MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing
-
Published:2023-10-30
Issue:1
Volume:24
Page:
-
ISSN:1474-760X
-
Container-title:Genome Biology
-
language:en
-
Short-container-title:Genome Biol
Author:
Lin Da, Zou Yanyan, Li Xinyu, Wang Jinyue, Xiao Qin, Gao Xiaochen, Lin Fei, Zhang Ningyuan, Jiao Ming, Guo Yu, Teng Zhaowei, Li Shiyi, Wei Yongchang, Zhou Fuling, Yin Rong, Zhang Siheng, Xing Lingyu, Xu Weize, Wu Xiaofeng, Yang Bing, Xiao Ke, Wu Chengchao, Tao Yingfeng, Yang Xiaoqing, Zhang Jing, Hu Sheng, Dong Shuang, Li Xiaoyu, Ye Shengwei, Hong Zhidan, Pan Yihang, Yang Yuqin, Sun Haixiang, Cao GangORCID
Abstract
AbstractGenomic 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.
Funder
National Natural Science Foundation of China
Publisher
Springer Science and Business Media LLC
Reference71 articles.
1. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang C-Z, Wala J, Mermel CH. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013;45:1134–40. 2. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet. 2018;50:1388–98. 3. Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh C-H, Zhang C, Ren X, Protopopov A, Chin L. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013;153:919–29. 4. Zorrilla M, Yatsenko AN. The genetics of infertility: current status of the field. Curr Genet Med Rep. 2013;1:247–60. 5. Harton GL, Tempest HG. Chromosomal disorders and male infertility. Asian J Androl. 2012;14:32.
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|