021) · European Urology · doi:10.1016/j.eururo.2021.09.030 · Cited by 37
Rodríguez-Rodríguez, L., Hirshfield, K. M., Rojas, V. A., DiPaola, R. S., Gibbon, D. G., Hellmann, M., Isani, S. S., Leiser, A., Riedlinger, G., Wagreich, A. R., et al. (2016) · Gynecologic Oncology · doi:10.1016/j.ygyno.2016.02.021 · Cited by 37
“Formalin-fixed, paraffin-embedded tumor specimens from patients in this trial underwent hybrid capture-based comprehensive genomic profiling (CGP) in a Clinical Laboratory Improvement Amendments (CLIA)-approved, New York State accredited commercial laboratory (Foundation Medicine, Inc, Cambridge, MA) [31].”
MethodPhenotypic and Genomic Determinants of Immunotherapy Response Associated with Squamousness
Goodman, A. M., Kato, S., Chattopadhyay, R., Okamura, R., Saunders, I. M., Montesion, M., Frampton, G. M., Miller, V. A., Daniels, G. A., & Kurzrock, R. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0716 · Cited by 35
“The methods and associated software information have been described previously (21).”
MethodGenomic alterations in cholangiocarcinoma: clinical significance and relevance to therapy
Carotenuto, M., Sacco, A., Forgione, L., & Normanno, N. (2022) · Exploration of Targeted Anti-tumor Therapy · doi:10.37349/etat.2022.00079 · Cited by 36
“00079 Page 208 Target enrichment via hybrid capture is achieved by using gene-specific hybridization probes to select the desired target sequences from shotgun genomic DNA libraries (DNA-based method) [110] or from libraries of expressed transcripts (RNA-based method) [116].”
MethodIdentification of Oncogenic and Drug-Sensitizing Mutations in the Extracellular Domain of FGFR2
Tanizaki, J., Ercan, D., Capelletti, M., Dodge, M. E., Xu, C., Bahcall, M., Tricker, E. M., Butaney, M., Calles, A., Sholl, L. M., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-3771 · Cited by 35
Pulse Afatinib for ERBB2 Exon 20 Insertion–Mutated Lung Adenocarcinomas
Costa, D. B., Jorge, S. E., Moran, J. P., Freed, J. A., Zerillo, J. A., Huberman, M. S., & Kobayashi, S. S. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.02.016 · Cited by 35
Goodman, A. M., Choi, M. P., Wieduwilt, M. J., Mulroney, C. M., Costello, C. L., Frampton, G. M., Miller, V. A., & Kurzrock, R. (2017) · JCO Precision Oncology · doi:10.1200/po.16.00004 · Cited by 35
Hilal, T., Nakazawa, M., Hodskins, J., Villano, J. L., Mathew, A., Goel, G., Wagner, L. M., Arnold, S. M., DeSimone, P. A., Anthony, L. B., et al. (2017) · BMC Cancer · doi:10.1186/s12885-017-3587-8 · Cited by 35
“The specificity is reported at >99% for all classes of genomic alterations [9].”
BackgroundLattanzi, M. W., Deng, F., Chiriboga, L. A., Femia, A. N., Meehan, S. A., Iyer, G., Voss, M. H., Sundatova, Y., Huang, W. C. W., & Balar, A. V. (2018) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-018-0415-x · Cited by 35
Clinical Applications of Next-Generation Sequencing in Precision Oncology
Karlovich, C., & Williams, P. M. (2019) · The Cancer Journal · doi:10.1097/ppo.0000000000000385 · Cited by 37
Taylor, S. E., Chu, T., Elvin, J. A., Edwards, R. P., & Zorn, K. K. (2019) · Gynecologic Oncology · doi:10.1016/j.ygyno.2019.10.029 · Cited by 36
A novel next generation sequencing approach to improve sarcoma diagnosis
Connell, L. M., Houghton, O. P., Stewart, P., Gazdová, J., Srivastava, S., Kim, C., Catherwood, M. A., Strobl, A., Flanagan, A. M., Oniscu, A., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-0488-1 · Cited by 36
“Due to the lower input requirements, sequencing costs and data storage, panel-based targeted sequencing is currently more suited to the clinical setting than more comprehensive approaches, such as whole genome sequencing (WGS), and there are many examples of the development and implementation of targeted sequencing pa…”
BackgroundAdvances in theranostic biomarkers for tumor immunotherapy
Bellesœur, A., Torossian, N., Amigorena, S., & Romano, E. (2020) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2020.02.005 · Cited by 34
Genetics and Genomics of Breast Cancer: update and translational perspectives
Biancolella, M., Testa, B., Salehi, L. B., D’Apice, M. R., & Novelli, G. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.03.013 · Cited by 34
