دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.
المؤلفون: Lin D; Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. da.lin@shgh.cn., Zou Y; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Informatics, Huazhong Agricultural University, Wuhan, China., Li X; Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Wang J; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Xiao Q; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China., Gao X; Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Lin F; Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China., Zhang N; Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China., Jiao M; Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Guo Y; Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Teng Z; The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China., Li S; Baylor College of Medicine, Houston, TX, USA.; Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China., Wei Y; Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.; Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China., Zhou F; Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China., Yin R; Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China., Zhang S; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Xing L; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Xu W; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Wu X; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Yang B; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Xiao K; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Wu C; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Tao Y; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China., Yang X; Hospital of Huazhong Agricultural University, Wuhan, China., Zhang J; Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China., Hu S; Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China., Dong S; Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China., Li X; Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China., Ye S; Department of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China., Hong Z; Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China., Pan Y; Precision Medicine Center, Scientific Research Center, School of Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China., Yang Y; Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China., Sun H; Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China. stevensunz@163.com., Cao G; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.; College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. gcao@mail.hzau.edu.cn.
المصدر: Genome biology [Genome Biol] 2023 Oct 30; Vol. 24 (1), pp. 247. Date of Electronic Publication: 2023 Oct 30.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: London, UK : BioMed Central Ltd
Original Publication: London : Genome Biology Ltd., c2000-
مواضيع طبية MeSH: DNA Copy Number Variations* , Oncogenes*, Genomics/methods ; Gene Expression Regulation ; DNA
مستخلص: 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).)
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فهرسة مساهمة: Keywords: Extrachromosomal DNA (ecDNA); Genomic abnormalities; Homogenously staining regions (HSRs); Spatial chromatin conformation; Structural variation (SV)
المشرفين على المادة: 9007-49-2 (DNA)
تواريخ الأحداث: Date Created: 20231031 Date Completed: 20231101 Latest Revision: 20231107
رمز التحديث: 20240513
مُعرف محوري في PubMed: PMC10614391
DOI: 10.1186/s13059-023-03081-x
PMID: 37904244
قاعدة البيانات: MEDLINE
الوصف
تدمد:1474-760X
DOI:10.1186/s13059-023-03081-x