The landscape and therapeutic relevance of cancer-associated transcript fusions
Open accessAbstract
Transcript fusions as a result of chromosomal rearrangements have been a focus of attention in cancer as they provide attractive therapeutic targets. To identify novel fusion transcripts with the potential to be exploited therapeutically, we analyzed RNA sequencing, DNA copy number and gene mutation data from 4366 primary tumor samples. To avoid false positives, we implemented stringent quality criteria that included filtering of fusions detected in RNAseq data from 364 normal tissue samples. Our analysis identified 7887 high confidence fusion transcripts across 13 tumor types. Our fusion prediction was validated by evidence of a genomic rearrangement for 78 of 79 fusions in 48 glioma samples where whole-genome sequencing data were available. Cancers with higher levels of genomic instability showed a corresponding increase in fusion transcript frequency, whereas tumor samples harboring fusions contained statistically significantly fewer driver gene mutations, suggesting an important role for tumorigenesis. We identified at least one in-frame protein kinase fusion in 324 of 4366 samples (7.4%). Potentially druggable kinase fusions involving ALK, ROS, RET, NTRK and FGFR gene families were detected in bladder carcinoma (3.3%), glioblastoma (4.4%), head and neck cancer (1.0%), low-grade glioma (1.5%), lung adenocarcinoma (1.6%), lung squamous cell carcinoma (2.3%) and thyroid carcinoma (8.7%), suggesting a potential for application of kinase inhibitors across tumor types. In-frame fusion transcripts involving histone methyltransferase or histone demethylase genes were detected in 111 samples (2.5%) and may additionally be considered as therapeutic targets. In summary, we described the landscape of transcript fusions detected across a large number of tumor samples and revealed fusion events with clinical relevance that have not been previously recognized. Our results support the concept of basket clinical trials where patients are matched with experimental therapies based on their genomic profile rather than the tissue where the tumor originated.
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A low ratio of chimeric to wild-type reads in the vicinity of the fusion boundary may indicate spurious mis-mapping of reads from a highly expressed gene.
“Finally, a low ratio of chimeric to wild-type reads in the vicinity of the fusion boundary may indicate spurious mis-mapping of reads from a highly expressed gene (the transcript allele fraction described by Yoshihara et al. [87]).”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [87]
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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 · see citing works
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 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
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 · see citing works
In silico prediction of protein-protein interactions in human macrophages
Souiai, O., Guerfali, F. Z., Miled, S. B., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,785 · see citing works
Significance analysis of microarrays applied to the ionizing radiation response
Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568 · 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
Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer
Soda, M., Choi, Y. L., Enomoto, M., Takada, S., Yamashita, Y., Ishikawa, S., Fujiwara, S.-I., Watanabe, H., Kurashina, K., Hatanaka, H., et al. (2007) · Nature · doi:10.1038/nature05945 · Cited by 5,439 · see citing works
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
The Cancer Genome Atlas Research Network (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1301689 · Cited by 5,078 · see citing works
The Somatic Genomic Landscape of Glioblastoma
Brennan, C. W., Verhaak, R. G. W., McKenna, A., Campos, B., Noushmehr, H., Salama, S. R., Zheng, S., Chakravarty, D., Sanborn, J. Z., Berman, S. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.09.034 · Cited by 5,016 · see citing works
Self-citationRecurrent Fusion of <i>TMPRSS2</i> and ETS Transcription Factor Genes in Prostate Cancer
Tomlins, S. A., Rhodes, D. R., Perner, S., Dhanasekaran, S. M., Mehra, R., Sun, X.-W., Varambally, S., Cao, X., Tchinda, J., Kuefer, R., et al. (2005) · Science · doi:10.1126/science.1117679 · Cited by 3,846 · see citing works
Comprehensive molecular characterization of clear cell renal cell carcinoma
The Cancer Genome Atlas Research Network (2013) · Nature · doi:10.1038/nature12222 · Cited by 3,485 · see citing works
Mermel, C. H., Schumacher, S. E., Hill, B., Meyerson, M. M., Beroukhim, R., & Getz, G. A. (2011) · Genome biology · doi:10.1186/gb-2011-12-4-r41 · Cited by 3,469 · see citing works
Crizotinib versus Chemotherapy in Advanced <i>ALK</i> -Positive Lung Cancer
