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

The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.

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

Open access

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

Open this paper in CoChat — free account

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nbt.2696

Cites

54 of 54 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950
Self-citation
dbSNP: the NCBI database of genetic variation
Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017
Comprehensive genomic characterization of squamous cell lung cancers
The Cancer Genome Atlas Research Network (2012) · Nature · doi:10.1038/nature11404 · Cited by 3,994
The cancer genome
Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
Systematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456

Flagged first, then by citations

Show all 54 references

Sorted by citations

Items 501–600 of 1,001

Molecular profiling of metastatic colorectal tumors using next-generation sequencing: a single-institution experience
Gong, J., Cho, M. T., Sy, M., Salgia, R., & Fakih, M. (2017) · Oncotarget · doi:10.18632/oncotarget.15030 · Cited by 117
“The NGS assay performed by FoundationOne has been previously described and validated [45].”
Method
Clinical Benefit in Response to Palbociclib Treatment in Refractory Uterine Leiomyosarcomas with a Common CDKN2A Alteration
Elvin, J. A., Gay, L. M., Ort, R., Shuluk, J., Long, J. M., Shelley, L. B., Lee, R. D., Chalmers, Z. R., Frampton, G. M., Ali, S. M., et al. (2017) · The Oncologist · doi:10.1634/theoncologist.2016-0310 · Cited by 61
“recurrent uLMS (Table 1), as described previously [10].”
Comprehensive Genomic Profiling of Esthesioneuroblastoma Reveals Additional Treatment Options
Gay, L. M., Kim, S., Fedorchak, K., Kundranda, M. N., Odia, Y., Nangia, C. S., Battiste, J. D., Colón‐Otero, G., Powell, S. F., Russell, J. S., et al. (2017) · The Oncologist · doi:10.1634/theoncologist.2016-0287 · Cited by 59
“The samples were assayed by adaptor ligation hybrid capture, performed for all coding exons of 236 (v1), 315 (v2), or 405 (v3) cancer-related genes plus select introns from 19 (v1), 28 (v2), or 31 (v3) genes frequently rearranged in cancer (supplemental online Tables 1–3) [19, 20].”
BackgroundMethodInfluential
Mutation load and an effector T-cell gene signature may distinguish immunologically distinct and clinically relevant lymphoma subsets
Bolen, C. R., McCord, R., Huet, S., Frampton, G. M., Bourgon, R., Jardin, F., Dartigues, P., Punnoose, E. A., Szafer‐Glusman, E., Xerri, L., et al. (2017) · Blood Advances · doi:10.1182/bloodadvances.2016000786 · Cited by 60
Genomic landscape of advanced basal cell carcinoma: Implications for precision treatment with targeted and immune therapies
Goodman, A. M., Kato, S., Cohen, P. R., Boichard, A., Frampton, G. M., Miller, V. A., Stephens, P. J., Daniels, G. A., & Kurzrock, R. (2017) · OncoImmunology · doi:10.1080/2162402x.2017.1404217 · Cited by 59
“The median TMB (mutations/mb) (range) for nine basal cell carcinoma samples was 90 (3-103) while the median TMB (range) for 1637 samples with cancers other than basal cell carcinoma was 4 (1-860) (P < 0.”
Background
A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5
White, B. S., Lanc, I., O’Neal, J., Gupta, H., Fulton, R. S., Schmidt, H. K., Fronick, C. C., Belter, E. A., Fiala, M. A., King, J. A., et al. (2018) · Blood Cancer Journal · doi:10.1038/s41408-018-0062-y · Cited by 59
A large collection of integrated genomically characterized patient‐derived xenografts highlighting the heterogeneity of triple‐negative breast cancer
Coussy, F., de Koning, L., Lavigne, M., Bernard, V., Ouine, B., Boulai, A., Botty, R. E., Dahmani, A., Montaudon, É., Assayag, F., et al. (2019) · International Journal of Cancer · doi:10.1002/ijc.32266 · Cited by 59
“, base substitutions and short insertions/deletions).(23) Deleterious genomic alterations were defined as follows: (i) for oncogenes, only mutations driving to gain of function were considered (i.”
Background
Germline mutations of SMARCA4 in small cell carcinoma of the ovary, hypercalcemic type and in SMARCA4-deficient undifferentiated uterine sarcoma: Clinical features of a single family and comparison of large cohorts
Connor, Y., Miao, D., Lin, D. I., Hayne, C. C., Howitt, B. E., Dalrymple, J. L., DeLeonardis, K. R., Hacker, M. R., Esselen, K. M., & Shea, M. (2020) · Gynecologic Oncology · doi:10.1016/j.ygyno.2019.10.031 · Cited by 58
FGFR inhibitors in cholangiocarcinoma: what’s now and what’s next?
Saborowski, A. L., Lehmann, U., & Vogel, A. (2020) · Therapeutic Advances in Medical Oncology · doi:10.1177/1758835920953293 · Cited by 58
Adult diffuse midline gliomas: Clinical, radiological, and genetic characteristics
Dono, A., Takayasu, T., Ballester, L. Y., & Esquenazi, Y. (2020) · Journal of Clinical Neuroscience · doi:10.1016/j.jocn.2020.10.005 · Cited by 58
Tumor Mutational Burden in Real-World Patients With Pancreatic Cancer: Genomic Alterations and Predictive Value for Immune Checkpoint Inhibitor Effectiveness
Quintanilha, J. C. F., Storandt, M. H., Graf, R. P., Li, G., Keller, R. B., Lin, D. I., Ross, J. S., Huang, R. S. P., Schrock, A. B., Oxnard, G. R., et al. (2023) · JCO Precision Oncology · doi:10.1200/po.23.00092 · Cited by 61
A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors
Park, S., Silva, E., Singhal, A., Kelly, M. R., Licon, K. S., Panagiotou, I., Fogg, C., Fong, S. H., Lee, J. J. Y., Zhao, X., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00740-1 · Cited by 60
“Genetic alteration data: a panel of 718 clinical genes was assembled from the union of genes assessed by FoundationOne CDx 20 , Tempus xT 21 , PALOMA-3 trial 61 or Project GENIE 22 , each of which assesses mutations and/or copy number aberrations.”
MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing
Hempelmann, J. A., Scroggins, S. M., Pritchard, C. C., & Salipante, S. J. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.05.008 · Cited by 59
Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
Heydt, C., Fassunke, J., Künstlinger, H., Ihle, M. A., König, K., Heukamp, L. C., Schildhaus, H., Odenthal, M., Büttner, R., & Merkelbach‐Bruse, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0104566 · Cited by 58
“Further, more and more FFPE samples are small biopsies, which are now analysed by massively parallel sequencing [6].”
Background
Response to mTOR and PI3K inhibitors in enzalutamide-resistant luminal androgen receptor triple-negative breast cancer patient-derived xenografts
Coussy, F., Lavigne, M., de Koning, L., Botty, R. E., Némati, F., Naguez, A., Bataillon, G., Ouine, B., Dahmani, A., Montaudon, É., et al. (2020) · Theranostics · doi:10.7150/thno.36182 · Cited by 62
“The genomic alterations detected included single-nucleotide variations of SMGs (i.e. base substitutions and short insertions/deletions) [20].”
The genomic landscape of metastatic breast cancer: Insights from 11,000 tumors
Rinaldi, J., Sokol, E. S., Hartmaier, R. J., Trabucco, S. E., Frampton, G. M., Goldberg, M. E., Albacker, L. A., Daemen, A., & Manning, G. (2020) · PLoS ONE · doi:10.1371/journal.pone.0231999 · Cited by 57
“Samples were processed in the protocol defined by solid tumors and hematological cancers as previously described [33,34].”
MethodInfluential
Achieving high-sensitivity for clinical applications using augmented exome sequencing
Patwardhan, A. J., Harris, J., Leng, N., Bartha, G. T., Church, D. M., Luo, S. J., Haudenschild, C. D., Pratt, M., Zook, J. M., Salit, M., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0197-4 · Cited by 57
“As recently demonstrated [11–13], this includes the calculation of false positive (FP) and false negative (FN) rates using wellcharacterized reference materials (RM) and the reporting of depth of coverage and breadth of coverage statistics.”
Background
Saturation genome editing of BAP1 functionally classifies somatic and germline variants
Waters, A. J., Brendler-Spaeth, T., Smith, D., Offord, V., Tan, H. K., Zhao, Y., Obolenski, S., Nielsen, M., van Doorn, R., Murphy, J.-E., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01799-3 · Cited by 64
“Finally, to further explore the use of SGE data and identify novel BAP1 variants, we queried tumor sequence data for a cohort of 394,756 patient samples in the Foundation Medicine database 29 and found 12,172 (3.1”
Influential
Spatially resolved transcriptomics reveal the determinants of primary resistance to immunotherapy in NSCLC with mature tertiary lymphoid structures
Peyraud, F., Guégan, J., Rey, C., Lara, O., Odin, O., Castillo, M. D., Vanhersecke, L., Coindre, J., Clot, E., Brunet, M., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.101934 · Cited by 69
Tumor mutational burden and survival on immune checkpoint inhibition in >8000 patients across 24 cancer types
Gandara, D. R., Agarwal, N., Gupta, S., Klempner, S. J., Andrews, M. C., Mahipal, A., Subbiah, V., Eskander, R. N., Carbone, D. P., Riess, J. W., et al. (2025) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2024-010311 · Cited by 67
Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST)
Astolfi, A., Urbini, M., Indio, V., Nannini, M., Genovese, C. G., Santini, D., Saponara, M., Mandrioli, A., Ercolani, G., Brandi, G., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1982-6 · Cited by 61
“Indeed we know that targeted sequencing of clinically relevant mutation panels has become a feasible approach, that is increasingly applied in clinical practice to aid diagnosis and treatment choice [10, 25].”
Background
Evolving landscape of tumor molecular profiling for personalized cancer therapy: a comprehensive review
Syn, N. L. X., Yong, W. P., Goh, B. C., & Lee, S. C. (2016) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1080/17425255.2016.1196187 · Cited by 59
“There is also a need to perform validation checks in different ethnic populations to ensure that the information generated is reliable [103,104].”
