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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“These panels use PCR capture-based NGS assay that allow deep targeted sequencing of genes of interest from limited formalin-fixed, paraffin-embedded (FFPE) specimens [6].”
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MET tyrosine kinase receptor expression and amplification as prognostic biomarkers of survival in gastroesophageal adenocarcinoma
Catenacci, D. V. T., Ang, A. L., Liao, W., Shen, J., O’Day, E., Loberg, R. D., Cecchi, F., Hembrough, T., Ruzzo, A., & Graziano, F. (2016) · Cancer · doi:10.1002/cncr.30437 · Cited by 46
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BackgroundMethod
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MethodInfluential
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Method
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Method
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Method
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Method
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“Extensive technical descriptions and validation of the genomic profiling assays used to analyze these samples in the course of clinical care have been published previously [48, 49].”
Background
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“New NGS-technologies allow the detection of a great variety of somatic mutations instead of just screening for known “hotspot”-mutations [28], improving survival without adding to the financial burden in cancer care [29].”
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Clinicopathological and genomic characterization of BCORL1-driven high-grade endometrial stromal sarcomas
Lin, D. I., Huang, R. S. P., Mata, D. A., Decker, B. J., Danziger, N. A., Lechpammer, M., Hiemenz, M., Ramkissoon, S. H., Ross, J. S., & Elvin, J. A. (2021) · Modern Pathology · doi:10.1038/s41379-021-00873-z · Cited by 43
Landscape of homologous recombination deficiencies in solid tumours: analyses of two independent genomic datasets
Lai, Z., Brosnan, M., Sokol, E. S., Xie, M., Dry, J. R., Harrington, E. A., Barrett, J. C., & Hodgson, D. (2022) · BMC Cancer · doi:10.1186/s12885-021-09082-y · Cited by 43
“Foundation Medicine Inc. FoundationOne®CDx Technical Information.”
MethodInfluential
ARID1A mutations confer intrinsic and acquired resistance to cetuximab treatment in colorectal cancer
Johnson, R. M., Qu, X., Lin, C.-F., Huw, L.-Y., Venkatanarayan, A., Sokol, E., Ou, F.-S., Ihuegbu, N., Zill, O. A., Kabbarah, O., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33172-5 · Cited by 42
PARP Inhibitor Insensitivity to BRCA1/2 Monoallelic Mutations in Microsatellite Instability-High Cancers
Sokol, E. S., Jin, D. X., Fine, A. D., Trabucco, S. E., Maund, S. L., Frampton, G. M., Molinero, L. L., & Antonarakis, E. S. (2022) · JCO Precision Oncology · doi:10.1200/po.21.00531 · Cited by 47
“METHODS Comprehensive Genomic Profiling Comprehensive genomic profiling for all classes of alterations in at least 324 genes was performed on all-comers during routine clinical care using hybrid capture-based next-generation sequencing in a Clinical Laboratory Improvement Amendments–certified laboratory as previously…”
Method
Biology and Targetability of the Extended Spectrum of PIK3CA Mutations Detected in Breast Carcinoma
Rugo, H. S., Raskina, K., Schrock, A. B., Madison, R. W., Graf, R. P., Sokol, E. S., Sivakumar, S., Lee, J., Fisher, V. A., Oxnard, G. R., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-2115 · Cited by 42
Next-generation sequencing for the diagnosis of hereditary pheochromocytoma and paraganglioma syndromes
Toledo, R. A., & Dahia, P. L. M. (2015) · Current Opinion in Endocrinology Diabetes and Obesity · doi:10.1097/med.0000000000000150 · Cited by 42
“NGS exhibits much greater sensitivity and specificity for detection of substitutions than it does for other sequence changes [5,41,42].”
Background
Cell-Cycle Gene Alterations in 4,864 Tumors Analyzed by Next-Generation Sequencing: Implications for Targeted Therapeutics
Helsten, T. L., Kato, S., Schwaederle, M. C., 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-16-0071 · Cited by 41
“Samples were required to have a surface area 25 mm(2), volume 1 mm(3), nucleated cellularity 80%, and tumor content 20% (20).”