Shaw, A. T., Kim, D.-W., Nakagawa, K., Seto, T., Crinó, L., Ahn, M.-J., De Pas, T., Besse, B., Solomon, B. J., Blackhall, F., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1214886 · Cited by 3,381 · see citing works
A census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184 · see citing works
Combined BRAF and MEK inhibition in melanoma with BRAF V600 mutations
Flaherty, K. T., Infante, J. R., Daud, A., Gonzalez, R., Kefford, R. F., Sosman, J., Hamid, O., Schuchter, L., Cebon, J., Ibrahim, N., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1210093 · Cited by 2,810 · see citing works
A minute chromosome in human chronic granulocytic leukemia
Nowell̀, P. C. (1960) · Science · Cited by 2,316 · see citing works
Pan-cancer patterns of somatic copy number alteration
Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C., Wala, J. A., Mermel, C. H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2760 · Cited by 1,843 · see citing works
Dasatinib versus Imatinib in Newly Diagnosed Chronic-Phase Chronic Myeloid Leukemia
Kantarjian, H. M., Shah, N. P., Hochhaus, A., Cortes, J. E., Shah, S. A., Ayala, M., Moiraghi, B., Shen, Z., Mayer, J., Pasqüini, R., et al. (2010) · New England Journal of Medicine · doi:10.1056/nejmoa1002315 · Cited by 1,572 · see citing works
Decitabine improves patient outcomes in myelodysplastic syndromes
Kantarjian, H. M., Issa, J. J., Rosenfeld, C. S., Bennett, J. M., Albitar, M. X., DiPersio, J. F., Klimek, V. M., Slack, J. L., de Castro, C., Ravandi, F., et al. (2006) · Cancer · doi:10.1002/cncr.21792 · Cited by 1,530 · see citing works
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1363 · Cited by 1,463 · see citing works
The impact of translocations and gene fusions on cancer causation
Mitelman, F., Johansson, B., & Mertens, F. (2007) · Nature Reviews Cancer · doi:10.1038/nrc2091 · Cited by 1,400 · see citing works
Epigenetic protein families: a new frontier for drug discovery
Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K., & Schapira, M. (2012) · Nature Reviews Drug Discovery · doi:10.1038/nrd3674 · Cited by 1,327 · see citing works
Advances in understanding cancer genomes through second-generation sequencing
Meyerson, M. M., Gabriel, S., & Getz, G. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,114 · see citing works
Olsen, E. A., Kim, Y. H., Kuzel, T. M., Pacheco, T. R., Foss, F. M., Parker, S. R. S., Frankel, S. R., Chen, C., Ricker, J. L., Arduino, J. M., et al. (2007) · Journal of Clinical Oncology · doi:10.1200/jco.2006.10.2434 · Cited by 1,057 · see citing works
Selective Killing of Mixed Lineage Leukemia Cells by a Potent Small-Molecule DOT1L Inhibitor
Daigle, S. R., Olhava, E. J., Therkelsen, C. A., Majer, C. R., Sneeringer, C. J., Song, J. J., Johnston, L. D., Scott, M. P., Smith, J. J., Xiao, Y., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.009 · Cited by 926 · see citing works
Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma
Singh, D., Chan, J., Zoppoli, P., Niola, F., Sullivan, R., Castano, A. M., Liu, E., Reichel, J. B., Porrati, P., Pellegatta, S., et al. (2012) · Science · doi:10.1126/science.1220834 · Cited by 777 · see citing works
Identification of Targetable FGFR Gene Fusions in Diverse Cancers
Wu, Y.-M., Su, F., Sundaram, S. K., Khazanov, N. A., Ateeq, B., Cao, X., Lonigro, R. J., Vats, P., Wang, R., Lin, S., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0050 · Cited by 748 · see citing works
Shern, J. F., Chen, L., Chmielecki, J., Wei, J. S., Patidar, R., Rosenberg, M. W., Ambrogio, L., Auclair, D., Wang, J., Song, Y. K., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0639 · Cited by 742 · see citing works
C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma
Parker, M. D., Mohankumar, K. M., Punchihewa, C., Weinlich, R., Dalton, J., Li, Y., Lee, R. P., Tatevossian, R., Phoenix, T. N., Thiruvenkatam, R., et al. (2014) · Nature · doi:10.1038/nature13109 · Cited by 668 · see citing works
Mechanistic insight into ALK receptor tyrosine kinase in human cancer biology
Hallberg, B., & Palmer, R. H. (2013) · Nature reviews. Cancer · doi:10.1038/nrc3580 · Cited by 643 · see citing works
Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer
Vaishnavi, A., Capelletti, M., Le, A. T., Kako, S. L., Butaney, M., Ercan, D., Mahale, S., Davies, K. D., Aisner, D. L., Pilling, A. B., et al. (2013) · Nature Medicine · doi:10.1038/nm.3352 · Cited by 615 · see citing works
The transcriptional landscape and mutational profile of lung adenocarcinomaPreprint
Seo, J., Ju, Y. S., Lee, W., Shin, J.-Y., Lee, J. J.-K., Bleazard, T., Lee, J., Jung, Y. J., Kim, J. O., Shin, J.-Y., et al. (2012) · Genome Research · doi:10.1101/gr.145144.112 · Cited by 589 · see citing works
Wells, S. A., Gosnell, J. E., Gagel, R. F., Moley, J. F., Pfister, D. G., Sosa, J. A., Skinner, M., Krebs, A. D., Vasselli, J. R., & Schlumberger, M. J. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.23.6604 · Cited by 518 · see citing works
TCPA: a resource for cancer functional proteomics data
