Copy number alterations unmasked as enhancer hijackers

Comprehensive molecular characterization of human colon and rectal cancer

The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11252 · Cited by 8,499 · see citing works

Recurrent 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

Massive genomic rearrangement acquired in a single catastrophic event during cancer development

Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., Pleasance, E. D., Lau, K. W., Beare, D., Stebbings, L. A., et al. (2011) · Cell · doi:10.1016/j.cell.2010.11.055 · Cited by 2,414 · 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

Punctuated Evolution of Prostate Cancer Genomes

Baca, S. C., Prandi, D., Lawrence, M. S., Mosquera, J. M., Romanel, A., Drier, Y., Park, K., Kitabayashi, N., MacDonald, T. Y., Ghandi, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.03.021 · Cited by 1,299 · see citing works

Activation of proto-oncogenes by disruption of chromosome neighborhoods

Hnisz, D., Weintraub, A. S., Day, D. S., Valton, A.-L., Bak, R. O., Li, C. H., Goldmann, J., Lajoie, B. R., Fan, Z. P., Sigova, A. A., et al. (2016) · Science · doi:10.1126/science.aad9024 · Cited by 1,042 · see citing works

Enhancer function: new insights into the regulation of tissue-specific gene expression

Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929 · see citing works

Structural alterations of the epidermal growth factor receptor gene in human gliomas.

Wong, A. J., Ruppert, J. M., Bigner, S. H., Grzeschik, C. H., Humphrey, P. A., Bigner, D. S., & Vogelstein, B. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.7.2965 · Cited by 851 · see citing works

The human c-myc oncogene: Structural consequences of translocation into the igh locus in Burkitt lymphoma

Battey, J., Moulding, C. T., Taub, R. A., Murphy, W., Stewart, T. A., Potter, H., Lenoir, G., & Leder, P. (1983) · Cell · doi:10.1016/0092-8674(83)90534-2 · Cited by 714 · see citing works

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.019 · Cited by 687 · see citing works

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., et al. (2014) · Nature · doi:10.1038/nature13379 · Cited by 642 · see citing works

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

Hnisz, D., Day, D. S., & Young, R. A. (2016) · Cell · doi:10.1016/j.cell.2016.10.024 · Cited by 420 · see citing works

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

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

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

Zhang, X., Choi, P. S., Francis, J. M., Imielinski, M. B., Watanabe, H., Cherniack, A. D., & Meyerson, M. M. (2015) · Nature Genetics · doi:10.1038/ng.3470 · Cited by 341 · see citing works

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

Bandopadhayay, P., Ramkissoon, L. A., Jain, P., Bergthold, G., Wala, J. A., Zeid, R., Schumacher, S. E., Urbanski, L. M., O’Rourke, R., Gibson, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3500 · Cited by 273 · see citing works

The role of 3D genome organization in development and cell differentiation

Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

Morton, A. R., Dogan-Artun, N., Faber, Z. J., MacLeod, G. D. A. H., Bartels, C. F., Piazza, M. S., Allan, K. C., Mack, S. C., Wang, X., Gimple, R. C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.039 · Cited by 336 · see citing works

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0564-y · Cited by 283 · see citing works

Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

Yang, J. H., & Hansen, A. S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00710-6 · Cited by 191 · see citing works

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor

Zhang, X., Choi, P. S., Francis, J. M., Gao, G. F., Campbell, J. D., Ramachandran, A., Mitsuishi, Y., Ha, G., Shih, J., Vázquez, F., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0532 · Cited by 123 · see citing works

Chromatin features constrain structural variation across evolutionary timescales

Fudenberg, G., & Pollard, K. S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1808631116 · Cited by 106 · see citing works

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

Sanders, A. D., Meiers, S., Ghareghani, M., Porubskỳ, D., Jeong, H., Vliet, A. V., Rausch, T., Richter‐Pechańska, P., Kunz, J. B., Jenni, S., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0366-x · Cited by 95 · see citing works

Structural Variation in Cancer: Role, Prevalence, and Mechanisms

Cosenza, M. R., Rodríguez–Martín, B., & Korbel, J. O. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120121-101149 · Cited by 92 · see citing works

When TADs go bad: Chromatin structure and nuclear organisation in human disease

Kaiser, V. B., & Semple, C. A. (2017) · F1000Research · doi:10.12688/f1000research.10792.1 · Cited by 64 · see citing works

Chromatin Conformation in Development and Disease

Boltsis, I., Grosveld, F. G., Giraud, G., & Kolovos, P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723859 · Cited by 56 · see citing works

Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration

Ain, Q., Schmeer, C. W., Wengerodt, D., Witte, O. W., & Kretz, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21072477 · Cited by 51 · see citing works