Germline and somatic DNA repair gene alterations in prostate cancer
Dall’Era, M., McPherson, J. D., Gao, A. C., White, R. D., Gregg, J. P., & Lara, P. N. (2020) · Cancer · doi:10.1002/cncr.32908 · Cited by 35
“To maximize the accuracy of mutation detection (sensitivity and specificity) in impure clinical specimens, the test previously was optimized and validated to detect base substitutions at a mutant allele frequency of ≥5%, indels with a ≥10% mutant allele frequency with ≥99% accuracy, and fusions occurring within baited…”
MethodERBB2 Pathway in Biliary Tract Carcinoma: Clinical Implications of a Targetable Pathway
Jacobi, O., Ross, J. S., Goshen‐Lago, T., Haddad, R., Moore, A., Sulkes, A., Brenner, B., & Ben‐Aharon, I. (2020) · Oncology Research and Treatment · doi:10.1159/000511919 · Cited by 35
Okamura, R., Piccioni, D. E., Boichard, A., Lee, S., Jimenez, R. E., Sicklick, J. K., Kato, S., & Kurzrock, R. (2021) · International Journal of Cancer · doi:10.1002/ijc.33481 · Cited by 37
Kikuchi, J., Ohhara, Y., Takada, K., Tanabe, H., Hatanaka, K., Amano, T., Hatanaka, K. C., Hatanaka, Y., Mitamura, T., Kato, M., et al. (2020) · Japanese Journal of Clinical Oncology · doi:10.1093/jjco/hyaa277 · Cited by 35
Kim, H. Y., Song, J., & Park, H. G. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113048 · Cited by 35
NTRK fusions and Trk proteins: what are they and how to test for them
Weiss, L. M., & Funari, V. A. (2021) · Human Pathology · doi:10.1016/j.humpath.2021.03.007 · Cited by 36
Ramos‐Paradas, J., Hernández-Prieto, S., Lora, D., Sanchez, E., Rosado, A., Caniego-Casas, T., Carrizo, N., Enguita, A. B., Muñoz-Jimenez, M. T., Rodriguez, B., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-001904 · Cited by 35
“These findings should have an immediate impact on clinical practice and in the personalized management of patients with lung cancer.”
Real-World Performance of a Comprehensive Genomic Profiling Test Optimized for Small Tumor Samples
Tomlins, S. A., Hovelson, D. H., Suga, J. M., Anderson, D. M., Koh, H. A., Dees, E. C., McNulty, B., Burkard, M. E., Guarino, M. J., Khatri, J., et al. (2021) · JCO Precision Oncology · doi:10.1200/po.20.00472 · Cited by 36
“To maximize reportability, most CGP tests have tumor size (generally in mm(2) of tumor surface area [TSA]), TC, and nucleic acid yield or input requirements.(3,5,15) However, tissue CGP test failure rates of 30%-50% in clinical trial cohorts, where testing is attempted on all received samples (or those received below…”
BackgroundMethodInfluentialTumor Infiltrating Lymphocyte Expression of PD-1 Predicts Response to Anti-PD-1/PD-L1 Immunotherapy
Bevins, N., Okamura, R., Montesion, M., Adashek, J. J., Goodman, A. M., & Kurzrock, R. (2022) · Journal of Immunotherapy and Precision Oncology · doi:10.36401/jipo-22-9 · Cited by 39
“99% of exons.([24]) Concordance between sample replicates in the validation assessment was 97%, and no significant differences between interbatch and intraResearch Article 91”
BackgroundLooking beyond drivers and passengers in cancer genome sequencing data
De, S., & Ganesan, S. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw677 · Cited by 36
“Foundation Medicine [82]) now offer targeted sequencing of known cancer-associated genes in cancer in clinical settings with high reliability.”
InfluentialWilliams, E. A., Ravindranathan, A., Gupta, R. K., Stevers, N. O., Suwala, A. K., Hong, C., Kim, S., Yuan, J. B., Wu, J., Barreto, J., et al. (2023) · Neuro-Oncology · doi:10.1093/neuonc/noad121 · Cited by 34
“23 See Supplementary Methods for further details.”
Genomic characterization of thymic epithelial tumors in a real-world dataset
Kurokawa, K., Shukuya, T., Greenstein, R. A., Kaplan, B. G., Wakelee, H. A., Ross, J. S., Miura, K., Furuta, K., Kato, S., Suh, J. H., et al. (2023) · ESMO Open · doi:10.1016/j.esmoop.2023.101627 · Cited by 36
“15,16 Additional fi ltering was applied to exclude common germline variants based on presence in public databases (e.g. dbSNP, ExAC, 1000 genomes); of note, known pathogenic germline variants (e.g. in BRCA1 , BRCA2 ) were considered as reportable.”