BackgroundMethod
Activity of c-Met/ALK Inhibitor Crizotinib and Multi-Kinase VEGF Inhibitor Pazopanib in Metastatic Gastrointestinal Neuroectodermal Tumor Harboring EWSR1-CREB1 Fusion
Subbiah, V., Holmes, O., Gowen, K. A., Spritz, D., Amini, B., Wang, W., Schrock, A. B., Meric‐Bernstam, F., Zinner, R., Piha-Paul, S. A., et al. (2016) · Oncology · doi:10.1159/000449204 · Cited by 41
Clinical Use of Precision Oncology Decision Support
Johnson, A. M., Khotskaya, Y. B., Brusco, L., Zeng, J., Holla, V. R., Bailey, A. M., Litzenburger, B. C., Sánchez, N., Shufean, M. A., Piha-Paul, S. A., et al. (2017) · JCO Precision Oncology · doi:10.1200/po.17.00036 · Cited by 42
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
Kato, M., Nakamura, H., Nagai, M., Kubo, T., Elzawahry, A., Totoki, Y., Tanabe, Y., Furukawa, E., Miyamoto, J., Sakamoto, H., et al. (2018) · Genome Medicine · doi:10.1186/s13073-018-0547-0 · Cited by 40
“Commercially developed algorithms for detecting SNVs/ indels and CNAs from FFPE-based sequencing data have been reported [6]; however, the software is not publicly available.”
BackgroundMethodInfluential
Degree of MDM2 Amplification Affects Clinical Outcomes in Dedifferentiated Liposarcoma
Bill, K. L. J., Seligson, N. D., Hays, J. L., Awasthi, A., Demoret, B., Stets, C. W., Duggan, M. C., Bupathi, M., Brock, G. N., Millis, S. Z., et al. (2019) · The Oncologist · doi:10.1634/theoncologist.2019-0047 · Cited by 46
“(FMI) data set contained 642 unique patients withMDM2-amplified DDLPS assayed as previously described [12].”
Method
Melanomas with activating RAF1 fusions: clinical, histopathologic, and molecular profiles
Williams, E. A., Shah, N., Montesion, M., Sharaf, R., Pavlick, D. C., Sokol, E. S., Alexander, B. M., Venstrom, J. M., Elvin, J. A., Ross, J. S., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-0510-7 · Cited by 41
Polyclonal BRCA2 mutations following carboplatin treatment confer resistance to the PARP inhibitor rucaparib in a patient with mCRPC: a case report
Simmons, A. D., Nguyen, M., & Pintus, E. (2020) · BMC Cancer · doi:10.1186/s12885-020-6657-2 · Cited by 41
Comprehensive genomic profiling for patients with chemotherapy‐naïve advanced cancer
Kondo, T., Matsubara, J., Quy, P. N., Fukuyama, K., Nomura, M., Funakoshi, T., Doi, K., Sakamori, Y., Yoshioka, M., Yokoyama, A., et al. (2020) · Cancer Science · doi:10.1111/cas.14674 · Cited by 41
Concomitant MEK and Cyclin Gene Alterations: Implications for Response to Targeted Therapeutics
Kato, S., Adashek, J. J., Shaya, J. A., Okamura, R., Jimenez, R. E., Lee, S., Sicklick, J. K., & Kurzrock, R. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3761 · Cited by 43
“The details of sample requirement, DNA extraction, and NGS were described previously (24).”
Method
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC
Zhao, X., Wang, A., Walter, V., Patel, N. M., Eberhard, D. A., Hayward, M. C., Salazar, A. H., Jo, H., Soloway, M. G., Wilkerson, M. D., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129280 · Cited by 44
Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center
Kytölä, V., Topaloĝlu, Ü., Miller, L. D., Bitting, R. L., Goodman, M. M., D`Agostino, R. B., Desnoyers, R. J., Albright, C. A., Yacoub, G., Qasem, S. A., et al. (2017) · Theranostics · doi:10.7150/thno.20355 · Cited by 40
“We quantified tumor clonal heterogeneity based on clustering of variant allele fractions (Figure S5A, B, see Methods).”
