{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,6]],"date-time":"2026-09-06T04:46:39Z","timestamp":1788669999227,"version":"build-2803163510"},"reference-count":45,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T00:00:00Z","timestamp":1656460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["31771402"],"award-info":[{"award-number":["31771402"]}]},{"name":"National Natural Science Foundation of China","award":["31970590"],"award-info":[{"award-number":["31970590"]}]},{"name":"National Natural Science Foundation of China","award":["2662017PY116"],"award-info":[{"award-number":["2662017PY116"]}]},{"name":"Fundamental Research Funds for the Central Universities","award":["31771402"],"award-info":[{"award-number":["31771402"]}]},{"name":"Fundamental Research Funds for the Central Universities","award":["31970590"],"award-info":[{"award-number":["31970590"]}]},{"name":"Fundamental Research Funds for the Central Universities","award":["2662017PY116"],"award-info":[{"award-number":["2662017PY116"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Complex chromosomal rearrangements such as translocations play a critical role in oncogenesis. Translocation detection is vital to decipher their biological role in activating cancer-associated mechanisms. High-throughput chromosomal conformations capture (Hi-C) data have shown promising progress in unveiling the genome variations in a disease condition. Until now, multiple structural data (Hi-C)-based methods are available that can detect translocations in cancer genomes. However, the consistency and specificity of Hi-C-based translocation results still need to be validated with conventional methods. This study used Hi-C data of cancerous cell lines, namely lung cancer (A549), Chronic Myelogenous Leukemia (K562), and Acute Monocytic Leukemia (THP-1), to detect the translocations. The results were cross-validated through whole-genome sequencing (WGS) and paired-read analysis. Moreover, PCR amplification validated the presence of translocated reads in different chromosomes. By integrating different data types, we showed that the results of Hi-C data are as reliable as WGS and can be utilized as an assistive method for detecting translocations in the diseased genome. Our findings support the utility of Hi-C technology to detect the translocations and study their effects on the three-dimensional architecture of the genome in cancer condition.<\/jats:p>","DOI":"10.3390\/genes13071170","type":"journal-article","created":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T20:47:56Z","timestamp":1656535676000},"page":"1170","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8937-074X","authenticated-orcid":false,"given":"Muhammad Muzammal","family":"Adeel","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30605, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khaista","family":"Rehman","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibeltal","family":"Arega","sequence":"additional","affiliation":[{"name":"Departments of Population Health & Environmental Medicine, New York University 180 Madison Ave., New York, NY 10016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1601-6640","authenticated-orcid":false,"given":"Guoliang","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China"},{"name":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s13059-019-1728-x","article-title":"Spatial chromatin architecture alteration by structural variations in human genomes at the population scale","volume":"20","author":"Sadowski","year":"2019","journal-title":"Genome Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrg1767","article-title":"Structural variation in the human genome","volume":"7","author":"Feuk","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1016\/j.ajhg.2008.02.007","article-title":"FISH Mapping of De Novo Apparently Balanced Chromosome Rearrangements Identifies Characteristics Associated with Phenotypic Abnormality","volume":"82","author":"Fantes","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.ajhg.2012.08.003","article-title":"Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease","volume":"91","author":"Soemedi","year":"2012","journal-title":"Am. J. Hum. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1038\/ng.162","article-title":"Strong association of de novo copy number mutations with sporadic schizophrenia","volume":"40","author":"Xu","year":"2008","journal-title":"Nat. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/s41576-018-0007-0","article-title":"Structural variation in the 3D genome","volume":"19","author":"Spielmann","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5473","DOI":"10.1073\/pnas.1418631112","article-title":"Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants","volume":"112","author":"Belkadi","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1038\/nrc.2017.82","article-title":"Genome-wide association studies of cancer: Current insights and future perspectives","volume":"17","author":"Sud","year":"2017","journal-title":"Nat. Rev. Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/nature13907","article-title":"Resolving the complexity of the human genome using single-molecule sequencing","volume":"517","author":"Chaisson","year":"2015","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1038\/nmeth.3454","article-title":"Assembly and diploid architecture of an individual human genome via single-molecule technologies","volume":"12","author":"Pendleton","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nature20098","article-title":"De novo assembly and phasing of a Korean human genome","volume":"538","author":"Seo","year":"2016","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"English, A.C., Salerno, W.J., and Reid, J.G. (2014). PBHoney: Identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-180"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1093\/bioinformatics\/btx664","article-title":"Identification of copy number variations and translocations in cancer cells from Hi-C data","volume":"34","author":"Chakraborty","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.3389\/fcell.2021.706375","article-title":"Structural Variations of the 3D Genome Architecture in Cervical Cancer Development","volume":"9","author":"Adeel","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1038\/s41588-018-0111-2","article-title":"Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture","volume":"50","author":"Lin","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"ref_18","unstructured":"Andrews, S. (2021, February 15). Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Hong, P., Jiang, H., Xu, W., Lin, D., Xu, Q., Cao, G., and Li, G. (2019). DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis. Genes, 11.","DOI":"10.1101\/764332"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","article-title":"HiC-Pro: An optimized and flexible pipeline for Hi-C data processing","volume":"16","author":"Servant","year":"2015","journal-title":"Genome Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization","volume":"9","author":"Imakaev","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/ng0496-368","article-title":"Karyotyping human chromosomes by combinatorial multi-fluor FISH","volume":"12","author":"Speicher","year":"1996","journal-title":"Nat. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4181","DOI":"10.1093\/nar\/gkp552","article-title":"Single nucleotide polymorphism arrays: A decade of biological, computational and technological advances","volume":"37","author":"LaFramboise","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s13059-020-01986-5","article-title":"HiNT: A computational method for detecting copy number variations and translocations from Hi-C data","volume":"21","author":"Wang","year":"2020","journal-title":"Genome Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative Genome Viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1038\/s41588-018-0195-8","article-title":"Integrative detection and analysis of structural variation in cancer genomes","volume":"50","author":"Dixon","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.3389\/fgene.2019.01313","article-title":"Location of Balanced Chromosome-Translocation Breakpoints by Long-Read Sequencing on the Oxford Nanopore Platform","volume":"10","author":"Hu","year":"2020","journal-title":"Front. Genet."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: Ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/ng1407","article-title":"Mutations in a new member of the chromodomain gene family cause CHARGE syndrome","volume":"36","author":"Vissers","year":"2004","journal-title":"Nat. Genet."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1002\/humu.22813","article-title":"Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions","volume":"36","author":"Lelieveld","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Hayes, M., and Li, J. (2013). Bellerophon: A hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-S5-S6"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/s13059-017-1253-8","article-title":"Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours","volume":"18","author":"Harewood","year":"2017","journal-title":"Genome Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1093\/jnci\/92.16.1355","article-title":"Chromosome 19 translocation, overexpression of Notch3, and human lung cancer","volume":"92","author":"Dang","year":"2000","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Rohrbeck, A., and Borlak, J. (2009). Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0007315"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/s12967-019-2068-z","article-title":"Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers","volume":"17","author":"Li","year":"2019","journal-title":"J. Transl. Med."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.omtm.2018.06.007","article-title":"Inferring Novel Tumor Suppressor Genes with a Protein-Protein Interaction Network and Network Diffusion Algorithms","volume":"10","author":"Chen","year":"2018","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Engreitz, J.M., Agarwala, V., and Mirny, L.A. (2012). Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0044196"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.ygeno.2019.05.009","article-title":"Hi-C detects novel structural variants in HL-60 and HL-60\/S4 cell lines","volume":"112","author":"Jacobson","year":"2020","journal-title":"Genomics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1084\/jem.20131121","article-title":"Synergy against PML-RARa: Targeting transcription, proteolysis, differentiation, and self-renewal in acute promyelocytic leukemia","volume":"210","author":"Kats","year":"2013","journal-title":"J. Exp. Med."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1007\/BF02981952","article-title":"Mechanisms of transformation by the BCR\/ABL oncogene","volume":"73","author":"Sattler","year":"2001","journal-title":"Int. J. Hematol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/7\/1170\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:40:19Z","timestamp":1760139619000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/7\/1170"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,29]]},"references-count":45,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["genes13071170"],"URL":"https:\/\/doi.org\/10.3390\/genes13071170","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,29]]}}}