Kerr, D. A., Cloutier, J. M., Margolis, M. L., Mata, D. A., Simoes, N. J. R., Faquin, W. C., Dias-Santagata, D. C., Chopra, S., Charville, G. W., Wangsiricharoen, S., et al. (2023) · Modern Pathology · doi:10.1016/j.modpat.2023.100386 · Cited by 34
Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples
Betge, J., Kerr, G., Miersch, T., Leible, S., Erdmann, G., Galata, C. L., Zhan, T., Gaiser, T., Post, S., Ebert, M. P. A., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127146 · Cited by 34
Shah, R. H., Scott, S. N., Brannon, A. R., Levine, D. A., Lin, O., & Berger, M. F. (2015) · Cancer Cytopathology · doi:10.1002/cncy.21522 · Cited by 34
Jeck, W. R., Parker, J. S., Carson, C. C., Shields, J. M., Sambade, M. J., Peters, E. C., Burd, C. E., Thomas, N. E., Chiang, D. Y., Liu, W., et al. (2014) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12238 · Cited by 35
“DNA quality from FFPE in general is adequate for capturebased NextGen sequencing, yielding results comparable to those obtained using frozen material [not shown and (Frampton et al., 2013)].”
ResultYang, M., Topaloĝlu, Ü., Petty, W. J., Pagni, M., Foley, K. L., Grant, S. C., Robinson, M., Bitting, R. L., Thomas, A., Alistar, A. T., et al. (2017) · Journal of Hematology & Oncology · doi:10.1186/s13045-017-0468-1 · Cited by 34
“Point mutations were identified by a Bayesian algorithm; short insertions and deletions determined by local assembly; gene copy number alterations identified by comparison to process-matched normal controls; and gene fusions/rearrangements determined by clustering chimeric reads mapped to targeted introns [33].”
BackgroundBoddu, S., Walko, C. M., Bienasz, S., Bui, M. M., Henderson‐Jackson, E., Naghavi, A. O., Mullinax, J. E., Joyce, D. M., Binitie, O. T., Letson, G. D., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.18.00096 · Cited by 34
Molinero, L. L., Li, Y., Chang, C., Maund, S. L., Berg, M., Harrison, J., Fassò, M., O'Hear, C. E., Hegde, P. S., & Emens, L. A. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0740-8 · Cited by 33
The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook
Lemus, E. H., Reyes-Gopar, H., Enríquez, J. E., & Ochoa, S. (2019) · Genes · doi:10.3390/genes10110865 · Cited by 33
“Although whole-genome sequencing has the advantage of uncovering the whole set of variations in a given tumor, sequencing a subset of the genome such as whole-exome or targeted regions is sometimes favored due to the lower cost and input DNA requirements, particularly in clinical settings [99].”
BackgroundPiha-Paul, S. A., Taylor, M. H., Spitz, D. L., Schwartzberg, L. S., Beck, J. T., Bauer, T. M., Meric‐Bernstam, F., Purkayastha, D., Karpiak, L., Szpakowski, S., et al. (2019) · Oncotarget · doi:10.18632/oncotarget.27251 · Cited by 34
“com lung cancer, with an overall response rate of 3% [14].”
BackgroundGilson, C., Ingleby, F. C., Gilbert, D. C., Parry, M., Atako, N. B., Ali, A., Hoyle, A. P., Clarke, N. W., Gannon, M. R., Wanstall, C., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00388 · Cited by 34
“The Foundation Medicine T7 hybrid-capture assay includes 395 cancer-related genes and reports singlenucleotide variants (SNVs), indels, copy-number alterations, and selected rearrangements.(18) We here report the pathogenic changes that occurred in 39 genes shown to be aberrant in prostate cancer on the basis of prior…”
BackgroundPrevalence of UV Mutational Signatures Among Cutaneous Primary Tumors
Mata, D. A., Williams, E. A., Sokol, E. S., Oxnard, G. R., Fleischmann, Z., Tse, J. Y., & Decker, B. J. (2022) · JAMA Network Open · doi:10.1001/jamanetworkopen.2022.3833 · Cited by 34
Framework for Adoption of Next-Generation Sequencing (NGS) Globally in the Oncology Area
Horgan, D., Hamdi, Y., Lal, J. A., Nyawira, T., Meyer, S., Kondji, D., Francisco, N. M., Guzman, R. B. D., Paul, A., Bernard, B., et al. (2023) · Healthcare · doi:10.3390/healthcare11030431 · Cited by 35
Genetic Heterogeneity and Tissue-specific Patterns of Tumors with Multiple PIK3CA Mutations
Sivakumar, S., Jin, D. X., Rathod, R., Ross, J. S., Cantley, L. C., Scaltriti, M., Chen, J. W., Hutchinson, K. E., Wilson, T. R., Sokol, E. S., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-2270 · Cited by 33
Spencer, K. R., Pappas, L., Baiev, I., Maurer, J. R., Bocobo, A. G., Zhang, K., Jain, A., Armas, A. D. D., Reyes, S., Le, T. M., et al. (2023) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djad046 · Cited by 33
“Tumor tissue underwent molecular profiling as a routine part of clinical care using FoundationOne (55) or institutional platforms (Supplementary Table 1, available online).”