Li, J., Lu, Y., Akbani, R., Ju, Z., Roebuck, P. L., Liu, W., Yang, J.-Y., Broom, B. M., Verhaak, R. G. W., Kane, D. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2650 · Cited by 513 · see citing works
Self-citationDetection of a Recurrent DNAJB1-PRKACA Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma
Honeyman, J. N., Simon, E. P., Robine, N., Chiaroni-Clarke, R. C., Darcy, D. G., Lim, I. I. P., Gleason, C. E., Murphy, J. M., Rosenberg, B. R., Teegan, L., et al. (2014) · Science · doi:10.1126/science.1249484 · Cited by 491 · see citing works
Emerging patterns of somatic mutations in cancer
Watson, I. R., Takahashi, K., Futreal, P. A., & Chin, L. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3539 · Cited by 481 · see citing works
Guo, G., Sun, X., Chen, C., Wu, S., Huang, P., Li, Z., Dean, M. C., Huang, Y. F., Jia, W., Zhou, Q., et al. (2013) · Nature Genetics · doi:10.1038/ng.2798 · Cited by 479 · see citing works
Histone lysine demethylases as targets for anticancer therapy
Højfeldt, J. W., Agger, K., & Helin, K. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4154 · Cited by 461 · see citing works
Phase II Clinical Trial of Sorafenib in Metastatic Medullary Thyroid Cancer
Lam, E. T., Ringel, M. D., Kloos, R. T., Prior, T. W., Knopp, M. V., Liang, J., Sammet, S., Hall, N. C., Wakely, P. E., Vasko, V. V., et al. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.25.0068 · Cited by 378 · see citing works
Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer
Mitelman, F., Johansson, B., & Mertens, F. (2004) · Nature Genetics · doi:10.1038/ng1335 · Cited by 361 · see citing works
TSGene: a web resource for tumor suppressor genes
Zhao, M., Sun, J., & Zhao, Z. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks937 · Cited by 325 · see citing works
Identification of fusion genes in breast cancer by paired-end RNA-sequencing
Edgren, H., Murumägi, A., Kangaspeska, S., Nicorici, D., Hongisto, V., Sahlberg, K. K., Rye, I. H., Nyberg, S., Wolf, M., Børresen‐Dale, A., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r6 · Cited by 313 · see citing works
Tyrosine kinase gene rearrangements in epithelial malignancies
Shaw, A. T., Hsu, P. P., Awad, M. M., & Engelman, J. A. (2013) · Nature reviews. Cancer · doi:10.1038/nrc3612 · Cited by 291 · see citing works
C11ORF95-RELA FUSIONS DRIVE ONCOGENIC NF-KB SIGNALING IN EPENDYMOMA
Gilbertson, R. J., Parker, M. D., Mohankumar, K. M., Punchihewa, C., Weinlich, R., Dalton, J. D., Li, Y., Lee, R. P., Tatevossian, R., Phoenix, T. N., et al. (2014) · Neuro-Oncology · doi:10.1093/neuonc/nou206.57 · Cited by 173 · see citing works
Histone Demethylase RBP2 Promotes Lung Tumorigenesis and Cancer Metastasis
Teng, Y., Lee, C.-F., Li, Y.-S., Chen, Y.-R., Hsiao, P., Chan, M.-Y., Lin, F., Huang, H., Chen, Y.-T., Jeng, Y., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-12-3165 · Cited by 154 · see citing works
PRADA: pipeline for RNA sequencing data analysis
Torres‐García, W., Zheng, S., Sivachenko, A., Vegesna, R., Wang, Q., Yao, R., Berger, M. F., Weinstein, J. N., Getz, G. A., & Verhaak, R. G. W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu169 · Cited by 154 · see citing works
Self-citationAsmann, Y. W., Hossain, A., Necela, B. M., Middha, S., Kalari, K. R., Sun, Z., Chai, H. S., Williamson, D. W., Radisky, D. C., Schroth, G. P., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr362 · Cited by 114 · see citing works
Gough, S. M., Lee, F., Yang, F., Walker, R. L., Zhu, Y. J., Pineda, M. A., Onozawa, M., Chung, Y. J., Bilke, S., Wagner, E. K., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0419 · Cited by 90 · see citing works
Shah, N., Lankerovich, M., Lee, H., Yoon, J., Schroeder, B., & Foltz, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-818 · Cited by 85 · see citing works
ChimerDB 2.0—a knowledgebase for fusion genes updated
Kim, P., Yoon, S., Kim, N., Lee, S., Ko, M., Lee, H., Kang, H., Kim, J., & Lee, S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp982 · Cited by 78 · see citing works
Sundaram, S. K., Shankar, S., DeRoo, S. C., Iyer, M. K., Palanisamy, N., Chinnaiyan, A. M., & Kumar‐Sinha, C. (2012) · Neoplasia · doi:10.1593/neo.12914 · Cited by 73 · see citing works
Wu, C., Wyatt, A. W., Lapuk, A. V., McPherson, A., McConeghy, B. J., Bell, R. H., Anderson, S. A., Haegert, A. M., Brahmbhatt, S., Shukin, R. J., et al. (2012) · The Journal of Pathology · doi:10.1002/path.3987 · Cited by 73 · see citing works
Zheng, S., Fu, J., Vegesna, R., Mao, Y., Heathcock, L. E., Torres‐García, W., Ezhilarasan, R., Wang, S., McKenna, A., Chin, L., et al. (2013) · Genes & Development · doi:10.1101/gad.213686.113 · Cited by 73 · see citing works
Self-citationCadot, B., Brunetti, M., Coppari, S., Fedeli, S., de Rinaldis, E., Russo, C. D., Gallinari, P., Francesco, R. D., Steinkühler, C., & Filocamo, G. (2009) · Cancer Research · doi:10.1158/0008-5472.can-08-2796 · Cited by 41 · see citing works
