Shotgun sequence assembly and recent segmental duplications within the human genome

Nature

Volumn 431, Issue 7011, 2004, Pages 927-930

  She, Xinwel ^a   Jiang, Zhaoshi ^a   Clark, Royden A ^b   Liu, Ge ^b   Cheng, Ze ^a   Tuzun, Eray ^a   Church, Deanna M ^c   Sutton, Granger ^d   Halpern, Aaron L ^e   Elchler, Evan E ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d Applied Biosystems   (United States)

^e Ctr for the Advancement of Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSEMBLY; BIOTECHNOLOGY; CLONING; MOLECULAR STRUCTURE;

EUKARYOTIC GENOMES; GENOME ASSEMBLIES; GENOME STRUCTURE; WHOLE-GENOME SHOTGUN (WGS) SEQUENCE;

GENES;

GENOME;

EUKARYOTE; GENE DUPLICATION; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN GENOME; HUMAN TISSUE; MOLECULAR CLONING; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; QUANTITATIVE ANALYSIS; REVIEW; SHOTGUN SEQUENCE ASSEMBLY; STATISTICAL SIGNIFICANCE; WHOLE GENOME SHOTGUN SEQUENCE ASSEMBLY;

ANIMALS; CHROMOSOMES, HUMAN; COMPUTATIONAL BIOLOGY; GENE DUPLICATION; GENES, DUPLICATE; GENOME, HUMAN; GENOMICS; HUMANS; MICE; PHYSICAL CHROMOSOME MAPPING; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EUKARYOTA; MAMMALIA;

EID: 7244247384     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03062     Document Type: Review

References (23)

1. Weber, J. L. & Myers, E. W. Human whole-genome shotgun sequencing. Genome Res. 7, 401-409 (1977).
2. Green, P. Against a whole-genome shotgun. Genome Res. 7, 410-417 (1997).
3. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
4. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
5. Waterston, R. H., Lander, E. S. & Sulston, J. E. More on the sequencing of the human genome. Proc. Natl Acad. Sci. USA 100, 3022-3024 (2003) author reply 3025-3026.
6. Rat Genome Sequencing Project Consortium, Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493-521 (2004).
7. Mouse Genome Sequencing Consortium, Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
8. Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl Acad. Sci. USA 101, 1916-1921 (2004).
9. International Human Genome Sequencing Consortium, Finishing the euchromatic sequence of the human genome. Nature doi:10.1038/nature03001 (this issue).
10. Bailey, J. A., Yavor, A. M., Massa, H. F., Trask, B. J. & Eichler, E. E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11, 1005-1017 (2001).
11. Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 4, R25 (2003).
12. International Human Genome sequencing Consortium, Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
13. Tuzun, E., Bailey, J. A. & Eichler, E. E. Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res. 14, 493-506 (2004).
14. Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
15. Cheung, V. G. et al. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409, 953-958 (2001).
16. Huang, X., Wang, J., Aluru, S., Yang, S. P. & Hillier, L. PCAP: a whole-genome assembly program. Genome Res. 13, 2164-2170 (2003).
17. Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177-189 (2002).
18. Bailey, J. A., Church, D. M., Ventura, M., Rocchi, M. & Eichler, E. E. Analysis of segmental duplications and genome assembly in the mouse. Genome Res. 14, 789-801 (2004).
19. Stankiewicz, P. & Lupski, J. R. Genomic architecture, rearrangements and genomic disorders. Trends Genet. 18, 74-82 (2002).
20. Armengol, L., Pujana, M. A., Cheung, J., Scherer, S. W. & Estivill, X. Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. Hum. Mol. Genet. 12, 2201-2208 (2003).
21. Bailey, J. A., Baertsch, R., Kent, W. J., Haussler, D. & Eichler, E. E. Hotspots of mammalian chromosomal evolution. Genome Biol. 5, R23 (2004).
22. Hillier, L. W. et al. The DNA sequence of human chromosome 7, Nature 424, 157-164 (2003).
23. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004).