Background
Comprehensive genomic profiling of malignant phyllodes tumors of the breast
Nozad, S., Sheehan, C. E., Gay, L. M., Elvin, J. A., Vergilio, J., Suh, J. H., Ramkissoon, S. H., Schrock, A. B., Hirshfield, K. M., Ali, N. Ş. M., et al. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4156-1 · Cited by 58
Next-generation sequencing of prostate cancer: genomic and pathway alterations, potential actionability patterns, and relative rate of use of clinical-grade testing
Ikeda, S., Elkin, S. K., Tomson, B. N., Carter, J. L., & Kurzrock, R. (2018) · Cancer Biology & Therapy · doi:10.1080/15384047.2018.1523849 · Cited by 59
Comprehensive characterization of PTEN mutational profile in a series of 34,129 colorectal cancers
Serebriiskii, I. G., Pavlov, V., Tricarico, R., Andrianov, G., Nicolas, E., Parker, M. I., Newberg, J., Frampton, G., Meyer, J. E., & Golemis, E. A. (2022) · Nature Communications · doi:10.1038/s41467-022-29227-2 · Cited by 55
Performance characteristics of next-generation sequencing in clinical mutation detection of colorectal cancers
Haley, L. M., Tseng, L., Zheng, G., Dudley, J. C., Anderson, D. A., Azad, N. S., Gocke, C. D., Eshleman, J. R., & Lin, M. (2015) · Modern Pathology · doi:10.1038/modpathol.2015.86 · Cited by 57
Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies
Hartmaier, R. J., Charo, J., Fabrizio, D. A., Goldberg, M. E., Albacker, L. A., Pao, W. J., & Chmielecki, J. (2017) · Genome Medicine · doi:10.1186/s13073-017-0408-2 · Cited by 57
“Samples were processed in one of two broad protocols generally defined by solid tumors or hematologic cancers as previously described [17, 18].”
Method
Phosphatidylinositol 3‐kinase pathway genomic alterations in 60,991 diverse solid tumors informs targeted therapy opportunities
Millis, S. Z., Jardim, D. L. F., Albacker, L. A., Ross, J. S., Miller, V. A., Ali, S. M., & Kurzrock, R. (2018) · Cancer · doi:10.1002/cncr.31921 · Cited by 56
“DNA was extracted from formalin-fixed, paraffin-embedded tissue, as previously described.(21) Patient identification was anonymized for the study.”
Method
Predictive Biomarkers of Immune Checkpoint Inhibition in Gastroesophageal Cancers
Sundar, R., Smyth, E. C., Peng, S., Yeong, J. P.-S., & Tan, P. B. O. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.00763 · Cited by 55
Role of ultraviolet mutational signature versus tumor mutation burden in predicting response to immunotherapy
Pham, T. V., Boichard, A., Goodman, A. M., Riviere, P. J., Yeerna, H., Tamayo, P., & Kurzrock, R. (2020) · Molecular Oncology · doi:10.1002/1878-0261.12748 · Cited by 57
Choosing tumor mutational burden wisely for immunotherapy: A hard road to explore
Li, R., Han, D., Shi, J., Han, Y., Tan, P., Zhang, R., & Li, J. (2020) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2020.188420 · Cited by 57
The role of PIM1 in the ibrutinib-resistant ABC subtype of diffuse large B-cell lymphoma.
Kuo, H.-P., Ezell, S. A., Hsieh, S., Schweighofer, K. J., Cheung, L. W. K., Wu, S., Apatira, M., Sirisawad, M., Eckert, K., Liang, Y., et al. (2016) · PubMed Central · Cited by 55
Loss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition?
Pawlyn, C., Loehr, A., Ashby, C., Tytarenko, R. G., Deshpande, S., Sun, J. X., Fedorchak, K., Mughal, T. I., Davies, F. E., Walker, B. A., et al. (2018) · Leukemia · doi:10.1038/s41375-018-0017-0 · Cited by 56
“DNA underwent targeted nextgeneration sequencing (FoundationOne Heme) interrogating 405 cancer-related genes and 3543 singlenucleotide polymorphisms (SNPs) across the genome as previously described [17, 18].”
Method
Association of ERBB Mutations With Clinical Outcomes of Afatinib- or Erlotinib-Treated Patients With Lung Squamous Cell Carcinoma: Secondary Analysis of the LUX-Lung 8 Randomized Clinical Trial
Goss, G. D., Felip, E., Cobo, M., Lu, S., Syrigos, K., Lee, K. H., Göker, E., Georgoulias, V., Li, W., Guclu, S., et al. (2018) · JAMA Oncology · doi:10.1001/jamaoncol.2018.0775 · Cited by 55
How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies
Gallon, R., Gawthorpe, P., Phelps, R., Hayes, C. M., Borthwick, G. M., Santibanez‐Koref, M., Jackson, M. S., & Burn, J. (2021) · Cancers · doi:10.3390/cancers13030406 · Cited by 57
Vulvar Squamous Cell Carcinoma: Comprehensive Genomic Profiling of HPV+ Versus HPV– Forms Reveals Distinct Sets of Potentially Actionable Molecular Targets
Williams, E. A., Werth, A. J., Sharaf, R., Montesion, M., Sokol, E. S., Pavlick, D. C., McLaughlin-Drubin, M., Erlich, R., Toma, H., Williams, K. J., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00406 · Cited by 54
Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures
Abbasi, A., & Alexandrov, L. B. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103200 · Cited by 59
A comprehensive genomic study of 390 H3F3A-mutant pediatric and adult diffuse high-grade gliomas, CNS WHO grade 4
Williams, E. A., Brastianos, P. K., Wakimoto, H., Zolal, A., Filbin, M. G., Cahill, D. P., Santagata, S., & Juratli, T. A. (2023) · Acta Neuropathologica · doi:10.1007/s00401-023-02609-6 · Cited by 59
“The samples were assayed by adaptor ligation hybrid capture, performed for all coding exons of 236 (v1), 315 (v2), or 405 (v3) cancer-related genes plus select introns from 19 (v1), 28 (v2), or 31 (v3) genes frequently rearranged in cancer [8, 10].”