Flagged first, then by citations
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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
Self-citationA survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,316 · see citing works
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Cancer Genome Atlas Research Network, Campbell, J. D., Alexandrov, A., Kim, J., Wala, J., Berger, A. H., Pedamallu, C. S., Shukla, S. A., Guo, G., Brooks, A. N., et al. (2016) · Nature Genetics · doi:10.1038/ng.3564 · Cited by 1,200 · see citing works
Self-citationGenomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Knijnenburg, T., Wang, L., Zimmermann, M. T., Chambwe, N., Gao, G. F., Cherniack, A. D., Fan, H., Shen, H., Way, G. P., Greene, C. S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.076 · Cited by 1,126 · see citing works
Cancer biomarkers: Emerging trends and clinical implications for personalized treatment
Passaro, A., Bakir, M. A., Hamilton, E. G., Diehn, M., André, F., Roy‐Chowdhuri, S., Mountzios, G., Wistuba, I. I., Swanton, C., & Peters, S. (2024) · Cell · doi:10.1016/j.cell.2024.02.041 · Cited by 703 · see citing works
The emerging complexity of gene fusions in cancer
Mertens, F., Johansson, B., Fioretos, T., & Mitelman, F. (2015) · Nature reviews. Cancer · doi:10.1038/nrc3947 · Cited by 675 · see citing works
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.04.002 · Cited by 657 · see citing works
Self-citationHaas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., & Regev, A. (2019) · Genome biology · doi:10.1186/s13059-019-1842-9 · Cited by 646 · see citing works
Systematic analysis of telomere length and somatic alterations in 31 cancer types
Barthel, F. P., Wei, W., Tang, M., Martinez-Ledesma, E., Hu, X., Amin, S. B., Akdemir, K. C., Seth, S., Song, X., Wang, Q., et al. (2017) · Nature Genetics · doi:10.1038/ng.3781 · Cited by 614 · see citing works
Self-citationKim, H., Nguyen, N., Turner, K. M., Wu, S., Gujar, A. D., Luebeck, J., Liu, J., Deshpande, V., Rajkumar, U., Namburi, S., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0678-2 · Cited by 596 · see citing works
Self-citationMolecular characterization of cancers with NTRK gene fusions
Gatalica, Z., Xiu, J., Swensen, J. J., & Vranić, S. (2018) · Modern Pathology · doi:10.1038/s41379-018-0118-3 · Cited by 488 · see citing works
Benayed, R., Offin, M. D., Mullaney, K. A., Sukhadia, P., Rios, K., Desmeules, P., Ptashkin, R. N., Won, H. H., Chang, J. C., Halpenny, D. F., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-0225 · Cited by 490 · see citing works
Glioblastoma targeted therapy: updated approaches from recent biological insights
Touat, M., Idbaïh, A., Sanson, M., & Ligon, K. L. (2017) · Annals of Oncology · doi:10.1093/annonc/mdx106 · Cited by 443 · see citing works
Suda, K., Nakaoka, H., Yoshihara, K., Ishiguro, T., Tamura, R., Mori, Y., Yamawaki, K., Adachi, S., Takahashi, T., Kase, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.07.037 · Cited by 414 · see citing works
Self-citationTargeting RET-driven cancers: lessons from evolving preclinical and clinical landscapes
Drilon, A. E. D. C., Hu, Z. I., Lai, G. G. Y., & Tan, D. S. W. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.175 · Cited by 409 · see citing works
Weischenfeldt, J., Dubash, T., Drainas, A. P., Mardin, B. R., Chen, Y., Stütz, A. M., Waszak, S. M., Bosco, G., Halvorsen, A. R., Raeder, B., et al. (2017) · Nature Genetics · doi:10.1038/ng.3722 · Cited by 404 · see citing works
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes
Zhao, M., Kim, P., Mitra, R., Zhao, J., & Zhao, Z. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1268 · Cited by 400 · see citing works
Fusions in solid tumours: diagnostic strategies, targeted therapy, and acquired resistance
Schram, A. M., Chang, M. T., Jonsson, P., & Drilon, A. E. D. C. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.127 · Cited by 328 · see citing works
Yasuhara, T., Kato, R., Hagiwara, Y., Shiotani, B., Yamauchi, M., Nakada, S., Shibata, A., & Miyagawa, K. (2018) · Cell · doi:10.1016/j.cell.2018.08.056 · Cited by 317 · see citing works
Proteogenomic Characterization of Human Early-Onset Gastric Cancer
Mun, D.-G., Bhin, J., Kim, S., Kim, H., Jung, J. H., Jung, Y., Jang, Y. E., Park, J. M., Kim, H., Jung, Y., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2018.12.003 · Cited by 294 · see citing works
Self-citationRubio-Perez, C., Tamborero, D., Schroeder, M. P., Antolín, A. A., Deu-Pons, J., Perez-Llamas, C., Mestres, J., Gonzalez-Perez, A., & Lopez-Bigas, N. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.02.007 · Cited by 296 · see citing works
STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-SeqPreprint
Haas, B. J., Dobin, A., Stransky, N., Li, B., Yang, X. F., Tickle, T. L., Bankapur, A., Ganote, C. L., Doak, T. G., Pochet, N. L. M. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/120295 · Cited by 284 · see citing works
