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MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing

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收录情况： ◇ SCIE

作者：
Da Lin[1] * ; Yanyan Zou[2,3] * ; Xinyu Li[1] ; Jinyue Wang [2,4,5] ; Qin Xiao[2,4,5] ; Xiaochen Gao [1] ; Fei Lin[6] ; Ningyuan Zhang[6] ; Ming Jiao[7] ; Yu Guo[7] ; Zhaowei Teng[8] ; Shiyi Li[9,10] ; Yongchang Wei[10,11] ; Fuling Zhou[12] ; Rong Yin[12] ; Siheng Zhang [2,13] ; Lingyu Xing[2,13] ; Weize Xu[2,13] ; Xiaofeng Wu[2,13] ; Bing Yang[2,13] ; Ke Xiao[2,13] ; Chengchao Wu[2,13] ; Yingfeng Tao [2,13] ; Xiaoqing Yang[14] ; Jing Zhang[15] ; Sheng Hu[15] ; Shuang Dong [15] ; Xiaoyu Li[15] ; Shengwei Ye[16] ; Zhidan Hong[17] ; Yihang Pan[18] ; Yuqin Yang[7] ; Haixiang Sun[6] ; Gang Cao[2,4,13,19] ;
机构： [1]Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, ShanghaiJiao Tong University School of Medicine, Shanghai, China [2]State Key Laboratory of Agricultural Microbiology, HuazhongAgricultural University, Wuhan, China [3]College of Informatics, Huazhong Agricultural University, Wuhan, China [4]Collegeof Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China [5]College of Life Science and Technology,Huazhong Agricultural University, Wuhan, China [6]Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affili-ated Hospital of Nanjing University Medical School, Nanjing, China [7]Department of Laboratory Animal Center, ShanghaiGeneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China [8]The First People’s Hospital of Yun-nan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China [9]Baylor Collegeof Medicine, Houston, TX, USA [10]Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University,Wuhan, China [11]Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan,China [12]Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China [13]College of VeterinaryMedicine, Huazhong Agricultural University, Wuhan, China [14]Hospital of Huazhong Agricultural University, Wuhan, China [15]Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Scienceand Technology, Wuhan, China [16]Department of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical Col-lege, Huazhong University of Science and Technology, Wuhan, China [17]Dapartment of Reproductive Medicine Center,Zhongnan Hospital of Wuhan University, Wuhan, China [18]Precision Medicine Center, Scientific Research Center, Schoolof Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China [19]Shenzhen Institute of AdvancedTechnology, Chinese Academy of Sciences, Shenzhen, China
出处：
DOI： 10.1186/s13059-023-03081-x
ISSN：

关键词： Extrachromosomal DNA (ecDNA) Homogenously staining regions (HSRs) Structural variation (SV) Genomic abnormalities Spatial chromatin conformation

摘要：
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.© 2023. The Author(s).

基金：
This work was supported by the National Natural Science Foundation of China (32221005 to G.C. and 31900432 to D.L.), the Fundamental Research Funds for the Central Universities (2662022SYPY001 to G.C.), the National Postdoc- toral Program for Innovative Talents (BX20180113 to D.L.) and the Shanghai Science and Technology Committee (201409002300 to Y.Y.).
语种：
外文
被引次数：
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PubmedID：
中科院(CAS)分区：
出版当年[2023]版：
大类 | 1 区 生物学
小类 | 1 区 生物工程与应用微生物 1 区 遗传学
最新[2023]版：
大类 | 1 区 生物学
小类 | 1 区 生物工程与应用微生物 1 区 遗传学
JCR分区：
出版当年[2022]版：
Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Q1 GENETICS & HEREDITY
最新[2023]版：
Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Q1 GENETICS & HEREDITY

影响因子： 最新[2023版] 最新五年平均 出版当年[2022版] 出版当年五年平均 出版前一年[2021版] 出版后一年[2023版]

第一作者：
第一作者机构： [1]Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, ShanghaiJiao Tong University School of Medicine, Shanghai, China
共同第一作者：
通讯作者：
通讯机构： [2]State Key Laboratory of Agricultural Microbiology, HuazhongAgricultural University, Wuhan, China [4]Collegeof Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China [13]College of VeterinaryMedicine, Huazhong Agricultural University, Wuhan, China [19]Shenzhen Institute of AdvancedTechnology, Chinese Academy of Sciences, Shenzhen, China
推荐引用方式(GB/T 7714)：
Da Lin,Yanyan Zou,Xinyu Li,et al.MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing[J].GENOME BIOLOGY.2023,24(1):247.doi:10.1186/s13059-023-03081-x.
APA：
Da Lin,Yanyan Zou,Xinyu Li,Jinyue Wang,Qin Xiao...&Gang Cao.(2023).MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.GENOME BIOLOGY,24,(1)
MLA：
Da Lin,et al."MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing".GENOME BIOLOGY 24..1(2023):247

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