Method
Cancer Driver Log (CanDL)
Damodaran, S., Miya, J., Kautto, E. A., Zhu, E. Y., Samorodnitsky, E., Datta, J., Reeser, J. W., & Roychowdhury, S. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.05.002 · Cited by 54
The minimal amount of starting DNA for Agilent’s hybrid capture-based targeted massively parallel sequencing
Chung, J., Son, D., Jeon, H.-J., Kim, K., Park, G., Ryu, G. H., Park, W., & Park, D. (2016) · Scientific Reports · doi:10.1038/srep26732 · Cited by 54
Individualized Molecular Analyses Guide Efforts (IMAGE): A Prospective Study of Molecular Profiling of Tissue and Blood in Metastatic Triple-Negative Breast Cancer
Parsons, H. A., Beaver, J. A., Cimino‐Mathews, A., Ali, S. M., Axilbund, J. E., Chu, D. T. W., Connolly, R. M., Cochran, R. L., Croessmann, S., Clark, T. A., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-1543 · Cited by 54
“Methods of the clinical cancer gene assay have been previously published, and assay performance has been rigorously validated (17).”
Method
Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests
Kim, J., Park, W., Kim, N. K. D., Jang, S. J., Chun, S., Sung, C. O., Choi, J., Ko, Y. H., Choi, Y., Shim, H. S., et al. (2017) · Journal of Pathology and Translational Medicine · doi:10.4132/jptm.2017.03.14 · Cited by 55
“regions.(23) During this type of validation, an adequate depth of coverage threshold(35) necessary to accurately call all expected variants can be empirically established by plotting false-positives and false-negatives as a function of coverage.”
Background
Comprehensive genomic profiling reveals inactivating SMARCA4 mutations and low tumor mutational burden in small cell carcinoma of the ovary, hypercalcemic-type
Lin, D. I., Chudnovsky, Y., Duggan, B., Zajchowski, D. A., Greenbowe, J. R., Ross, J. S., Gay, L. M., Ali, S. M., & Elvin, J. A. (2017) · Gynecologic Oncology · doi:10.1016/j.ygyno.2017.09.031 · Cited by 54
Intratumor heterogeneity inferred from targeted deep sequencing as a prognostic indicator
Oh, B. Y., Shin, H., Yun, J. W., Kim, K., Kim, J.-H., Bae, J. S., Cho, Y. B., Lee, W. Y., Yun, S. H., Park, Y. A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-41098-0 · Cited by 54
Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer
Han, C., Sasson, A., Srinivasan, S., Golhar, R., Greenawalt, D. M., Geese, W. J., Green, G. A., Zerba, K. E., Kirov, S. A., & Szustakowski, J. D. (2019) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-019-00408-y · Cited by 56
“12 into TMB tertiles based on their WES-derived somatic missense mutations (low [0–100], medium [100–242], high [≥243]).”
BackgroundMethod
Targeting ERBB2 ( HER2 ) Amplification Identified by Next-Generation Sequencing in Patients With Advanced or Metastatic Solid Tumors Beyond Conventional Indications
Dumbrava, E. E. I., Balaji, K., Raghav, K. P. S., Hess, K. R., Javle, M. M., Blum-Murphy, M. A., Ajani, J. A., Kopetz, S., Broaddus, R. R., Routbort, M. J., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00345 · Cited by 56
“HER2 amplification determined by NGS was defined according to each platform’s analytic pipeline, was based on the resulting reports and validation, and varied between greater than five to greater than seven estimated copy numbers for reporting high-confidence amplification.(29,30) For patients who underwent cfDNA anal…”
Method
Predictive Biomarkers for Immune Checkpoint Inhibitors in Metastatic Breast Cancer
Sivapiragasam, A., Kumar, P. A., Sokol, E. S., Albacker, L. A., Killian, J. K., Ramkissoon, S. H., Huang, R. S. P., Severson, E. A., Brown, C. A., Danziger, N. A., et al. (2020) · Cancer Medicine · doi:10.1002/cam4.3550 · Cited by 54
A retrospective observational study of the natural history of advanced non–small-cell lung cancer in patients with KRAS p.G12C mutated or wild-type disease
Spira, A. I., Tu, H., Aggarwal, S., Hsu, H., Carrigan, G. J., Wang, X., Ngarmchamnanrith, G., Chia, V., & Gray, J. E. (2021) · Lung Cancer · doi:10.1016/j.lungcan.2021.05.026 · Cited by 55
Comprehensive Genomic Profiling Reveals Diverse but Actionable Molecular Portfolios across Hematologic Malignancies: Implications for Next Generation Clinical Trials
Galanina, N., Bejar, R. L., Choi, M. Y., Goodman, A. M., Wieduwilt, M. J., Mulroney, C. M., Kim, L., Yeerna, H., Tamayo, P., Vergilio, J., et al. (2018) · Cancers · doi:10.3390/cancers11010011 · Cited by 54
“F1H is a validated clinical laboratory improvement amendments (CLIA)-approved, NY-state approved assay, and the methods used have been previously reported in detail [58,59].”