Cancer transcriptome profiling at the juncture of clinical translation
Cieslik, M. P., & Chinnaiyan, A. M. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.96 · Cited by 261 · see citing works
The kinome 'at large' in cancer
Fleuren, E. D. G., Zhang, L., Wu, J., & Daly, R. J. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2015.18 · Cited by 260 · see citing works
TumorFusions: an integrative resource for cancer-associated transcript fusions
Hu, X., Wang, Q., Tang, M., Barthel, F. P., Amin, S. B., Yoshihara, K., Lang, F., Martínez-Ledesma, E., Lee, S. H., Zheng, S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1018 · Cited by 239 · see citing works
Self-citationRecurrent MET fusion genes represent a drug target in pediatric glioblastoma
Bender, S., Gröbner, S. N., Pfaff, E., Kool, M., Northcott, P. A., Sturm, D., Worst, B. C., Pfister, S. M., Jones, D. T. W., van Tilburg, C. M., et al. (2016) · Nature Medicine · doi:10.1038/nm.4204 · Cited by 233 · see citing works
Hsiao, S. J., Zehir, A., Sireci, A. N., & Aisner, D. L. (2019) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2019.03.008 · Cited by 225 · see citing works
Recurrent chimeric fusion RNAs in non-cancer tissues and cells
Babiceanu, M., Qin, F., Xie, Z., Jia, Y., Lopez, K., Janus, N., Facemire, L., Kumar, S., Pang, Y., Qi, Y., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw032 · Cited by 202 · see citing works
Discovering and understanding oncogenic gene fusions through data intensive computational approaches
Latysheva, N. S., & Babu, M. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw282 · Cited by 194 · see citing works
A metabolic function of FGFR3-TACC3 gene fusions in cancer
Frattini, V., Pagnotta, S. M., Tala, Fan, J. J., Russo, M. V., Lee, S. B., Garofano, L., Zhang, J., Shi, P., Lewis, G., et al. (2018) · Nature · doi:10.1038/nature25171 · Cited by 189 · see citing works
Testing algorithm for identification of patients with TRK fusion cancer
Penault-Llorca, F. M., Rudzinski, E. R., & Sepulveda, A. R. (2019) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2018-205679 · Cited by 177 · see citing works
Precision therapy for RET-altered cancers with RET inhibitors
Thein, K. Z., Velcheti, V., Mooers, B. H. M., Wu, J., & Subbiah, V. (2021) · Trends in cancer · doi:10.1016/j.trecan.2021.07.003 · Cited by 175 · see citing works
The RNA Atlas expands the catalog of human non-coding RNAs
Lorenzi, L., Chiu, H., Cobos, F. A., Gross, S., Volders, P., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00936-1 · Cited by 161 · see citing works
Landscape of gene fusions in epithelial cancers: seq and ye shall find
Kumar‐Sinha, C., Sundaram, S. K., & Chinnaiyan, A. M. (2015) · Genome Medicine · doi:10.1186/s13073-015-0252-1 · Cited by 154 · see citing works
Genomic disorders 20 years on—mechanisms for clinical manifestations
Harel, T., & Lupski, J. R. (2017) · Clinical Genetics · doi:10.1111/cge.13146 · Cited by 142 · see citing works
Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes
Mertens, F., Antonescu, C. R., & Mitelman, F. (2015) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22335 · Cited by 143 · see citing works
FGFR-TACC gene fusions in human glioma
Lasorella, A., Sanson, M., & Iavarone, A. (2016) · Neuro-Oncology · doi:10.1093/neuonc/now240 · Cited by 141 · see citing works
Cheng, C., Zhou, Y., Li, H., Xiong, T., Li, S. C., Bi, Y., Kong, P., Wang, F., Cui, H., Li, Y., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.12.013 · Cited by 139 · see citing works
Gene Fusions in Thyroid Cancer
Yakushina, V. D., Lerner, L. V., & Лавров, А. В. (2017) · Thyroid · doi:10.1089/thy.2017.0318 · Cited by 138 · see citing works
Molecular and clinicopathologic features of gliomas harboring NTRK fusions
Torre, M., Vasudevaraja, V., Serrano, J., DeLorenzo, M., Malinowski, S. W., Blandin, A.-F., Pagès, M., Ligon, A. H., Dong, F., Meredith, D. M., et al. (2020) · Acta Neuropathologica Communications · doi:10.1186/s40478-020-00980-z · Cited by 138 · see citing works
Lee, J., Li, C., Huang, H.-Y., Zhu, M.-J., Mariño‐Enríquez, A., Lee, C., Ou, W., Hornick, J. L., & Fletcher, J. A. (2016) · The Journal of Pathology · doi:10.1002/path.4836 · Cited by 134 · see citing works
FGFR Fusions in Cancer: From Diagnostic Approaches to Therapeutic Intervention
Luca, A. D., Abate, R. E., Rachiglio, A. M., Maiello, M. R., Esposito, C., Schettino, C., Izzo, F., Nasti, G., & Normanno, N. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186856 · Cited by 131 · see citing works
Thind, A., Monga, I., Thakur, P., Kumari, P., Dindhoria, K., Krzak, M., Ranson, M., & Ashford, B. (2021) · Briefings Bioinform. · doi:10.1093/bib/bbab259 · Cited by 106 · see citing works
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Griffith, M., Walker, J., Spies, N. C., Ainscough, B. J., & Griffith, O. L. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004393 · Cited by 123 · see citing works