MethodTung, N., Dougherty, K. C., Gatof, E. S., DeLeonardis, K., Hogan, L., Tukachinsky, H., Gornstein, E. L., Oxnard, G. R., McGregor, K., & Keller, R. B. (2023) · npj Precision Oncology · doi:10.1038/s41698-023-00429-1 · Cited by 35
Vokes, N. I., Galán‐Cobo, A., Fernandez-Chas, M., Molkentine, D. P., Treviño, S., Druker, V., Qian, Y., Patel, S. A., Schmidt, S., Hong, L., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-1122 · Cited by 35
“Genomic alterations were identi fi ed via CGP of > 300 cancer-related genes on FMI ’ s NGS test FoundationOne CDx (34 – 36).”
Zhao, X., Singhal, A., Park, S., Kong, J., Bachelder, R. E., & Ideker, T. (2024) · Cancer Discovery · doi:10.1158/2159-8290.cd-23-0641 · Cited by 35
“To model responses to RSi drugs, we focused on the set of 718 genes assessed by current clinical cancer gene panels, including one or more of FoundationOne CDx (40), Tem-pus xT (41), and Project GENIE (42).”
MethodKRAS Allelic Variants in Biliary Tract Cancers
Moffat, G. T., Hu, Z. I., Meric‐Bernstam, F., Kong, E., Pavlick, D., Ross, J. S., Murugesan, K., Kwong, L. N., Armas, A. D. D., Korkut, A., et al. (2024) · JAMA Network Open · doi:10.1001/jamanetworkopen.2024.9840 · Cited by 32
Folch, E. E., Costa, D. B., WRIGHT, J. P., & VanderLaan, P. A. (2015) · PubMed · doi:10.3978/j.issn.2218-6751.2015.08.02 · Cited by 35
“Therefore, a shift towards multiplexed panels seems inevitable in future (21).”
Background
Metadata
- Authors
- Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., An, P., Sun, J., Juhn, F., Brennan, K., Iwanik, K., Maillet, A., Buell, J., White, E., Zhao, M., Balasubramanian, S., Terzic, S., Richards, T., Banning, V., Garcia, L., Mahoney, K., Zwirko, Z., Donahue, A., Beltran, H., Mosquera, J. M., Rubin, M. A., Dogan, S., Hedvat, C. V., Berger, M. F., Pusztai, L., Lechner, M., Boshoff, C., Jarosz, M., Vietz, C., Parker, A., Miller, V. A., Ross, J. S., Curran, J., Cronin, M. T., Stephens, P. J., Lipson, D., & Yelensky, R.
- Affiliations
- Foundation Medicine (United States) (US)
- NewYork–Presbyterian Hospital (US)
- Memorial Sloan Kettering Cancer Center (US)
- Yale Cancer Center (US)
- University College London (GB)
- Corresponding author
- Lipson, Doron
- Yelensky, Roman
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2013-11
- Volume
- 31
- Issue
- 11
- Pages
- 1023-1031
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC5710001
- OpenAlex
- W2160981405
- Cited by
- 2,157
- References
- 54
- Citations by year
- 2026: 91 · 2025: 122 · 2024: 139 · 2023: 215 · 2022: 208 · 2021: 188 · 2020: 213 · 2019: 185 · 2018: 195 · 2017: 180 · 2016: 182 · 2015: 159 · 2014: 76 · 2013: 2
- FWCI
- 49.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust (WT093855MA)
- National Cancer Institute (P30CA008748)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Keywords
- tumor genomic profiling, analytical method validation, formalin-fixed paraffin-embedded tissue, copy number alterations, indels, gene fusion, actionable mutations, mutant allele frequency, sensitivity and specificity, precision oncology
- MeSH terms
- DNA Mutational Analysis, Gene Frequency, Humans, Neoplasms, Sensitivity and Specificity, Reproducibility of Results, Sequence Analysis, DNA, Molecular Diagnostic Techniques, DNA Copy Number Variations
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