Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays

Nature Genetics

Volumn 22, Issue 2, 1999, Pages 164-167

  Hacia, Joseph G ^a   Fan, Jian Bing ^b   Ryder, Oliver ^c   Jin, Li ^d,e   Edgemon, Keith ^a   Ghandour, Ghassan ^b   Mayer, R Aeryn ^a   Sun, Bryan ^a   Hsie, Linda ^b   Robbins, Christiane M ^a   Brody, Lawrence C ^a   Wang, David ^f   Lander, Eric S ^f   Lipshutz, Robert ^b   Fodor, Stephen P A ^b   Collins, Francis S ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b Thermo Fisher Scientific   (United States)

^c INSTITUTE FOR CONSERVATION RESEARCH   (United States)

^d FUDAN UNIVERSITY   (China)

^e UNIVERSITY OF TEXAS   (United States)

^f WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHIMPANZEE; DNA MICROARRAY; DNA POLYMORPHISM; EVOLUTION; GENE FREQUENCY; GENETIC VARIABILITY; GORILLA; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SPECIES DIFFERENCE;

EID: 0033039498     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/9674     Document Type: Article

References (28)

1. Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-1082 (1998).
2. Ruvolo, M. A new approach to studying modern human origins: hypothesis testing with coalescence time distributions. Mol. Phylogenet. Evol. 5, 202-219 (1996).
3. Goodman, M. et al. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9, 585-598 (1998).
4. Hacia, J.G. et al. Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nature Genet. 18, 155-158 (1998).
5. Savatier, P. et al. Evolution of the primate β-globin gene region. High rate of variation in CpG dinucleotides and in short repeated sequences between man and chimpanzee. J. Mol. Biol. 182, 21-29 (1985).
6. Sved, J. & Bird, A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc. Natl Acad. Sci. USA 12, 4692-4696 (1990).
7. Yang, A.S. et al. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J. Mol. Biol. 258, 240-250 (1996).
8. Watterson, G.A. & Guess, H.A. Is the most frequent allele the oldest? Theor. Popul. Biol. 11, 141-160 (1977).
9. Watkins, D.I. The evolution of major histocompatibility class I genes in primates. Crit. Rev. Immunol. 15, 1-29 (1995).
10. Brown, W.M., Prager, E.M., Wang, A. & Wilson, A.C. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18, 225-239 (1982).
11. Garner, K.J. & Ryder, O.A. Mitochondrial DNA diversity in gorillas. Mol. Phylogenet. Evol. 6, 39-48 (1996).
12. Crouau-Roy, B., Service, S., Slatkin, M. & Freimer, N. A fine-scale comparison of the human and chimpanzee genomes: linkage, linkage disequilibrium and sequence analysis. Hum. Mol. Genet. 5, 1131-1137 (1996).
13. Wise, C.A., Sraml, M., Rubinsztein, D.C. & Easteal, S. Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees. Mol. Biol. Evol. 14, 707-716 (1997).
14. Cooper, G., Rubinsztein, D.C. & Amos, W. Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Hum. Mol. Genet. 7, 1425-1429 (1998).
15. Mountain, J.L. & Cavalli-Sforza, L.L. Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Natl Acad. Sci. USA 91, 6515-6519 (1994).
16. Martinko, J.M., Vincek, V., Klein, D. & Klein, J. Primate ABO glycotransferases: evidence for trans-species evolution. Immunogenetics 37, 274-278 (1993).
17. Deeb, S.S., Jorgensen, A.L., Battisti, L., Iwasaki, L. & Motulsky, A.G. Sequence divergence of the red and green visual pigments in great apes and humans. Proc. Natl Acad. Sci. USA 91, 7262-7266 (1994).
18. Jaeger, E.E.M. et al. Characterization of chimpanzee TCRV gene polymorphism: how old are human TCRV alleles? Immunogenetics 47, 115-123 (1998).
19. Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983).
20. Bergstrom, T.F., Josefsson, A., Erlich, H.A. & Gyllensten, U. Recent origin of HLADRB1 alleles and implications for human evolution. Nature Genet. 18, 237-242 (1998).
21. Clark, A.G. Neutral behavior of shared polymorphism. Proc. Natl Acad. Sci. USA 94, 7730-7734 (1997).
22. Chee, M.S. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610-614 (1996).
23. Hacia, J.G. et al. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nature Genet. 14, 441-447 (1996).
24. Morin, P.A. et al. Kin selection, social structure, gene flow, and the evolution of chimpanzees. Science 265, 1193-1201 (1994).
25. Collins, F.S., Guyer, M.S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580-1581 (1997).
26. Kruglyak, L. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17, 21-24 (1997).
27. Nickerson D.A. et al. DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nature Genet. 19, 233-240 (1998).
28. Lai, E., Riley, J., Purvis, I. & Roses, A. A 4-Mb high-density single nucleotide polymorphism-based map around human APOE. Genomics 54, 31-38 (1998).