Wang, K., Russell, J. S., McDermott, J. D., Elvin, J. A., Khaira, D., Johnson, A., Jennings, T. A., Ali, S. M., Murray, M., Marshall, C. B., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2568 · Cited by 123 · see citing works
Yakirevich, E., Resnick, M. B., Mangray, S., Wheeler, M., Jackson, C. L., Lombardo, K. A., Lee, J., Kim, K., Gill, A. J., Wang, K., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-3000 · Cited by 121 · see citing works
In vivo CRISPR/Cas9 targeting of fusion oncogenes for selective elimination of cancer cells
Martínez-Lage, M., Torres-Ruiz, R., Puig-Serra, P., Moreno-Gaona, P., Martín, M. C., Moya, F., Bustamante, O. Q., Garcı́a-Silva, S., Carcaboso, A. M., Petazzi, P., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18875-x · Cited by 117 · see citing works
Tian, L., Li, Y., Edmonson, M. N., Zhou, X., Newman, S., McLeod, C., Thrasher, A., Liu, Y., Tang, B., Rusch, M., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02043-x · Cited by 115 · see citing works
Comprehensive analysis of PD-L1 expression in glioblastoma multiforme
Heiland, D. H., Haaker, G., Delev, D., Mercas, B., Masalha, W., Heynckes, S., Gaebelein, A., Pfeifer, D., Carro, M. S., Weyerbrock, A., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.15031 · Cited by 111 · see citing works
Genetic Heterogeneity of BRAF Fusion Kinases in Melanoma Affects Drug Responses
Botton, T., Talevich, E., Mishra, V. K., Zhang, T., Shain, A. H., Berquet, C., Gagnon, A., Judson, R. L., Ballotti, R., Ribas, A., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.009 · Cited by 110 · see citing works
The translational challenges of precision oncology
Pich, O., Bailey, C., Watkins, T. B. K., Zaccaria, S., Jamal‐Hanjani, M., & Swanton, C. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.04.002 · Cited by 111 · see citing works
Docking, R., Parker, J., Jädersten, M., Duns, G., Chang, L., Jiang, J., Pilsworth, J. A., Swanson, L., Chan, S. K., Chiu, R., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22625-y · Cited by 106 · see citing works
Dellino, G. I., Palluzzi, F., Chiariello, A. M., Piccioni, R., Bianco, S., Furia, L., Conti, G. D., Bouwman, B. A. M., Melloni, G. E. M., Guido, D., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0421-z · Cited by 104 · see citing works
The convergent roles of the nuclear factor I transcription factors in development and cancer
Chen, K., Lim, J. W. C., Richards, L. J., & Bunt, J. (2017) · Cancer Letters · doi:10.1016/j.canlet.2017.09.015 · Cited by 98 · see citing works
TissGDB: tissue-specific gene database in cancer
Kim, P., Park, A., Han, G., Sun, H., Jia, P., & Zhao, Z. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx850 · Cited by 102 · see citing works
Erdem‐Eraslan, L., van den Bent, M. J., Hoogstrate, Y., Naz-Khan, H., Stubbs, A., van der Spek, P. J., Böttcher, R., Gao, Y., de Wit, M., Taal, W., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-0776 · Cited by 99 · see citing works
TRK Inhibition: A New Tumor-Agnostic Treatment Strategy
Kummar, S., & Lassen, U. (2018) · Targeted Oncology · doi:10.1007/s11523-018-0590-1 · Cited by 98 · see citing works
Primary and Metastatic Melanoma With NTRK Fusions
Lezcano, C. M., Shoushtari, A. N., Ariyan, C. E., Hollmann, T. J., & BUSAM, K. J. (2018) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001070 · Cited by 96 · see citing works
The landscape of chimeric RNAs in non-diseased tissues and cells
Singh, S., Qin, F., Kumar, S., Elfman, J., Lin, E., Pham, L.-P., Yang, A. X., & Li, H. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz1223 · Cited by 95 · see citing works
A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer
Kloosterman, W. P., van den Braak, R. R. J. C., Pieterse, M., van Roosmalen, M. J., Sieuwerts, A. M., Stangl, C., Brunekreef, R., Lalmahomed, Z. S., Ooft, S., van Galen, A., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-16-3563 · Cited by 94 · see citing works
Jung, S., Kim, M. S., Jung, C. K., Park, H.-C., Kim, S. Y., Liu, J., Bae, J. S., Lee, S. H., Kim, T., Lee, S. H., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.11922 · Cited by 86 · see citing works
Zhang, Y., Yang, L., Kucherlapati, M. H., Chen, F., Hadjipanayis, A. G., Pantazi, A., Bristow, C. A., Lee, E. A., Mahadeshwar, H. S., Tang, J., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.025 · Cited by 80 · see citing works
Lee, M., Lee, K., Yu, N., Jang, I., Choi, I., Kim, P., Jang, Y. E., Kim, B., Kim, S., Lee, B., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1083 · Cited by 80 · see citing works
Zhang, J., Fujiwara, Y., Yamamoto, S., & Shibuya, H. (2019) · Nature Communications · doi:10.1038/s41467-019-08676-2 · Cited by 81 · see citing works
A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing
Beadling, C., Wald, A. I., Warrick, A., Neff, T. L., Zhong, S., Nikiforov, Y. E., Corless, C. L., & Nikiforova, M. N. (2015) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2015.10.002 · Cited by 79 · see citing works
Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy
Laumont, C. M., & Perreault, C. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2628-4 · Cited by 77 · see citing works
HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncologyPreprint
Shrestha, R., Hodzic, E., Sauerwald, T., Dao, P., Wang, K., Yeung, J., Anderson, S. A., Vandin, F., Haffari, G., Collins, C. C., et al. (2017) · Genome Research · doi:10.1101/gr.221218.117 · Cited by 77 · see citing works
Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors
Reeser, J. W., Patacsil, D., Miya, J., Kautto, E. A., Lyon, E., Zhu, E. Y., Wing, M. R., Smith, A. M., Reeder, M., Samorodnitsky, E., et al. (2017) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2017.05.006 · Cited by 76 · see citing works
Liu, H., Murphy, C. J., Karreth, F. A., Emdal, K. B., White, F. M., Elemento, O., Toker, A., Wulf, G. M., & Cantley, L. C. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0679 · Cited by 73 · see citing works
Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs
Yan, Z., Huang, N., Wu, W., Chen, W., Jiang, Y., Chen, J., Huang, X., Wen, X., Xu, J., Jin, Q., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1819788116 · Cited by 75 · see citing works
Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer
Latysheva, N. S., Oates, M. E., Maddox, L., Flock, T., Gough, J., Buljan, M., Weatheritt, R. J., & Babu, M. M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.07.008 · Cited by 74 · see citing works
Identification of a novel PARP14‐TFE3 gene fusion from 10‐year‐old FFPE tissue by RNA‐seq
Huang, W., Goldfischer, M., Babayeva, S., Mao, Y., Volyanskyy, K. Y., Dimitrova, N., Fallon, J. T., & Zhong, M. (2015) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22261 · Cited by 72 · see citing works
Jain, P., Fierst, T. M., Han, H. J., Smith, T. L., Vakil, A., Storm, P. B., Resnick, A. C., & Waanders, A. J. (2017) · Oncogene · doi:10.1038/onc.2017.276 · Cited by 72 · see citing works
Molecular characterization of the histiocytoses: Neoplasia of dendritic cells and macrophages
Durham, B. H. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.03.002 · Cited by 71 · see citing works
Knott, M. M. L., Hölting, T. L. B., Ohmura, S., Kirchner, T., Cidre‐Aranaz, F., & Grünewald, T. G. P. (2019) · Cancer and Metastasis Reviews · doi:10.1007/s10555-019-09839-9 · Cited by 71 · see citing works
The CLIP1–LTK fusion is an oncogenic driver in non‐small‐cell lung cancer
Izumi, H., Matsumoto, S., Liu, J., Tanaka, K., Mori, S., Hayashi, K., Kumagai, S., Shibata, Y., Hayashida, T., Watanabe, K., et al. (2021) · Nature · doi:10.1038/s41586-021-04135-5 · Cited by 70 · see citing works
Glioblastoma: To Target the Tumor Cell or the Microenvironment?
Vleeschouwer, S. D., & Bergers, G. (2017) · Codon Publications eBooks · doi:10.15586/codon.glioblastoma.2017.ch16 · Cited by 71 · see citing works
Mutation accumulation in cancer genes relates to nonoptimal outcome in chronic myeloid leukemia
Adnan Awad, S., Kankainen, M., Ojala, T., Koskenvesa, P., Eldfors, S., Ghimire, B., Kumar, A., Kytölä, S., Kamel, M. M., Heckman, C. A., et al. (2020) · Blood Advances · doi:10.1182/bloodadvances.2019000943 · Cited by 67 · see citing works
The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters
Gorini, F., Scala, G., Di Palo, G., Dellino, G. I., Cocozza, S., Pelicci, P. G., Lania, L., Majello, B., & Amente, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa175 · Cited by 67 · see citing works
Subbiah, V., Berry, J., Roxas, M., Guha‐Thakurta, N., Subbiah, I. M., Ali, S. M., McMahon, C., Miller, V. A., Cascone, T., Pai, S., et al. (2015) · Lung Cancer · doi:10.1016/j.lungcan.2015.04.004 · Cited by 67 · see citing works
Relevance of Fusion Genes in Pediatric Cancers: Toward Precision Medicine
Dupain, C., Harttrampf, A. C., Urbinati, G., Geoerger, B., & Massaad-Massade, L. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.01.005 · Cited by 66 · see citing works
Fusion Genes and RNAs in Cancer Development
Taniue, K., & Akimitsu, N. (2021) · Non-Coding RNA · doi:10.3390/ncrna7010010 · Cited by 66 · see citing works
Picco, G., Petti, C., Centonze, A., Torchiaro, E., Crisafulli, G., Novara, L., Acquaviva, A., Bardelli, A., & Médico, E. (2017) · EMBO Molecular Medicine · doi:10.15252/emmm.201606773 · Cited by 64 · see citing works
Identification of recurrent fusion genes across multiple cancer types
Yu, Y., Liu, P., Nelson, J. B., Hamilton, R. L., Bhargava, R., Michalopoulos, G. K., Chen, Q., Zhang, J., Ma, D., Pennathur, A., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-38550-6 · Cited by 63 · see citing works
Novel therapeutic strategy for cervical cancer harboring FGFR3-TACC3 fusions
Tamura, R., Yoshihara, K., Saito, T., Ishimura, R., Martínez-Ledesma, E., Hu, X., Ishiguro, T., Mori, Y., Yamawaki, K., Suda, K., et al. (2018) · Oncogenesis · doi:10.1038/s41389-017-0018-2 · Cited by 60 · see citing works
