Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies

PLoS Genetics

Volumn 1, Issue 4, 2005, Pages 0489-0498

  Feuk, Lars ^a,b   MacDonald, Jeffrey R ^a   Tang, Terence ^a   Carson, Andrew R ^a,b   Li, Martin ^a   Rao, Girish ^a   Khaja, Razi ^a   Scherer, Stephen W ^a,b  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGY; CHROMOSOME INVERSION; COMPARATIVE STUDY; EVOLUTION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC POLYMORPHISM; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; PAN TROGLODYTES; POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION; EVOLUTION, MOLECULAR; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INVERSION, CHROMOSOME; PAN TROGLODYTES; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SPECIES SPECIFICITY;

EID: 34147145526     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0010056     Document Type: Article

References (33)

1. Fujiyama A, Watanabe H, Toyoda A, Taylor TD, Itoh T, et al. (2002) Construction and analysis of a human-chimpanzee comparative clone map. Science 295: 131-134.
2. Li WH, Saunders MA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
3. Ebersberger I, Metzler D, Schwarz C, Paabo S (2002) Genome-wide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet 70: 1490-1497.
4. Hacia JG, Makalowski W, Edgemon K, Erdos MR, Robbins CM, et al. (1998) Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nat Genet 18: 155-158.
5. Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, et al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-793.
6. Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, et al. (2004) DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429: 382-388.
7. Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci U S A 99:13633-13635.
8. Yunis JJ, Prakash O (1982) The origin of man: A chromosomal pictorial legacy. Science 215: 1525-1530.
9. Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, et al. (2004) Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2: E207. DOI: 10.1371/journal.pbio.0020207
10. Locke DP, Segraves R, Carbone L, Archidiacono N, Albertson DG, et al. (2003) Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 13: 347-357.
11. Tuzun E, Bailey JA, Eichler EE (2004) Recent segmental duplications in the working draft assembly of the brown Norway rat. Genome Res 14: 493-506.
12. Cheung J, Wilson MD, Zhang J, Khaja R, MacDonald JR, et al. (2003) Recent segmental and gene duplications in the mouse genome. Genome Biol 4: R47.
13. Armengol L, Pujana MA, Cheung J, Scherer SW, Estivill X (2003) 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.
14. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE (2004) Hotspots of mammalian chromosomal evolution. Genome Biol 5: R23.
15. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
16. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, et al. (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437: 88-93.
17. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
18. Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, et al. (2005) Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77: 78-88.
19. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, et al. (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727-732.
20. Navarro A, Barton NH (2003) Chromosomal speciation and molecular divergence - accelerated evolution in rearranged chromosomes. Science 300: 321-324.
21. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129-137.
22. Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, et al. (2003) Human chromosome 7: DNA sequence and biology. Science 300: 767-772.
23. Fredman D, White SJ, Potter S, Eichler EE, Dunnen JT, et al. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 36: 861-866.
24. Papadopoulos N, Nicolaides NC, Wei YF, Ruben SM, Carter KC, et al. (1994) Mutation of a mutL homolog in hereditary colon cancer. Science 263: 1625-1629.
25. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789-796.
26. Muller S, Finelli P, Neusser M, Wienberg J (2004) The evolutionary history of human chromosome 7. Genomics 84: 458-467.
27. Pevzner P, Tesler G (2003) Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A 100: 7672-7677.
28. Osborne LR, Li M, Pober B, Chitayat D, Bodurtha J, et al. (2001) A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat Genet 29: 321-325.
29. Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, et al. (2003) Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet 12: 849-858.
30. Visser R, Shimokawa O, Harada N, Kinoshita A, Ohta T, et al. (2005) Identification of a 3.0-kb major recombination hotspot in patients with sotos syndrome who carry a common 1.9-Mb microdeletion. Am J Hum Genet 76: 52-67.
31. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
32. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, et al. (2003) Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol 4: R25.
33. Kozik A, Kochetkova E, Michelmore R (2002) GenomePixelizer - a visualization program for comparative genomics within and between species. Bioinformatics 18: 335-336.