MethodInfluential
Broad Detection of Alterations Predicted to Confer Lack of Benefit from EGFR Antibodies or Sensitivity to Targeted Therapy in Advanced Colorectal Cancer
Rankin, A., Klempner, S. J., Erlich, R., Sun, J. X., Grothey, A., Fakih, M., George, T. J., Lee, J., Ross, J. S., Stephens, P. J., et al. (2016) · The Oncologist · doi:10.1634/theoncologist.2016-0148 · Cited by 40
Outcomes According to ALK Status Determined by Central Immunohistochemistry or Fluorescence In Situ Hybridization in Patients With ALK-Positive NSCLC Enrolled in the Phase 3 ALEX Study
Mok, T. S. K., Peters, S., Camidge, D. R., Noé, J., Gadgeel, S. M., Ou, S. I., Kim, D., Konopa, K., Pozzi, E., Liu, T., et al. (2020) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2020.10.007 · Cited by 42
Circulating kidney injury molecule-1 (KIM-1) and association with outcome to adjuvant immunotherapy in renal cell carcinoma
Rini, B. I., Albiges, L. K., Tang, X., Koeppen, H., Bex, A., Suárez, C., Uzzo, R. G., Hamidi, H., Assaf, Z. J. F., Dubey, S., et al. (2025) · Annals of Oncology · doi:10.1016/j.annonc.2025.08.007 · Cited by 43
Network-based stratification analysis of 13 major cancer types using mutations in panels of cancer genes
Zhong, X. Y., Yang, H., Zhao, S., Shyr, Y., & Li, B. (2015) · BMC Genomics · doi:10.1186/1471-2164-16-s7-s7 · Cited by 41
“In routine research and clinical application, instead of exome sequencing, a viable cost-effective alternative is to screen mutations in a panel of pre-selected cancer genes [19,20].”
Background
Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing
Bolognesi, C., Forcato, C., Buson, G., Fontana, F., Mangano, C., Doffini, A., Sero, V., Lanzellotto, R., Signorini, G., Calanca, A., et al. (2016) · Scientific Reports · doi:10.1038/srep20944 · Cited by 41
Validity of Targeted Next-Generation Sequencing in Routine Care for Identifying Clinically Relevant Molecular Profiles in Non–Small-Cell Lung Cancer
Legras, A., Barritault, M., Tallet, A., Fabre, E., Guyard, A., Rance, B., Digan, W. E., Pécuchet, N., Leprieur, E. G., Julié, C., et al. (2018) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2018.04.002 · Cited by 42
Real world data analysis of next generation sequencing and protein expression in metastatic breast cancer patients
Hempel, D., Ebner, F. K., Garg, A., Trepotec, Ž., Both, A., Stein, W., Gaumann, A. K. A., Güttler, L., Janni, W., deGregorio, A., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-67393-9 · Cited by 42
Unique Genomic Landscape of High-Grade Neuroendocrine Cervical Carcinoma: Implications for Rethinking Current Treatment Paradigms
Eskander, R. N., Elvin, J. A., Gay, L. M., Ross, J. S., Miller, V. A., & Kurzrock, R. (2020) · JCO Precision Oncology · doi:10.1200/po.19.00248 · Cited by 42
“The sequencing methods used for comprehensive genomic profiling have been validated and reported previously (Appendix).(12,13) The optimized loci used to evaluate MSI status were selected from a total set of 1,897 that have adequate coverage on all versions of the assay.”
BackgroundMethodInfluential
MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting
Schubart, C., Stöhr, R., Tögel, L., Fuchs, F. S., Sı̂rbu, H., Seitz, G., Seggewiß-Bernhardt, R., Leistner, R., Sterlacci, W., Vieth, M. W., et al. (2021) · Cancers · doi:10.3390/cancers13195023 · Cited by 41
“0 gene copies of the MET gene as amplified [23].”
Constructing germline research cohorts from the discarded reads of clinical tumor sequences
Gusev, A., Groha, S., Taraszka, K., Semenov, Y. R., & Zaitlen, N. (2021) · Genome Medicine · doi:10.1186/s13073-021-00999-4 · Cited by 33
Genomic testing among patients with newly diagnosed advanced non-small cell lung cancer in the United States: A contemporary clinical practice patterns study
Paz-Ares, L. G., Gondos, Á., Saldaña, D., Thomas, M., Mascaux, C., Bubendorf, L., & Barlési, F. (2022) · Lung Cancer · doi:10.1016/j.lungcan.2022.01.021 · Cited by 42
An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer
Haynes, B. C., Blidner, R., Cardwell, R. D., Zeigler, R., Gokul, S., Thibert, J. R., Chen, L., Fujimoto, J., Papadimitrakopoulou, V. A., Wistuba, I. I., et al. (2019) · Translational Oncology · doi:10.1016/j.tranon.2019.02.012 · Cited by 40
P16 immunohistochemistry is a sensitive and specific surrogate marker for CDKN2A homozygous deletion in gliomas
Vij, M., Cho, B. B., Yokoda, R. T., Rashidipour, O., Umphlett, M., Richardson, T. E., & Tsankova, N. M. (2023) · Acta Neuropathologica Communications · doi:10.1186/s40478-023-01573-2 · Cited by 43
“This profile was then corrected for GC bias, segmented, and used to estimate copy number at each segment, purity- and ploidy-adjusted [29, 30].”