Self-citationCroce, S., Lesluyes, T., Delespaul, L., Bonhomme, B., Pérot, G., Velasco, V., Mayeur, L., Rebier, F., Rejeb, H. B., Guyon, F., et al. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22694 · Cited by 57 · see citing works
Tang, R., Chen, W., He, R., Zeng, J., Liang, L., Li, S., Ma, J., Luo, D., & Chen, G. (2017) · Oncotarget · doi:10.18632/oncotarget.17098 · Cited by 56 · see citing works
Challenges and best practices in omics benchmarking
Brooks, T. G., Lahens, N. F., Mrčela, A., & Grant, G. R. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-023-00679-6 · Cited by 53 · see citing works
Condensates induced by transcription inhibition localize active chromatin to nucleoli
Yasuhara, T., Xing, Y., Bauer, N. C., Lee, L., Dong, R., Yadav, T., Soberman, R. J., Rivera, M. N., & Zou, L. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.05.010 · Cited by 53 · see citing works
Gene Fusion in Malignant Glioma: An Emerging Target for Next-Generation Personalized Treatment
Xu, T., Wang, H., Huang, X., Li, W., Huang, Q., Yan, Y., & Chen, J. (2018) · Translational Oncology · doi:10.1016/j.tranon.2018.02.020 · Cited by 53 · see citing works
Fusion genes: A promising tool combating against cancer
Dai, X., Theobard, R., Cheng, H., Xing, M., & Zhang, J. (2018) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2017.12.003 · Cited by 52 · see citing works
The oncogenic fusion landscape in pediatric CNS neoplasms
Roosen, M. M., Odé, Z., Bunt, J., & Kool, M. (2022) · Acta Neuropathologica · doi:10.1007/s00401-022-02405-8 · Cited by 52 · see citing works
Guo, T. W., Gaykalova, D. A., Considine, M., Wheelan, S. J., Pallavajjala, A., Bishop, J. A., Westra, W. H., Ideker, T. E., Koch, W. M., Khan, Z. H., et al. (2016) · International Journal of Cancer · doi:10.1002/ijc.30081 · Cited by 51 · see citing works
Veeraraghavan, J., Ma, J., Hu, Y., & Wang, X.-S. (2016) · Breast Cancer Research and Treatment · doi:10.1007/s10549-016-3876-y · Cited by 50 · see citing works
Recurrent TRIO Fusion in Nontranslocation–Related Sarcomas
Delespaul, L., Lesluyes, T., Pérot, G., Brulard, C., Lartigue, L., Baud, J., Lagarde, P., Guellec, S. L., Neuville, A., Terrier, P., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-16-0290 · Cited by 50 · see citing works
Maguire, S. L., Peck, B., Wai, P. T., Campbell, J., Barker, H. E., Gulati, A., Daley, F. M., Vyse, S., Huang, P. H., Lord, C. J., et al. (2016) · The Journal of Pathology · doi:10.1002/path.4778 · Cited by 49 · see citing works
Fluorescence in situ hybridization in surgical pathology: principles and applications
Liang Cheng, C., Zhang, S., Wang, L., MacLennan, G. T., & Davidson, D. D. (2017) · The Journal of Pathology Clinical Research · doi:10.1002/cjp2.64 · Cited by 50 · see citing works
Recurrent EP300-BCOR Fusions in Pediatric Gliomas With Distinct Clinicopathologic Features
Torre, M., Meredith, D. M., Dubuc, A. M., Solomon, D. A., Perry, A., Vasudevaraja, V., Serrano, J., Snuderl, M., Ligon, K. L., & Alexandrescu, S. (2019) · Journal of Neuropathology & Experimental Neurology · doi:10.1093/jnen/nlz011 · Cited by 50 · see citing works
Glioblastomas harboring gene fusions detected by next-generation sequencing
Woo, H. Y., Na, K., Yoo, J., Chang, J. H., Park, Y. N., Shim, H. S., & Kim, S. H. (2020) · Brain Tumor Pathology · doi:10.1007/s10014-020-00377-9 · Cited by 50 · see citing works
- Authors
- Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H., & Verhaak, R. G. W.
- Affiliations
- The University of Texas MD Anderson Cancer Center (US)
- Corresponding author
- Verhaak, R G W
- Venue
- Oncogene
- Published
- 2014-12-15
- Volume
- 34
- Issue
- 37
- Pages
- 4845-4854
- ISSN
- 0950-9232 (ISSN-L)
- 1476-5594
- PMC
- PMC4468049
- OpenAlex
- W2042337609
- Cited by
- 450
- References
- 56
- Citations by year
- 2026: 8 · 2025: 26 · 2024: 38 · 2023: 23 · 2022: 41 · 2021: 59 · 2020: 37 · 2019: 56 · 2018: 43 · 2017: 54 · 2016: 48 · 2015: 16 · 2014: 1
- FWCI
- 12.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Oncogene (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Mary K. Chapman Foundation
- California Department of Transportation
- National Cancer Institute (CA083639, CA143883, U24CA143883, P50CA083639, P30CA016672)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- fusion transcripts, chromosomal rearrangements, kinase fusions, anaplastic lymphoma kinase, reactive oxygen species, RET, NTRK, fibroblast growth factor receptor, genomic instability, driver mutations, kinase inhibitors, glioma, bladder cancer, thyroid cancer, lung adenocarcinoma, lung squamous cell carcinoma, head and neck cancer, low-grade glioma, glioblastoma
- MeSH terms
- Cell Transformation, Neoplastic, DNA Mutational Analysis, Humans, Neoplasms, RNA, Messenger, RNA, Neoplasm, Oncogene Proteins, Fusion, Sequence Alignment, Genetic Heterogeneity, Computational Biology, Gene Expression Profiling, Chromatin Assembly and Disassembly, Molecular Targeted Therapy
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