Institutional implementation of clinical tumor profiling on an unselected cancer population
Open accessAbstract
BACKGROUND. Comprehensive genomic profiling of a patient’s cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. METHODS. We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested. RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR , associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a “cancer-agnostic” approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS. Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).
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
Cites
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?
Only a small proportion of patients, approximately 10-20%, have an actionable alteration that can be coupled to a specific intervention.
“However, as shown in several clinical trials161–165, only a small proportion of patients (approx. 10–20%) have an actionable alteration that can be coupled to a specific intervention161.”
From Organoids (2022) · cites this paper as [163]
The pan-cancer results report that 19% of alterations could inform standard-of-care therapeutic decisions, consistent with the claim’s approximate range for that narrower category. But they also report that 73% of the cohort had a clinically actionable or informative alteration, including alterations that could guide trial enrollment. The claim does not make that distinction and understates the broader proportion. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455 · see citing works
Self-citationIntegrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160 · see citing works
Self-citationGefitinib or Carboplatin–Paclitaxel in Pulmonary Adenocarcinoma
Mok, T. S., Wu, Y.-L., Thongprasert, S., Yang, C.-H., Chu, D.-T., Saijo, N., Sunpaweravong, P., Han, B., Margono, B., Ichinose, Y., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0810699 · Cited by 8,261 · see citing works
Improved survival with vemurafenib in melanoma with BRAF V600E mutation
Chapman, P. B., Hauschild, A., Robert, C., Haanen, J. B., Ascierto, P., Larkin, J., Dummer, R., Garbe, C., Testori, A., Maio, M., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1103782 · Cited by 7,720 · see citing works
Mutational heterogeneity in cancer and the search for new cancer-associated genes
Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) · Nature · doi:10.1038/nature12213 · Cited by 5,461 · see citing works
Self-citationEfficacy and safety of imatinib mesylate in advanced gastrointestinal stromal tumors
Demetri, G. D., von Mehren, M., Blanke, C. D., Van den Abbeele, A. D., Eisenberg, B., Roberts, P. J., Heinrich, M. C., Tuveson, D. A., Singer, S., Janicek, M., et al. (2002) · New England Journal of Medicine · doi:10.1056/nejmoa020461 · Cited by 4,389 · see citing works
Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr–Abl positive cells
Druker, B. J., Tamura, S., Buchdunger, E., Ohno-Jones, S., Segal, G. M., Fanning, S., Zimmermann, J., & Lydon, N. (1996) · Nature Medicine · doi:10.1038/nm0596-561 · Cited by 3,618 · see citing works
Cobleigh, M., Vogel, C. L., Tripathy, D., Robert, N. J., Scholl, S., Fehrenbacher, L., Wolter, J. M., Paton, V. E., Shak, S., Lieberman, G., et al. (1999) · Journal of Clinical Oncology · doi:10.1200/jco.1999.17.9.2639 · Cited by 2,767 · see citing works
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., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2696 · Cited by 2,157 · cited 1× · see citing works
“Discussion In recent years, a number of academic cancer centers, hospitals, and commercial entities have established genomic profiling programs (11, 12, 16, 17, 20, 24, 26, 40) that differ in terms of technology and gene panel content (varying from tens to hundreds or thousands of genes) as well as target patient popu…”
BackgroundMemorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)
Cheng, D. T., Mitchell, T. N., Zehir, A., Shah, R. H., Benayed, R., Syed, A., Chandramohan, R., Liu, Z. Y., Won, H. H., Scott, S. N., et al. (2015) · The Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.12.006 · Cited by 2,119 · see citing works
Using Multiplexed Assays of Oncogenic Drivers in Lung Cancers to Select Targeted Drugs
Kris, M. G., Johnson, B. E., Berry, L. D., Kwiatkowski, D. J., Iafrate, A. J., Wistuba, I. I., Varella-Garcia, M., Franklin, W. A., Aronson, S. L., Su, P.-F., et al. (2014) · JAMA · doi:10.1001/jama.2014.3741 · Cited by 1,724 · see citing works
Self-citationActivation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer
Zhang, Z., Lee, J. C., Lin, L., Olivas, V., Au, V., LaFramboise, T., Abdel-Rahman, M., Wang, X., Levine, A. D., Rho, J. K., et al. (2012) · Nature Genetics · doi:10.1038/ng.2330 · Cited by 1,224 · see citing works
Le Tourneau, C., Delord, J.-P., Gonçalves, A., Gavoille, C., Dubot, C., Isambert, N., Campone, M., Trédan, O., Massiani, M.-A., Mauborgne, C., et al. (2015) · The Lancet Oncology · doi:10.1016/s1470-2045(15)00188-6 · Cited by 1,137 · see citing works
Jackman, D., Pao, W., Riely, G. J., Engelman, J. A., Kris, M. G., Jänne, P. A., Lynch, T., Johnson, B. E., & Miller, V. A. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.24.7049 · Cited by 793 · see citing works
Self-citationAwad, M. M., Oxnard, G. R., Jackman, D. M., Savukoski, D. O., Hall, D., Shivdasani, P., Heng, J. C., Dahlberg, S. E., Janne, P. A., Verma, S., et al. (2016) · Journal of Clinical Oncology · doi:10.1200/jco.2015.63.4600 · Cited by 697 · see citing works
Self-citationGenome Sequencing Identifies a Basis for Everolimus Sensitivity
Iyer, G., Hanrahan, A. J., Milowsky, M. I., Al‐Ahmadie, H. A., Scott, S. N., Janakiraman, M., Pirun, M., Sander, C., Socci, N. D., Ostrovnaya, I., et al. (2012) · Science · doi:10.1126/science.1226344 · Cited by 688 · see citing works
Hoff, D. D. V., Stephenson, J. J., Rosen, P. J., Loesch, D. M., Borad, M. J., Anthony, S. P., Jameson, G., Brown, S., Cantafio, N. A., Richards, D., et al. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.26.5983 · Cited by 650 · see citing works
Yasuda, H., Park, E., Yun, C.-H., Sng, N. J., Lucena-Araujo, A. R., Yeo, W.-L., Huberman, M. S., Cohen, D. W., Nakayama, S., Ishioka, K., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3007205 · Cited by 571 · see citing works
Self-citationPersonalized Medicine in a Phase I Clinical Trials Program: The MD Anderson Cancer Center Initiative
Tsimberidou, A. M., Iskander, N. G., Hong, D. S., Wheler, J. J., Falchook, G. S., Fu, S., Piha-Paul, S. A., Naing, A., Jankú, F., Luthra, R., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-1627 · Cited by 538 · see citing works
Allen, E. M. V., Wagle, N., Stojanov, P., Perrin, D., Cibulskis, K., Marlow, S., Jané‐Valbuena, J., Friedrich, D. C., Kryukov, G. V., Carter, S. L., et al. (2014) · Nature Medicine · doi:10.1038/nm.3559 · Cited by 533 · see citing works
Self-citationWagle, N., Berger, M. F., Davis, M. J., Blumenstiel, B. S., DeFelice, M. T., Pochanard, P., Ducar, M. D., Hummelen, P. V., MacConaill, L. E., Hahn, W. C., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0184 · Cited by 526 · see citing works
Self-citationMeric-Bernstam, F., Brusco, L., Shaw, K., Horombe, C., Kopetz, S., Davies, M. A., Routbort, M., Piha-Paul, S. A., Janku, F., Ueno, N., et al. (2015) · Journal of Clinical Oncology · doi:10.1200/jco.2014.60.4165 · Cited by 424 · see citing works
Personalized genomic analyses for cancer mutation discovery and interpretation
Jones, S., Anagnostou, V., Lytle, K., Parpart-Li, S. T., Nesselbush, M. C., Riley, D. R. J., Shukla, M., Chesnick, B., Kadan, M., Papp, E., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa7161 · Cited by 413 · see citing works
