Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data
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...
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MDPI AG
2022-06-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/7/1170 |
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| author | Muhammad Muzammal Adeel Khaista Rehman Yan Zhang Yibeltal Arega Guoliang Li |
| author_facet | Muhammad Muzammal Adeel Khaista Rehman Yan Zhang Yibeltal Arega Guoliang Li |
| author_sort | Muhammad Muzammal Adeel |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T10:18:15Z |
| format | Article |
| id | doaj.art-60d21f72c32e46358d7027b40b2e4779 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T10:18:15Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-60d21f72c32e46358d7027b40b2e47792023-12-01T22:11:28ZengMDPI AGGenes2073-44252022-06-01137117010.3390/genes13071170Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture DataMuhammad Muzammal Adeel0Khaista Rehman1Yan Zhang2Yibeltal Arega3Guoliang Li4National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, ChinaState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, ChinaNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, ChinaDepartments of Population Health & Environmental Medicine, New York University 180 Madison Ave., New York, NY 10016, USANational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, ChinaComplex 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.https://www.mdpi.com/2073-4425/13/7/11703D-genometranslocations detectioncancersWGSPCRHi-C |
| spellingShingle | Muhammad Muzammal Adeel Khaista Rehman Yan Zhang Yibeltal Arega Guoliang Li Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data Genes 3D-genome translocations detection cancers WGS PCR Hi-C |
| title | Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data |
| title_full | Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data |
| title_fullStr | Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data |
| title_full_unstemmed | Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data |
| title_short | Chromosomal Translocations Detection in Cancer Cells Using Chromosomal Conformation Capture Data |
| title_sort | chromosomal translocations detection in cancer cells using chromosomal conformation capture data |
| topic | 3D-genome translocations detection cancers WGS PCR Hi-C |
| url | https://www.mdpi.com/2073-4425/13/7/1170 |
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