Method
Progress in Thyroid Cancer Genomics: A 40-Year Journey
Fagin, J. A., & Nikiforov, Y. E. (2023) · Thyroid · doi:10.1089/thy.2023.0045 · Cited by 43
A Comprehensive Clinicopathologic and Molecular Reappraisal of GLI1-altered Mesenchymal Tumors with Pooled Outcome Analysis Showing Poor Survival in GLI1- amplified Versus GLI1-rearranged Tumors
Saoud, C., Agaimy, A., Dermawan, J. K. T. K., Chen, J., Rosenblum, M. K., Dickson, B. C., Dashti, N. K., Michal, M., Kösemehmetoğlu, K., Din, N. U., et al. (2024) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000002272 · Cited by 40
Integrated proteo-genomic approach for early diagnosis and prognosis of cancer
Shukla, H. D., Mahmood, J., & Vujašković, Ž. (2015) · Cancer Letters · doi:10.1016/j.canlet.2015.08.003 · Cited by 42
Comprehensive Genomic Profiling Identifies Frequent Drug-Sensitive EGFR Exon 19 Deletions in NSCLC not Identified by Prior Molecular Testing
Schrock, A. B., Frampton, G. M., Herndon, D., Greenbowe, J. R., Wang, K., Lipson, D., Yelensky, R., Chalmers, Z. R., Chmielecki, J., Elvin, J. A., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1668 · Cited by 39
“, base pair substitutions, insertions/deletions, copy number alterations, and rearrangements), and then matches clinically relevant alterations to targeted treatment options (8, 9).”
Background
TPD52L1-ROS1, a new ROS1 fusion variant in lung adenosquamous cell carcinoma identified by comprehensive genomic profiling
Zhu, V. W., Upadhyay, D., Schrock, A. B., Gowen, K. A., Ali, S. M., & Ou, S. I. (2016) · Lung Cancer · doi:10.1016/j.lungcan.2016.04.013 · Cited by 42
“s part of our routine practice, tissue was sent for comprehenive genomic profiling (CGP) as previously described (Foundation edicine, Cambridge, MA, USA) [4].”
Method
Challenges in identifying cancer genes by analysis of exome sequencing data
Hofree, M., Carter, H. K., Kreisberg, J. F., Bandyopadhyay, S., Mischel, P. S., Friend, S. H., & Ideker, T. (2016) · Nature Communications · doi:10.1038/ncomms12096 · Cited by 40
Oncologist use and perception of large panel next-generation tumor sequencing
Schram, A. M., Reales, D. N., Galle, J., Cambria, R., Durany, R., Feldman, D. R., Sherman, E. J., Rosenberg, J. E., D’Andrea, G. M., Baxi, S. S., et al. (2017) · Annals of Oncology · doi:10.1093/annonc/mdx294 · Cited by 42
Next generation sequencing of lung adenocarcinoma subtypes with intestinal differentiation reveals distinct molecular signatures associated with histomorphology and therapeutic options
Jurmeister, P. S., Vollbrecht, C., Behnke, A., Frost, N., Arnold, A., Treue, D., Rückert, J., Neudecker, J., Schweizer, L., Klauschen, F., et al. (2019) · Lung Cancer · doi:10.1016/j.lungcan.2019.10.005 · Cited by 40
Pan-sarcoma genomic analysis of KMT2A rearrangements reveals distinct subtypes defined by YAP1–KMT2A–YAP1 and VIM–KMT2A fusions
Massoth, L. R., Hung, Y. P., Nardi, V., Nielsen, G. P., Hasserjian, R. P., Louissaint, A., Fisch, A. S., Deshpande, V., Zukerberg, L. R., Lennerz, J. K., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-0582-4 · Cited by 41
Phase I Basket Study of Taselisib, an Isoform-Selective PI3K Inhibitor, in Patients with PIK3CA -Mutant Cancers
Jhaveri, K. L., Chang, M. T., Juric, D., Saura, C., Gambardella, V., Melnyk, A., Patel, M. R., Ribrag, V., Ma, C. X., Aljumaily, R. M., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-2657 · Cited by 40
Effectiveness of Alpelisib + Fulvestrant Compared with Real-World Standard Treatment Among Patients with HR+, HER2–, PIK3CA-Mutated Breast Cancer
Turner, S. J., Chia, S., Kanakamedala, H., Hsu, W., Park, J., Chandiwana, D., Ridolfi, A., Yu, C., Zarate, J. P., & Rugo, H. S. (2021) · The Oncologist · doi:10.1002/onco.13804 · Cited by 41
Comprehensive Genomic Profiling of 274 Thymic Epithelial Tumors Unveils Oncogenic Pathways and Predictive Biomarkers
Girard, N., Basse, C., Schrock, A. B., Ramkissoon, S. H., Killian, K. J., & Ross, J. S. (2022) · The Oncologist · doi:10.1093/oncolo/oyac115 · Cited by 41
Immune Checkpoint Inhibition in Metastatic Urothelial Cancer
Powles, T., Smith, K., Stenzl, A., & Bedke, J. (2017) · European Urology · doi:10.1016/j.eururo.2017.03.047 · Cited by 40
“A correlation between mutational burden (eg, estimated using Foundation One, which covers approximately 3% of the genome [15]) and outcome has been established for atezolizumab [3].”