Brannon, A. R., Vakiani, E., Sylvester, B. E., Scott, S. N., McDermott, G. C., Shah, R. H., Kania, K., Viale, A. J., Oschwald, D. M., Vacic, V., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0454-7 · Cited by 369 · see citing works
Genomics-Driven Oncology: Framework for an Emerging Paradigm
Garraway, L. A. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.46.8934 · Cited by 339 · see citing works
Self-citationWhole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response
Beltran, H., Eng, K., Mosquera, J. M., Sigaras, A., Romanel, A., Rennert, H., Kossaï, M., Pauli, C., Faltas, B. M., Fontugne, J., et al. (2015) · JAMA Oncology · doi:10.1001/jamaoncol.2015.1313 · Cited by 287 · see citing works
Wagle, N., Grabiner, B. C., Allen, E. M. V., Hodis, E., Jacobus, S. J., Supko, J. G., Stewart, M. L., Choueiri, T. K., Gandhi, L., Cleary, J. M., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0353 · Cited by 281 · see citing works
Self-citationDrilon, A., Wang, L., Arcila, M. E., Balasubramanian, S., Greenbowe, J. R., Ross, J. S., Stephens, P., Lipson, D., Miller, V. A., Kris, M. G., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2683 · Cited by 274 · see citing works
Physicians' Attitudes About Multiplex Tumor Genomic Testing
Gray, S. W., Hicks-Courant, K., Cronin, A. M., Rollins, B. J., & Weeks, J. C. (2014) · Journal of Clinical Oncology · doi:10.1200/jco.2013.52.4298 · Cited by 241 · see citing works
Self-citationLopez-Chavez, A., Thomas, A., Rajan, A., Raffeld, M., Morrow, B., Kelly, R., Carter, C. A., Guha, U., Killian, K., Lau, C. C., et al. (2015) · Journal of Clinical Oncology · doi:10.1200/jco.2014.58.2007 · Cited by 233 · see citing works
Harris, M. H., DuBois, S. G., Glade Bender, J. L., Kim, A., Crompton, B. D., Parker, E., Dumont, I. P., Hong, A. L., Guo, D., Church, A., et al. (2016) · JAMA Oncology · doi:10.1001/jamaoncol.2015.5689 · Cited by 206 · see citing works
Self-citationGandhi, L., Bahleda, R., Tolaney, S. M., Kwak, E. L., Cleary, J. M., Pandya, S. S., Hollebecque, A., Abbas, R., Ananthakrishnan, R., Berkenblit, A., et al. (2014) · Journal of Clinical Oncology · doi:10.1200/jco.2012.47.2787 · Cited by 198 · see citing works
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine
Garofalo, A., Sholl, L. M., Reardon, B. M., Taylor-Weiner, A. N., Amin‐Mansour, A., Miao, D., Liu, D., Oliver, N. M., MacConaill, L. E., Ducar, M. D., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0333-9 · Cited by 178 · see citing works
Self-citationRho, J. K., Choi, Y. J., Kim, S. Y., Kim, T. W., Choi, E. K., Yoon, S.-J., Park, B. M., Park, E., Bae, J. H., Choi, C., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-1103 · Cited by 144 · see citing works
Spencer, D. H., Abel, H., Lockwood, C. M., et al. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.08.001 · Cited by 142 · see citing works
Building a Personalized Medicine Infrastructure at a Major Cancer Center
Meric‐Bernstam, F., Farhangfar, C. J., Mendelsohn, J. M., & Mills, G. B. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.45.3043 · Cited by 112 · see citing works
Johnson, D. B., Dahlman, K. H., Knol, J., Gilbert, J., Puzanov, I., Means-Powell, J., Balko, J., Lovly, C., Murphy, B., Goff, L., et al. (2014) · The Oncologist · doi:10.1634/theoncologist.2014-0011 · Cited by 110 · see citing works
Seifert, B. A., O’Daniel, J. M., Amin, K. D., Marchuk, D. S., Patel, N. M., Parker, J. S., Hoyle, A. P., Mose, L. E., Marron, A., Hayward, M. C., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-0015 · Cited by 95 · see citing works
KRAS and NKX2-1 Mutations in Invasive Mucinous Adenocarcinoma of the Lung