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma

Dubois, F. P. B., Shapira, O., Greenwald, N. F., Zack, T. I., Wala, J. A., Tsai, J. W., Crane, A., Baguette, A., Hadjadj, D., Harutyunyan, A. S., et al. (2022) · Nature Cancer · doi:10.1038/s43018-022-00403-z · Cited by 39 · see citing works

Enhancer dysfunction in leukemia

Bhagwat, A. S., Lu, B., & Vakoc, C. R. (2018) · Blood · doi:10.1182/blood-2017-11-737379 · Cited by 44 · see citing works

Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells

Willi, M., Yoo, K. H., Reinisch, F., Kuhns, T. M., Lee, H., Wang, C., & Hennighausen, L. G. (2017) · Nature Communications · doi:10.1038/ncomms16069 · Cited by 36 · see citing works

Effective normalization for copy number variation in Hi-C data

Servant, N., Varoquaux, N., Heard, E., Barillot, E., & Vert, J.-P. (2017) · BMC Bioinformatics · doi:10.1186/s12859-018-2256-5 · Cited by 34 · see citing works

Revisiting 3D chromatin architecture in cancer development and progression

Feng, Y., & Pauklin, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa747 · Cited by 36 · see citing works

A unifying model for extrachromosomal circular DNA load in eukaryotic cells

Arrey, G., Keating, S. T., & Regenberg, B. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.03.002 · Cited by 33 · see citing works

Enhancer-gene rewiring in the pathogenesis of Quebec Platelet Disorder

Liang, M., Soomro, A., Tasneem, S., Abatti, L. E., Alizada, A., Yuan, X., Uusküla-Reimand, L., Antounians, L., Alvi, S. A., Paterson, A. D., et al. (2020) · Blood · doi:10.1182/blood.2020005394 · Cited by 28 · see citing works

Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Gillani, R., Seong, B. K. A., Crowdis, J. P., Conway, J. R., Dharia, N. V., Alimohamed, S. I., Haas, B. J., Han, K., Park, J., Dietlein, F., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-0791 · Cited by 25 · see citing works

Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken

Chen, X., Bai, X., Liu, H., Zhao, B., Yan, Z., Hou, Y., & Chu, Q. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.830393 · Cited by 28 · see citing works

Identification and Characterization of Extrachromosomal Circular DNA in Human Placentas With Fetal Growth Restriction

Yang, H., He, J., Huang, S., Yang, H., Yi, Q., Tao, Y., Chen, M., Zhang, X., & Qi, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.780779 · Cited by 26 · see citing works

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancersPreprint

Mikulášová, A., Kent, D., Trevisán-Herraz, M., Karataraki, N., Fung, K. T. M., Ashby, C., Cieślak, A., Yaccoby, S., van Rhee, F., Zangari, M., et al. (2021) · Genome Research · doi:10.1101/gr.276042.121 · Cited by 22 · see citing works

Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes

Hung, S., Saiakhova, A., Faber, Z. J., Bartels, C. F., Neu, D., Bayles, I., Ojo, E. O., Hong, E. S., Pontius, W., Morton, A. R., et al. (2019) · eLife · doi:10.7554/elife.40760 · Cited by 22 · see citing works

Cardio-Metabolic Disease Genetic Risk Factors in Iran: Twenty Years of Tehran Lipid and Glucose Study

DANESHPOUR, M. S., Hedayati, M., Sedaghati-khayat, B., Guity, K., Zarkesh, M., Akbarzadeh, M., Javanrooh, N., Zadeh–Vakili, A., & Azizi, F. (2018) · Intern J Endocrinol Metab · doi:10.5812/ijem.84744 · Cited by 11 · see citing works

G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency

Kim, S., & Hwang, S. (2022) · Genes · doi:10.3390/genes13030391 · Cited by 8 · see citing works

Genomic copy number gains of ErbB family members predict poor clinical outcomes in glioma patients

Liu, R., Qu, Y., Chen, L., Pu, J., Ma, S., Zhang, X., Yang, Q., Shi, B., Hou, P., & Ji, M. (2017) · Oncotarget · doi:10.18632/oncotarget.21228 · Cited by 7 · see citing works

Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines

Khalil, A. I. S., Muzaki, S. R. B. M., Chattopadhyay, A., & Sanyal, A. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03832-8 · Cited by 7 · see citing works

A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data

Luo, F. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3266-7 · Cited by 7 · see citing works

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology

(2025) · doi:10.1038/s41467-024-54176-3 · Cited by 4 · see citing works

Effective normalization for copy number variation in Hi-C dataPreprint

Servant, N., Varoquaux, N., Heard, É., Vert, J., & Barillot, E. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/167031 · Cited by 3 · see citing works