Method
Systematic pan-cancer analysis of mutation–treatment interactions using large real-world clinicogenomics data
Liu, R., Rizzo, S., Waliany, S., Garmhausen, M. R., Pal, N., Huang, Z., Chaudhary, N., Wang, L. E., Harbron, C. G., Neal, J. W., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01873-5 · Cited by 55
Phase II Clinical Trial of Axitinib and Avelumab in Patients With Recurrent/Metastatic Adenoid Cystic Carcinoma
Ferrarotto, R., de Sousa, L. G., Feng, L., Mott, F. E., Blumenschein, G. R., Altan, M., Bell, D., Bonini, F., Li, K., Marques-Piubelli, M. L., et al. (2023) · Journal of Clinical Oncology · doi:10.1200/jco.22.02221 · Cited by 57
Abemaciclib Is Effective in Palbociclib-Resistant Hormone Receptor–Positive Metastatic Breast Cancers
Navarro-Yepes, J., Kettner, N. M., Rao, X., Bishop, C. S., Bui, T. N., Wingate, H. F., Raghavendra, A. S., Wang, Y., Wang, J., Şahin, A. A., et al. (2023) · Cancer Research · doi:10.1158/0008-5472.can-23-0705 · Cited by 55
Activating PIK3CA Mutations Induce an Epidermal Growth Factor Receptor (EGFR)/Extracellular Signal-regulated Kinase (ERK) Paracrine Signaling Axis in Basal-like Breast Cancer*
Young, C. D., Zimmerman, L. J., Hoshino, D., Formisano, L., Hanker, A. B., Gatza, M. L., Morrison, M. M., Moore, P. D., Whitwell, C. A., Dave, B., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.049783 · Cited by 53
“DNA was extracted from the primary breast tumor and the recurrent lung metastasis and subjected to deep sequencing evaluating 3769 exons of 236 cancer-related genes and 47 introns from 19 genes that are frequently rearranged in cancer using the Illumina HiSeq 2000 to at an average depth exceeding 500 as previously des…”
Method
Molecular Alterations and Buparlisib Efficacy in Patients with Squamous Cell Carcinoma of the Head and Neck: Biomarker Analysis from BERIL-1
Soulières, D., Licitra, L. F., Mesı́a, R., Remenár, É., Li, S.-H., Karpenko, A., Chol, M., Wang, Y. A., Solovieff, N., Bourdeau, L., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-2644 · Cited by 54
“Extraction and processing of tumor DNA from FFPE archival tissue and ctDNA from plasma samples was performed using standard procedures as described previously (39, 40).”
Rare but Recurrent ROS1 Fusions Resulting From Chromosome 6q22 Microdeletions are Targetable Oncogenes in Glioma
Davare, M. A., Henderson, J. J., Agarwal, A., Wagner, J. P., Iyer, S. R., Shah, N., Woltjer, R. L., Somwar, R., Gilheeney, S. W., DeCarvalo, A., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1052 · Cited by 54
“Specifically, we referred to the NGS data generated by the Memorial Sloan Kettering Cancer Center (MSKCC) MSK–IMPACT (31, 32), and the Foundation Medicine genomic sequencing panels (33, 34) that conducted massively parallel DNA sequencing of 341 and 287 cancer-related genes, respectively.”
Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study
Glicksberg, B. S., Burns, S., Currie, R., Griffin, A., Wang, Z. J., Haussler, D. H., Goldstein, T. C., & Collisson, E. A. (2019) · Journal of Medical Internet Research · doi:10.2196/16810 · Cited by 53
“…sequencing of tumor specimens was ordered by the supervising physician (EC) as standard of care using either a commercial (Foundation Medicine; FMI [28]) or in-house panel (UCSF 500) [29]; 13 patients were sequenced and analyzed by Foundation Medicine [30] and 4 patients by the UCSF 500 [31]…”
Method
A recurrent endometrial stromal sarcoma harbors the novel fusion JAZF1-BCORL1
Allen, A. J., Ali, S. M., Gowen, K. A., Elvin, J. A., & Pejovic, T. B. (2017) · Gynecologic Oncology Reports · doi:10.1016/j.gore.2017.03.002 · Cited by 52
ctDNA Predicts Overall Survival in Patients With NSCLC Treated With PD-L1 Blockade or With Chemotherapy
Zou, W., Yaung, S. J., Fuhlbrück, F., Ballinger, M. D., Peters, E. J., Palma, J. F., Shames, D. S., Gandara, D. R., Jiang, Y., & Patil, N. S. (2021) · JCO Precision Oncology · doi:10.1200/po.21.00057 · Cited by 52
Comparative Genomic Analysis of Intrahepatic Cholangiocarcinoma: Biopsy Type, Ancestry, and Testing Patterns
Israel, M. A., Danziger, N. A., McGregor, K., Murugesan, K., Gjoerup, O. V., Sokol, E. S., Tukachinsky, H., Kurzrock, R., Kato, S., Sicklick, J. K., et al. (2021) · The Oncologist · doi:10.1002/onco.13844 · Cited by 51
A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors
Conroy, J. M., Pabla, S., Glenn, S. T., Seager, R. J., Roey, E. V., Gao, S., Burgher, B., Andreas, J., Giamo, V., Mallon, M., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0260089 · Cited by 52
“CGP by NGS can be performed using DNA and/or RNA for detecting different types of molecular changes including small variants (substitutions, insertions, deletions and indels), copy number alterations (gain and loss), and rearrangements (fusion and splice variant transcripts) [1, 3, 19].”
Method
Tumor mutation burden in the prognosis and response of lung cancer patients to immune-checkpoint inhibition therapies
Vryza, P., Fischer, T., Mistakidi, E., & Zaravinos, A. (2023) · Translational Oncology · doi:10.1016/j.tranon.2023.101788 · Cited by 55
“40 Mb which represent < 5 % of the whole coding sequence [38].”
Background
Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types
Kasi, P. M., Lee, J., Pasquina, L. W., Decker, B. J., Borre, P. V., Pavlick, D. C., Allen, J. M., Parachoniak, C. A., Quintanilha, J. C. F., Graf, R. P., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-2693 · Cited by 53
“Tissue biopsies from patients with the same cancer types as those analyzed for LBx that were ordered within the United States between January 2017 and January 2023 during routine clinical care ( N ¼ 295,592) were analyzed using FoundationOneCDx as described previously (18, 19).”