Hwang, D. H., Sholl, L. M., Rojas‐Rudilla, V., Hall, D. L., Shivdasani, P., Garcia, E. P., MacConaill, L. E., Vivero, M., Hornick, J. L., Kuo, F. C., et al. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.01.010 · Cited by 93 · see citing works
Self-citationSchwaederle, M., Daniels, G. A., Piccioni, D. E., Fanta, P. T., Schwab, R. B., Shimabukuro, K. A., Parker, B. A., & Kurzrock, R. (2015) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-14-1061 · Cited by 90 · see citing works
Prospective Enterprise-Level Molecular Genotyping of a Cohort of Cancer Patients
MacConaill, L. E., Garcia, E., Shivdasani, P., Ducar, M. D., Adusumilli, R., Breneiser, M., Byrne, M. N., Chung, L. P., Conneely, J., Crosby, L., et al. (2014) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.06.004 · Cited by 87 · see citing works
Self-citationClinical and Molecular Characteristics of NF1 -Mutant Lung Cancer
Redig, A. J., Capelletti, M., Dahlberg, S. E., Sholl, L. M., Mach, S. L., Fontes, C., Shi, Y., Chalasani, P., & Janne, P. A. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2377 · Cited by 84 · see citing works
Self-citationJameson, G., Petricoin, E. F., Sachdev, J. C., et al. (2014) · Breast Cancer Research and Treatment · doi:10.1007/s10549-014-3117-1 · Cited by 82 · see citing works
Won, H. H., Scott, S. N., Brannon, A. R., Shah, R. H., & Berger, M. F. (2013) · Journal of Visualized Experiments · doi:10.3791/50710 · Cited by 65 · see citing works
Clinical Implications of Variant ALK FISH Rearrangement Patterns
Gao, X., Sholl, L. M., Nishino, M., et al. (2015) · Journal of Thoracic Oncology · doi:10.1097/jto.0000000000000665 · Cited by 58 · see citing works
Self-citationChau, N. G., Li, Y. Y., Jo, V. Y., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2314 · Cited by 57 · see citing works
Lee, J. J., Sholl, L. M., Lindeman, N. I., Granter, S. R., Laga, A. C., Shivdasani, P., Chin, G., Luke, J. J., Ott, P. A., Hodi, F. S., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0091-3 · Cited by 56 · see citing works
Self-citationRamkissoon, S. H., Bi, W. L., Schumacher, S. E., Ramkissoon, L. A., Haidar, S., Knoff, D. S., Dubuc, A. M., Brown, L. E., Burns, M., Cryan, J. B., et al. (2015) · Neuro-Oncology · doi:10.1093/neuonc/nov015 · Cited by 51 · see citing works
Self-citationClinical next generation sequencing to identify actionable aberrations in a phase I program
Boland, G. M., Piha-Paul, S. A., Subbiah, V., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.4040 · Cited by 48 · see citing works
Axl Receptor Axis: A New Therapeutic Target in Lung Cancer
Levin, P. A., Brekken, R. A., Byers, L. A., Heymach, J. V., & Gerber, D. E. (2016) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2016.04.015 · Cited by 46 · see citing works
Mason, E. F., Brown, R. D., Szeto, D. P., et al. (2016) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.1080/10428194.2016.1185786 · Cited by 46 · see citing works
Identification 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 · see citing works
Self-citationDoyle, L. A., Wong, K., Bueno, R., et al. (2014) · Cancer Genetics · doi:10.1016/j.cancergen.2014.08.004 · Cited by 18 · see citing works
Mandelker, D. L., Cin, P. D., Jacene, H. A., et al. (2015) · Experimental Hematology and Oncology · doi:10.1186/s40164-015-0026-x · Cited by 8 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., Srinivasan, P., Gao, J., Chakravarty, D., Devlin, S. M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4333 · Cited by 3,380 · see citing works
Oncogenic Signaling Pathways in The Cancer Genome Atlas
Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.035 · Cited by 3,201 · see citing works
Self-citationGenetic and transcriptional evolution alters cancer cell line drug response
Ben-David, U., Siranosian, B., Ha, G., Tang, H., Oren, Y., Hinohara, K., Strathdee, C. A., Dempster, J., Lyons, N. J., Burns, R., et al. (2018) · Nature · doi:10.1038/s41586-018-0409-3 · Cited by 931 · see citing works