Background
Genomic landscape of non‐small‐cell lung cancer with methylthioadenosine phosphorylase ( MTAP ) deficiency
Kumar, P. A., Graziano, S. L., Danziger, N. A., Pavlick, D. C., Severson, E. A., Ramkissoon, S. H., Huang, R. S. P., Decker, B. J., & Ross, J. S. (2022) · Cancer Medicine · doi:10.1002/cam4.4971 · Cited by 38
Methylthioadenosine Phosphorylase Genomic Loss in Advanced Gastrointestinal Cancers
Ngoi, N. Y. L., Tang, T., Gaspar, C. F., Pavlick, D. C., Buchold, G. M., Scholefield, E. L., Parimi, V., Huang, R. S. P., Janovitz, T., Danziger, N. A., et al. (2024) · The Oncologist · doi:10.1093/oncolo/oyae011 · Cited by 45
“22 Unless otherwise specified, short variants (single nucleotide variants and short insertion/deletions) were included in the analysis if they were annotated as either “Known Pathogenic” or “Likely Pathogenic.””
Method
Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision making
Weiss, G. J., Hoff, B. R., Whitehead, R. P., Sangal, A., Gingrich, S. A., Penny, R., Mallery, D. W., Morris, S., Thompson, E. J., Loesch, D. M., et al. (2015) · OncoTargets and Therapy · doi:10.2147/ott.s81995 · Cited by 39
“Tumor specimens and clinical annotation FFPE tumor tissues were ordered by the treating physician when deemed clinically appropriate for F1 testing and were submitted for commercial testing according to Foundation Medicine’s commercial laboratory standards.(8) Clinically appropriate testing was defined as (i) patient…”
Method
Integrative molecular profiling of routine clinical prostate cancer specimens
Grasso, C. S., Cani, A. K., Hovelson, D. H., Quist, M. J., Douville, N. J., Yadati, V., Amin, A. M., Nelson, P., Betz, B. L., Liu, C.-J., et al. (2015) · Annals of Oncology · doi:10.1093/annonc/mdv134 · Cited by 41
“Liu1, K. E. Knudsen11,12,13, K. A. Cooney4,7, F. Y. Feng5,7, A. S. McDaniel1 & S. A. Tomlins1,6,7* 1Michigan Center for Translational Pathology, Department of Pathology; Departments of 2Computational Medicine & Bioinformatics; 3Anesthesiology; 4Internal Medicine; 5Radiation Oncology; 6Urology; 7Comprehensive Cancer Ce…”
Background
Challenges Posed to Pathologists in the Detection of KRAS Mutations in Colorectal Cancers
Dudley, J. C., Tseng, L., Rooper, L. M., Harris, M., Haley, L. M., Chen, G., Gocke, C. D., Eshleman, J. R., & Lin, M. (2015) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2013-0649-oa · Cited by 39
“In the clinical molecular diagnostics setting, specimens from unselected patients often have a low tumor cellularity and therefore require assays with higher analytic sensitivity.(24) Improvement of sensitivity can also be achieved at the preanalytic step by macrodissection or microdissection.”
Next-generation sequencing in the clinic
Park, J. Y., Kricka, L. J., & Fortina, P. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2743 · Cited by 39

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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