Genome Biology (Oct 2023)
MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing
- Da Lin,
- Yanyan Zou,
- Xinyu Li,
- Jinyue Wang,
- Qin Xiao,
- Xiaochen Gao,
- Fei Lin,
- Ningyuan Zhang,
- Ming Jiao,
- Yu Guo,
- Zhaowei Teng,
- Shiyi Li,
- Yongchang Wei,
- Fuling Zhou,
- Rong Yin,
- Siheng Zhang,
- Lingyu Xing,
- Weize Xu,
- Xiaofeng Wu,
- Bing Yang,
- Ke Xiao,
- Chengchao Wu,
- Yingfeng Tao,
- Xiaoqing Yang,
- Jing Zhang,
- Sheng Hu,
- Shuang Dong,
- Xiaoyu Li,
- Shengwei Ye,
- Zhidan Hong,
- Yihang Pan,
- Yuqin Yang,
- Haixiang Sun,
- Gang Cao
Affiliations
- Da Lin
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Xinyu Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Xiaochen Gao
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Fei Lin
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
- Ningyuan Zhang
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
- Ming Jiao
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Yu Guo
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Zhaowei Teng
- The First People’s Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology
- Shiyi Li
- Baylor College of Medicine
- Yongchang Wei
- Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University
- Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University
- Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University
- Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Ke Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Yingfeng Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- Xiaoqing Yang
- Hospital of Huazhong Agricultural University
- Jing Zhang
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology
- Sheng Hu
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology
- Shuang Dong
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology
- Xiaoyu Li
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology
- Shengwei Ye
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology
- Zhidan Hong
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University
- Yihang Pan
- Precision Medicine Center, Scientific Research Center, School of Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University
- Yuqin Yang
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine
- Haixiang Sun
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School
- Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University
- DOI
- https://doi.org/10.1186/s13059-023-03081-x
- Journal volume & issue
-
Vol. 24,
no. 1
pp. 1 – 20
Abstract
Abstract Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method — multiple genetic abnormality sequencing (MGA-Seq) — to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA’s transcriptional regulatory function.
Keywords
- Extrachromosomal DNA (ecDNA)
- Homogenously staining regions (HSRs)
- Structural variation (SV)
- Genomic abnormalities
- Spatial chromatin conformation