Self-citationZhao, Z., Chen, X., Dowbaj, A. M., Sljukic, A., Bratlie, K., Lin, L., Fong, E. L. S., Balachander, G. M., Chen, Z., Soragni, A., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00174-y · Cited by 1,001 · see citing works
Oxnard, G. R., Hu, Y., Mileham, K. F., Husain, H., Costa, D. B., Tracy, P., Feeney, N., Sholl, L. M., Dahlberg, S. E., Redig, A. J., et al. (2018) · JAMA Oncology · doi:10.1001/jamaoncol.2018.2969 · Cited by 686 · see citing works
Self-citationMicroenvironment drives cell state, plasticity, and drug response in pancreatic cancer
Raghavan, S., Winter, P. S., Navia, A. W., Williams, H. L., DenAdel, A., Lowder, K. E., Galvez-Reyes, J., Kalekar, R. L., Mulugeta, N., Kapner, K. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.11.017 · Cited by 592 · see citing works
Self-citationReal-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine
Aguirre, A. J., Nowak, J. A., Camarda, N. D., Moffitt, R. A., Ghazani, A. A., Hazar-Rethinam, M., Raghavan, S., Kim, J., Brais, L. K., Ragon, D., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0275 · Cited by 367 · see citing works
Self-citationFunctional precision cancer medicine—moving beyond pure genomics
Letai, A. (2017) · Nature Medicine · doi:10.1038/nm.4389 · Cited by 366 · see citing works
Cas9 activates the p53 pathway and selects for p53-inactivating mutations
Enache, O. M., Rendo, V., Abdusamad, M., Lam, D., Davison, D., Pal, S., Currimjee, N., Hess, J., Pantel, S., Nag, A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0623-4 · Cited by 285 · see citing works
Self-citationKonstantinopoulos, P. A., Barry, W. T., Birrer, M., Westin, S. N., Cadoo, K. A., Shapiro, G. I., Mayer, E. L., O'Cearbhaill, R. E., Coleman, R. L., Kochupurakkal, B., et al. (2019) · The Lancet Oncology · doi:10.1016/s1470-2045(18)30905-7 · Cited by 263 · see citing works
Self-citationIntrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity
Mahadevan, N. R., Knelson, E. H., Wolff, J. O., Vajdi, A., Saigí, M., Campisi, M., Hong, D., Thai, T. C., Piel, B., Han, S., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0913 · Cited by 227 · see citing works
Self-citationClinical potential of mass spectrometry-based proteogenomics
Zhang, B., Whiteaker, J. R., Hoofnagle, A. N., Baird, G. S., Rodland, K. D., & Paulovich, A. G. (2019) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-018-0135-7 · Cited by 210 · see citing works
Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer
Wasko, U. N., Jiang, J., Dalton, T. C., Curiel-Garcia, A., Edwards, A. C., Wang, Y., Lee, B., Orlen, M., Tian, S., Stalnecker, C. A., et al. (2024) · Nature · doi:10.1038/s41586-024-07379-z · Cited by 209 · see citing works
Self-citationAisner, D. L., Sholl, L. M., Berry, L. D., Rossi, M. R., Chen, H., Fujimoto, J., Moreira, A. L., Ramalingam, S. S., Villaruz, L. C., Otterson, G. A., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-2289 · Cited by 206 · see citing works
Self-citationRakaee, M., Adib, E., Ricciuti, B., Sholl, L. M., Shi, W., Alessi, J. V., Cortellini, A., Fulgenzi, C. A. M., Viola, P., Pinato, D. J., et al. (2023) · JAMA Oncology · doi:10.1001/jamaoncol.2022.4933 · Cited by 141 · see citing works
Self-citationNassar, A. H., Adib, E., Abou Alaiwi, S., El Zarif, T., Groha, S., Akl, E. W., Nuzzo, P. V., Mouhieddine, T. H., Perea-Chamblee, T., Taraszka, K., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.08.022 · Cited by 121 · see citing works
Self-citationDevelopment of genome-derived tumor type prediction to inform clinical cancer care
Penson, A., Camacho, N., Zheng, Y., Varghese, A. M., Al-Ahmadie, H., Razavi, P., Chandarlapaty, S., Vallejo, C. E., Vakiani, E., Gilewski, T., et al. (2020) · JAMA Oncology · doi:10.1001/jamaoncol.2019.3985 · Cited by 115 · see citing works