BackgroundMethod
Assessing the clinical value of targeted massively parallel sequencing in a longitudinal, prospective population-based study of cancer patients
Wong, S. Q., FELLOWES, A. P., Doig, K. M., Ellul, J., Bosma, T. J., Irwin, D. E., Vedururu, R., Tan, A., Weiss, J. M., Chan, K. S., et al. (2015) · British Journal of Cancer · doi:10.1038/bjc.2015.80 · Cited by 52
“Moreover, unlike the amplicon-based approach used in this study, many of the platforms utilised require much larger amounts of input DNA with turnaround times in excess of desirable practice (Wagle et al, 2012; Frampton et al, 2013; Pritchard et al, 2014).”
Method
FDA Perspective on Companion Diagnostics: An Evolving Paradigm
Mansfield, E. A. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-1954 · Cited by 52
“Clin Cancer Res; 20(6) March 15, 2014 Clinical Cancer Research 1454”
BackgroundMethodInfluential
Genomic Characterization of Testicular Germ Cell Tumors Relapsing After Chemotherapy
Necchi, A., Bratslavsky, G., Corona, R. J., Chung, J., Millis, S. Z., Elvin, J. A., Vergilio, J., Suh, J. H., Ramkissoon, S. H., Severson, E. A., et al. (2018) · European Urology Focus · doi:10.1016/j.euf.2018.07.013 · Cited by 52
Entrectinib in TRK and ROS1 Fusion-Positive Metastatic Pancreatic Cancer
Pishvaian, M. J., Garrido‐Laguna, I., Liu, S. V., Multani, P. S., Chow‐Maneval, E., & Rolfo, C. D. (2018) · JCO Precision Oncology · doi:10.1200/po.18.00039 · Cited by 53
Deep Learning-based Identification of Cancer or Normal Tissue using Gene Expression Data
Ahn, T., Goo, T., Lee, C., Kim, S. M., Han, K., Park, S., & Park, T. (2018) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2018.8621108 · Cited by 55
“B. Genes for training To build a prediction model using gene expression data, we prepared five gene sets to represent a different selection strategy: (1) the top 3,000 genes based on the rank of variance across all training samples (VAR_3000), (2) the top 3,000 genes with high mean expression values (Mean_3000), (3) t…”
Method
Genomic Assessment of Blood-Derived Circulating Tumor DNA in Patients With Colorectal Cancers: Correlation With Tissue Sequencing, Therapeutic Response, and Survival
Kato, S., Schwaederlé, M. C., Fanta, P. T., Okamura, R., Leichman, L., Lippman, S. M., Lanman, R. B., Raymond, V. M., Talasaz, A., & Kurzrock, R. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00158 · Cited by 52
Serial Profiling of Circulating Tumor DNA Identifies Dynamic Evolution of Clinically Actionable Genomic Alterations in High-Risk Neuroblastoma
Bosse, K. R., Giudice, A. M., Lane, M. V., McIntyre, B., Schürch, P. M., Pascual-Pasto, G., Buongervino, S. N., Suresh, S., Fitzsimmons, A., Hyman, A., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-22-0287 · Cited by 51
A Phase Ib/II, open-label, multicenter study of INC280 (capmatinib) alone and in combination with buparlisib (BKM120) in adult patients with recurrent glioblastoma
van den Bent, M. J., Azaro, A., Vos, F. D., Sepúlveda-Sánchez, J. M., Yung, W. K. A., Wen, P. Y., Lassman, A. B., Joerger, M., Tabatabai, G., Rodon, J. A., et al. (2019) · Journal of Neuro-Oncology · doi:10.1007/s11060-019-03337-2 · Cited by 51
Renal carcinoma associated with a novel succinate dehydrogenase A mutation: a case report and review of literature of a rare subtype of renal carcinoma
Özlük, Y., Taheri, D., Matoso, A., Şanlı, Ö., Berker, N. K., Yakirevich, E., Balasubramanian, S., Ross, J. S., Ali, S. M., & Netto, G. J. (2015) · Human Pathology · doi:10.1016/j.humpath.2015.07.027 · Cited by 51
Incidence and clinical significance of ESR1 mutations in heavily pretreated metastatic breast cancer patients
Niu, J., Andres, G., Kramer, K., Kundranda, M. N., Alvarez, R., Klimant, E., Parikh, A. R., Tan, B. A., Staren, E. D., & Markman, M. M. (2015) · OncoTargets and Therapy · doi:10.2147/ott.s92443 · Cited by 52
“The targeted NGS platform FO has been previously described and validated.(16) FO testing utilizes NGS to identify alterations in genes known to be somatically altered”
PARP Inhibitors in Reproductive System Cancers: Current Use and Developments
Coyne, G. O., Chen, A. P., Meehan, R. S., & Doroshow, J. H. (2017) · Drugs · doi:10.1007/s40265-016-0688-7 · Cited by 51
“Specificity exceeded 99% for all genomic alterations tested: base substitutions ([99% when mutant allele frequency [MAF] C5%), indels ([97% when MAF C10%), CNAs ([95%), and rearrangements ([90%) [48, 73].”
Background
High-affinity peptide ligand LXY30 for targeting α3β1 integrin in non-small cell lung cancer
Xiao, W., Ma, W., Wei, S., Li, Q., Liu, R., Carney, R. P., Yang, K., Lee, J., Nyugen, A., Yoneda, K. Y., et al. (2019) · Journal of Hematology & Oncology · doi:10.1186/s13045-019-0740-7 · Cited by 52
“Currently, tumor genomic profiling assays by NGS (such as FoundationOne CDx assay) require tumor cells to be present in at least 20% of cells in the cell block derived from pleural effusion or archived tumor specimens [41].”