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancerPreprint

Song, Y., Li, F., Wang, S., Wang, Y., Lai, C., Chen, L., Jiang, N., Li, J., Chen, X., Bailey, S. D., et al. (2024) · Genome Research · doi:10.1101/gr.278418.123 · Cited by 2 · see citing works

Transcriptome sequencing identifies novel EVX fusions involved in transcriptional activation of HOX family genes in pediatric immature T-cell acute lymphoblastic leukemia: two cases reports and a literature review

Zhang, X., Cui, B., Li, Y., Li, Z., Zheng, J., Chu, X., Xiao, P., Lu, J., Wang, Z., Cen, J., et al. (2023) · International Journal of Hematology · doi:10.1007/s12185-023-03619-6 · Cited by 1 · see citing works

Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC

Dong, Y., Xia, W., Yang, Z.-T., Ren, L., Wang, H.-R., Zhou, Y.-Y., Li, Q.-C., Chen, Z., Xia, Z., Zheng, Y., et al. (2026) · npj Digital Medicine · doi:10.1038/s41746-025-02186-w · Cited by 2 · see citing works

Compare Copy Number Alterations Detection Methods on Real Cancer Data

Luo, F., & Zhu, Y. (2018) · Lecture notes in computer science · doi:10.1007/978-3-319-95930-6_57 · Cited by 1 · see citing works

Whole-genome Sequencing-based Lung Cancer Precision Medicine in Japan

Kohno, T. (2022) · Haigan · doi:10.2482/haigan.62.10 · Cited by 1 · see citing works

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processesPreprint

Sanders, A. D., Meiers, S., Ghareghani, M., Porubskỳ, D., Jeong, H., van Vliet, M. A. C. C., Rausch, T., Richter‐Pechańska, P., Kunz, J. B., Jenni, S., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/849604 · Cited by 1 · see citing works

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology

Zhang, Y., Leung, A. K., Kang, J. J., Sun, Y., Wu, G., Li, L., Sun, J., Cheng, L., Qiu, T., Zhang, J., et al. (2023) · doi:10.1101/2023.03.06.531441

Identifying Regulators from Multiple Types of Biological Data in Cancer

Baur, B. A. (2017) · e-Publications@Marquette (Marquette University)

Digital karyotyping of cancer cell lines from NGS data

Khalil, A. I. S. (2020) · doi:10.32657/10356/138176

Faculty Opinions recommendation of Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes.

Hannenhalli, S. S. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735088954.793558203

EagleC Explorer: A desktop application for interactively detecting and visualizing SVs and enhancer hijacking on Hi-C contact mapsPreprint

Fu, Y., Wang, X., & Yue, F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.07.552228 · Cited by 1 · see citing works

FuSViz—visualization and interpretation of structural variation using cancer genomics and transcriptomics data

Zhao, S., Nakken, S., Vodák, D., & Hovig, E. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf078

Nanopore Sequencing Unveils Somatic Structural Variations as Biomarkers in Laryngeal squamous cell carcinoma GenomesPreprint

Liu, X., Xia, L., Qiao, Y., Li, Y., Huang, Y., Yue, B., Liang, X., Yang, X., Zhang, H., Zhang, J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.12.659252

The Cancer Genome in the Long Reads Era

Ermini, L. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4702-8_15

Additional file 1 of Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines

Khalil, A. I. S., Muzaki, S. R. B. M., Chattopadhyay, A., & Sanyal, A. (2020) · Figshare · doi:10.6084/m9.figshare.13204750

Spatio-temporal organisation of histone variants : from nucleosomes to nuclei

Karagyozova, T. (2023) · doi:10.70675/9bc458efze7cbz44d3zb793z581bbc0e800c

integrated analysis of copy number alterations

Cáceres, R., Armengol, L., Villatoro, S., & González, J. R. (2013)

Enhancer hijacking: a new direction of research on oncogenesis mechanism

Tang, L., & Wu, N. (2018) · Int J Genet · doi:10.3760/cma.j.issn.1673-4386.2018.06.007

Abstract 6599: 3D genomic analysis reveals novel enhancer hijacking mechanisms caused by complex structural alterations that drive oncogene overexpression

Mortenson, K. L., Dawes, C., Wilson, E. R., Patchen, N. E., Johnson, H., Gertz, J., Bailey, S. D., Liu, Y., Varley, K. E., & Zhang, X. (2024) · Cancer Research · doi:10.1158/1538-7445.am2024-6599 · Cited by 1 · see citing works

Additional file 1 of Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes

Khalil, A. I. S., Khyriem, C., Chattopadhyay, A., & Sanyal, A. (2020) · Figshare · doi:10.6084/m9.figshare.12144288

Modeling recurrent DNA copy number alterations

Shah, S. P., Lam, W. L., Ng, R. T., & Murphy, K. P. (2013)