Genome-wide mapping of somatic mutation rates uncovers drivers of cancer
Sherman, M. A., Yaari, A. U., Priebe, O., Dietlein, F., Loh, P.-R., & Berger, B. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01353-8 · Cited by 80 · see citing works
Natural Language Processing to Ascertain Cancer Outcomes from Medical Oncologist Notes
Kehl, K. L., Xu, W., Lepisto, E., Elmarakeby, H., Hassett, M. J., Van Allen, E. M., Johnson, B. E., & Schrag, D. (2020) · JCO Clinical Cancer Informatics · doi:10.1200/cci.20.00020 · Cited by 90 · see citing works
Self-citationMadanat-Harjuoja, L. M., Renfro, L. A., Klega, K., Tornwall, B., Thorner, A. R., Nag, A., Dix, D., Dome, J. S., Diller, L. R., Fernandez, C. V., et al. (2022) · Journal of Clinical Oncology · doi:10.1200/jco.22.00098 · Cited by 41 · see citing works
Self-citation
- Authors
- Sholl, L. M., Do, K., Shivdasani, P., Cerami, E., Dubuc, A. M., Kuo, F. C., Garcia, E. P., Jia, Y., Davineni, P., Abo, R. P., Pugh, T. J., van Hummelen, P., Thorner, A. R., Ducar, M., Berger, A. H., Nishino, M., Janeway, K. A., Church, A., Harris, M., Ritterhouse, L. L., Campbell, J. D., Rojas-Rudilla, V., Ligon, A. H., Ramkissoon, S., Cleary, J. M., Matulonis, U., Oxnard, G. R., Chao, R., Tassell, V., Christensen, J., Hahn, W. C., Kantoff, P. W., Kwiatkowski, D. J., Johnson, B. E., Meyerson, M., Garraway, L. A., Shapiro, G. I., Rollins, B. J., Lindeman, N. I., & MacConaill, L. E.
- Affiliations
- Brigham and Women's Hospital (US)
- Department of Biostatistics and Computational Biology, and
- University Health Network (CA)
- Dana-Farber/Harvard Cancer Center (US)
- Broad Institute (US)
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center (US)
- Boston Children's Hospital (US)
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA.
- Mirati Therapeutics (United States) (US)
- Lank Center for Genitourinary Oncology and
- Corresponding author
- MacConaill, Laura E.
- ORCID
- Sholl, Lynette M.
- Do, Khanh
- Cerami, Ethan
- Dubuc, Adrian M.
- Kuo, Frank C.
- Garcia, Elizabeth P.
- Davineni, Phani
- Pugh, Trevor J.
- Thorner, Aaron R.
- Ducar, Matthew
- Berger, Alice H.
- Nishino, Mizuki
- Janeway, Katherine A.
- Church, Alanna
- Harris, Marian
- Ritterhouse, Lauren L.
- Campbell, Joshua D.
- Ligon, Azra H.
- Cleary, James M.
- Matulonis, Ursula
- Oxnard, Geoffrey R.
- Chao, Richard
- Christensen, James
- Hahn, William C.
- Kantoff, Philip W.
- Kwiatkowski, David J.
- Johnson, Bruce E.
- Meyerson, Matthew
- Garraway, Levi A.
- Shapiro, Geoffrey I.
- Rollins, Barrett J.
- Lindeman, Neal I.
- MacConaill, Laura E.
- Venue
- JCI Insight
- Published
- 2016-11-17
- Volume
- 1
- Issue
- 19
- Pages
- e87062-e87062
- ISSN
- 2379-3708 (ISSN-L)
- PMC
- PMC5111542
- OpenAlex
- W2551013093
- Cited by
- 450
- References
- 54
- Citations by year
- 2026: 20 · 2025: 36 · 2024: 27 · 2023: 63 · 2022: 44 · 2021: 58 · 2020: 63 · 2019: 53 · 2018: 56 · 2017: 29
- FWCI
- 19.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- JCI Insight (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- American Association for Cancer Research
- Dana-Farber Cancer Institute
- National Institutes of Health (5k23ca157631-02)
- National Cancer Institute (K23-CA157631, R33CA155554, 5K23CA157631, 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
- comprehensive genomic profiling, clinical implementation, actionable alterations, hybrid capture sequencing, OncoPanel, precision oncology, AXL, EGFR, rare tumor, treatment stratification, diagnostic revision, targeted therapy response
- MeSH terms
- DNA Mutational Analysis, Humans, Mutation, Neoplasms, Retrospective Studies, Genomics, Precision Medicine, High-Throughput Nucleotide Sequencing
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
