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Scanning the human genome at kilobase resolution
Jun Chen1; Yeong C. Kim1; Yong-Chul Jung1; Zhenyu Xuan2; Geoff Dworkin3; Yanming Zhang4; Michael Q. Zhang2; San Ming Wang1,5
2008
Source PublicationGenome Research
ISSN1088-9051
Volume18Issue:5Pages:751–762
Abstract

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.

DOIhttp://dx.doi.org/10.1101/gr.068304.107
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000255504600007
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Cited Times [WOS]:14   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionFaculty of Health Sciences
Institute of Chinese Medical Sciences
Corresponding AuthorSan Ming Wang
Affiliation1.Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA
2.Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
3.Glenbrook High School, Northbrook, Illinois 60062, USA
4.Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, Illinois 60637, USA
5.Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, USA
Recommended Citation
GB/T 7714
Jun Chen,Yeong C. Kim,Yong-Chul Jung,et al. Scanning the human genome at kilobase resolution[J]. Genome Research,2008,18(5):751–762.
APA Jun Chen.,Yeong C. Kim.,Yong-Chul Jung.,Zhenyu Xuan.,Geoff Dworkin.,...&San Ming Wang.(2008).Scanning the human genome at kilobase resolution.Genome Research,18(5),751–762.
MLA Jun Chen,et al."Scanning the human genome at kilobase resolution".Genome Research 18.5(2008):751–762.
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