Evidence map›Paper›PMID 37904244›Full record

ArticleGenome biology2023

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 and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Mutational separation and clinical outcomes ofWorld journal of gastrointestinal surgery · 2023
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

34 authors.

Da Lin *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.
Yanyan Zou *State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Xinyu LiPrecision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Jinyue WangState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Qin XiaoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Xiaochen GaoPrecision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Fei LinReproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
Ningyuan ZhangReproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
Ming JiaoDepartment of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Yu GuoDepartment of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Zhaowei TengThe First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China.
Shiyi LiBaylor College of Medicine, Houston, TX, USA.
Yongchang WeiDepartment of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.
Fuling ZhouDepartment of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China.
Rong YinDepartment of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China.
Siheng ZhangState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Lingyu XingState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Weize XuState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Xiaofeng WuState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Bing YangState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Ke XiaoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Chengchao WuState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Yingfeng TaoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
Xiaoqing YangHospital of Huazhong Agricultural University, Wuhan, China.
Jing ZhangDepartment of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Sheng HuDepartment of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Shuang DongDepartment of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Xiaoyu LiDepartment of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Shengwei YeDepartment of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Zhidan HongDapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
Yihang PanPrecision Medicine Center, Scientific Research Center, School of Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China.
Yuqin YangDepartment of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Haixiang SunReproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China. stevensunz@163.com.
Gang CaoState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. gcao@mail.hzau.edu.cn.ORCID 0000-0002-3020-5379

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

DNA Copy Number VariationsOncogenesDNAGene Expression RegulationGenomicsDNAExtrachromosomal DNA (ecDNA)Genomic abnormalitiesHomogenously staining regions (HSRs)Spatial chromatin conformationStructural variation (SV)

Identifiers

PMID37904244
PMCPMC10614391

What OpenQuestion holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.