Method
STK11 alterations in the pan-cancer setting: prognostic and therapeutic implications
Krishnamurthy, N., Goodman, A. M., Barkauskas, D. A., & Kurzrock, R. (2021) · European Journal of Cancer · doi:10.1016/j.ejca.2021.01.050 · Cited by 51
Genomic profiling reveals high frequency of DNA repair genetic aberrations in gallbladder cancer
Abdel‐Wahab, R., Yap, T. A., Madison, R. W., Pant, S., Cooke, M. B., Wang, K., Zhao, H., Bekaii‐Saab, T., Karatas, E., Kwong, L. N., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-77939-6 · Cited by 51
Efficacy of osimertinib plus bevacizumab in glioblastoma patients with simultaneous EGFR amplification and EGFRvIII mutation
Cardona, A. F., Jaramillo-Velásquez, D., Ruíz-Patiño, A., Polo, C., Jiménez, E., Hakim, F., Gómez, D., Ramón, J. F., Cifuentes, H., Mejía, J. A., et al. (2021) · Journal of Neuro-Oncology · doi:10.1007/s11060-021-03834-3 · Cited by 51
KRAS Mutation Status and Treatment Outcomes in Patients With Metastatic Pancreatic Adenocarcinoma
Norton, C., Shaw, M. S., Rubnitz, Z., Smith, J. L., Soares, H. P., Nevala-Plagemann, C., Garrido‐Laguna, I., & Florou, V. (2025) · JAMA Network Open · doi:10.1001/jamanetworkopen.2024.53588 · Cited by 50
Circulating tumor DNA as a liquid biopsy target for detection of pancreatic cancer
Takai, E., & Yachida, S. (2016) · World Journal of Gastroenterology · doi:10.3748/wjg.v22.i38.8480 · Cited by 53
Tumor Mutational Burden Guides Therapy in a Treatment Refractory POLE-Mutant Uterine Carcinosarcoma
Bhangoo, M. S., Boasberg, P. D., Mehta, P., Elvin, J. A., Ali, S. M., Wu, W., & Klempner, S. J. (2018) · The Oncologist · doi:10.1634/theoncologist.2017-0342 · Cited by 50
“Genotyping Results and the Interpretation of the Molecular Results Formalin-fixed, paraffin-embedded material from the April 2016 biopsy was sent for CGP using another commercial platform, as previously described [16, 17].”
Method
Somatic genetic aberrations in gallbladder cancer: comparison between Chinese and US patients
Yang, P., Javle, M. M., Pang, F., Wei, Z., Abdel‐Wahab, R., Chen, X., Meric‐Bernstam, F., Chen, H., Borad, M. J., Liu, Y., et al. (2019) · HepatoBiliary Surgery and Nutrition · doi:10.21037/hbsn.2019.04.11 · Cited by 49
“HepatoBiliary Surg Nutr 2019;8(6):604-614 | http://dx.”
Method
Clinical implications of plasma circulating tumor DNA in gynecologic cancer patients
Charo, L. M., Eskander, R. N., Okamura, R., Patel, S. P., Nikanjam, M., Lanman, R. B., Piccioni, D. E., Kato, S., McHale, M. T., & Kurzrock, R. (2020) · Molecular Oncology · doi:10.1002/1878-0261.12791 · Cited by 50
Hyperactivation of TORC1 drives resistance to the pan-HER tyrosine kinase inhibitor neratinib in HER2-mutant cancers
Sudhan, D. R., Guerrero-Zotano, A., Won, H., González Ericsson, P., Servetto, A., Huerta-Rosario, M., Ye, D., Lee, K.-M., Formisano, L., Guo, Y., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2019.12.013 · Cited by 49
“Tissue based targeted capture next-generation DNA sequencing was performed by Foundation medicine using the FoundationOneTM panel as described previously (Frampton et al., 2013).”
Method
Clinical and Immunological Implications of Frameshift Mutations in Lung Cancer
Chae, Y. K., de Viveiros, P. A. H., Junior, G. L. L., Sukhadia, B., Sheikh, M. M., Saravia, D., Florou, V., Sokol, E. S., Frampton, G. M., Chalmers, Z. R., et al. (2019) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2019.06.016 · Cited by 48
Frequent inactivating mutations of the PBAF complex gene PBRM1 in meningioma with papillary features
Williams, E. A., Wakimoto, H., Shankar, G. M., Barker, F. G., Brastianos, P. K., Santagata, S., Sokol, E. S., Pavlick, D. C., Shah, N., Reddy, A. K., et al. (2020) · Acta Neuropathologica · doi:10.1007/s00401-020-02161-7 · Cited by 49
A new generation of cancer genome diagnostics for routine clinical use: overcoming the roadblocks to personalized cancer medicine
Heuckmann, J. M., & Thomas, R. K. (2015) · Annals of Oncology · doi:10.1093/annonc/mdv184 · Cited by 48
Tissue-based next generation sequencing: application in a universal healthcare system
Hynes, S. O., Pang, B., James, J. A., Maxwell, P., & Salto‐Tellez, M. (2017) · British Journal of Cancer · doi:10.1038/bjc.2016.452 · Cited by 47
Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer
Raghav, K. P. S., Shen, J. P., Jacome, A. A. D. A., Guerra, J. L., Scally, C. P., Taggart, M. W., Foo, W. C., Matamoros, A., Shaw, K. R. M., Fournier, K. F., et al. (2020) · British Journal of Cancer · doi:10.1038/s41416-020-1015-3 · Cited by 48
A primer on precision medicine informatics
Sboner, A., & Elemento, O. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv032 · Cited by 50
Targeted sequencing identifies genetic alterations that confer primary resistance to EGFR tyrosine kinase inhibitor (Korean Lung Cancer Consortium)
Lim, S. M., Kim, H. R., Cho, E. K., Min, Y. J., Ahn, J. S., Ahn, M., Park, K., Cho, B. C., Lee, J.-H., Jeong, H. C., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.8904 · Cited by 48
“These panels use PCR capture-based NGS assay that allow deep targeted sequencing of genes of interest from limited formalinfixed, paraffin-embedded (FFPE) specimens [13].”
