Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags
文献类型：期刊论文
| 作者 | Gong,Qiang1,2; Tao,Yong1; Yang,Jian-Rong3; Cai,Jun1; Yuan,Yunfei4; Ruan,Jue1; Yang,Jin5; Liu,Hailiang3; Li,Wanghua1,2; Lu,Xuemei1,5 |
| 刊名 | Bmc genomics
 |
| 出版日期 | 2013-01-24 |
| 卷号 | 14期号:1 |
| 关键词 | Medium-sized deletion Restriction enzymes Next generation sequencing Structural variation |
| ISSN号 | 1471-2164 |
| DOI | 10.1186/1471-2164-14-51 |
| 通讯作者 | Wu,chung-i(wuci@big.ac.cn) |
| 英文摘要 | Abstractbackgroundgenomic deletions are known to be widespread in many species. variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-sized regions are limited when the sequencing coverage is low.resultswe present a cost-effective method for identifying medium-sized deletions in genomic regions with low genomic coverage. two mate-paired libraries were separately constructed from human cancerous tissue to generate paired short reads (ditags) from restriction fragments digested with a 4-base restriction enzyme. a total of 3 gb of paired reads (1.0× genome size) was collected, and 175 deletions were inferred by identifying the ditags with disorder alignments to the reference genome sequence. sanger sequencing results confirmed an overall detection accuracy of 95%. good reproducibility was verified by the deletions that were detected by both libraries.conclusionswe provide an approach to accurately identify medium-sized deletions in large genomes with low sequence coverage. it can be applied in studies of comparative genomics and in the identification of germline and somatic variants. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/1471-2164-14-51 |
| 出版者 | BioMed Central |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2374295 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Wu,Chung-I |
| 作者单位 | 1.Chinese Academy of Sciences; Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics 2.University of Chinese Academy of Sciences 3.Sun Yat-sen University; Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Science 4.Sun Yat-sen University; Department of Hepatobiliary Oncology, Cancer Center 5.Chinese Academy of Sciences; Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics 6.University of Nebraska Medical Center; Department of Genetics, Cell Biology & Anatomy, College of Medicine 7.University of Chicago; Department of Ecology and Evolution |
| 推荐引用方式 GB/T 7714 | Gong,Qiang,Tao,Yong,Yang,Jian-Rong,et al. Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags[J]. Bmc genomics,2013,14(1). |
| APA | Gong,Qiang.,Tao,Yong.,Yang,Jian-Rong.,Cai,Jun.,Yuan,Yunfei.,...&Wu,Chung-I.(2013).Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.Bmc genomics,14(1). |
| MLA | Gong,Qiang,et al."Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags".Bmc genomics 14.1(2013). |
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来源：中国科学院大学
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