Method
Correlation of tumor mutational burden and treatment outcomes in patients with colorectal cancer
Pai, S. G., Carneiro, B. A., Chae, Y. K., Costa, R. L. B., Kalyan, A., Shah, H. A., Helenowski, I., RADEMAKER, A. W., Mahalingam, D., & Giles, F. J. (2017) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo.2017.06.20 · Cited by 47
“Extraction of DNA and NGS At least 50 ng DNA was extracted from archival formalinfixed, paraffin embedded tumor tissue and mutational data obtained by using hybridization capture of 3,769 exons of 315 cancer-related genes plus introns from 28 genes commonly rearranged in cancer (15,16).”
Method
Exceptional Response to Pembrolizumab in a Metastatic, Chemotherapy/Radiation-Resistant Ovarian Cancer Patient Harboring a PD-L1-Genetic Rearrangement
Bellone, S., Buza, N., Choi, J., Zammataro, L. A., Gay, L. M., Elvin, J. A., Rimm, D. L., Liu, Y., Ratner, E., Schwartz, P. E., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-1805 · Cited by 49
Value-based genomics
Gong, J., Pan, K., Fakih, M., Pal, S. K., & Salgia, R. (2018) · Oncotarget · doi:10.18632/oncotarget.24353 · Cited by 48
“fusions, copy number variations MSI TMB 5800 USD 14 days 2011 [50, 57]”
Background
Distinctive features of immunostaining and mutational load in primary pulmonary enteric adenocarcinoma: implications for differential diagnosis and immunotherapy
Chen, M., Liu, P., Yan, F., Xu, S., Jiang, Q., Pan, J., He, M., & Shen, P. (2018) · Journal of Translational Medicine · doi:10.1186/s12967-018-1449-z · Cited by 48
“The experimental procedure was performed as described previously [7].”
Association of Somatic Driver Alterations With Prognosis in Postmenopausal, Hormone Receptor–Positive, HER2-Negative Early Breast Cancer
Luen, S. J., Asher, R., Lee, C. K., Savas, P. S., Kammler, R., Dell’Orto, P., Biasi, O., Demanse, D., JeBailey, L., Dolan, S., et al. (2018) · JAMA Oncology · doi:10.1001/jamaoncol.2018.1778 · Cited by 48
Novel MXD4–NUTM1 fusion transcript identified in primary ovarian undifferentiated small round cell sarcoma
Tamura, R., Nakaoka, H., Yoshihara, K., Mori, Y., Yachida, N., Nishikawa, N., Motoyama, T., Okuda, S., Inoue, I., & Enomoto, T. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22668 · Cited by 46
“A threshold of ≥6 copies for gene amplification was used.(23) Cancer-associated genes that were annotated in OncoKB(24) were focused in this study.”
Background
Genomic Features of Metastatic Testicular Sex Cord Stromal Tumors
Necchi, A., Bratslavsky, G., Shapiro, O., Elvin, J. A., Vergilio, J., Killian, J. K., Ngo, N., Ramkissoon, S. H., Severson, E. A., Hemmerich, A. C., et al. (2019) · European Urology Focus · doi:10.1016/j.euf.2019.05.012 · Cited by 48
Integrating Genomics Into Clinical Pediatric Oncology Using the Molecular Tumor Board at the Memorial Sloan Kettering Cancer Center
Ortiz, M. V., Kobos, R., Walsh, M. F., Slotkin, E. K., Roberts, S. S., Berger, M. F., Hameed, M., Solit, D. B., Ladanyi, M., Shukla, N. N., et al. (2016) · Pediatric Blood & Cancer · doi:10.1002/pbc.26002 · Cited by 48
Prognostic impact of somatic mutations in diffuse large B-cell lymphoma and relationship to cell-of-origin: data from the phase III GOYA study
Bolen, C. R., Klánová, M., Trněný, M., Sehn, L. H., He, J., Tong, J., Paulson, J. N., Kim, E., Vitolo, U., Rocco, A. D., et al. (2019) · Haematologica · doi:10.3324/haematol.2019.227892 · Cited by 50
“Samples were submitted to a central laboratory for NGS-based genomic profiling and processed as previously described.(21,22)”
Method
MAPK Pathway Alterations Correlate with Poor Survival and Drive Resistance to Therapy in Patients with Lung Cancers Driven by ROS1 Fusions
Sato, H., Schoenfeld, A. J., Siau, E., Lu, Y. C., Tai, H., Suzawa, K., Kubota, D., Lui, A. J. W., Qeriqi, B., Mattar, M. S., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-3321 · Cited by 49
“MSK-IMPACT (13) was the primary platform, but results from other methods such as FoundationOne (14) were also included if performed.”
Method

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks