Genome-wide SNP typing reveals signatures of population history

Genomics

Volumn 92, Issue 1, 2008, Pages 1-8

  Hughes, Austin L ^a   Welch, Robert ^b,c   Puri, Vinita ^b,c   Matthews, Casey ^b,c   Haque, Kashif ^b,c   Chanock, Stephen J ^c   Yeager, Meredith ^b,c  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

^b SAIC FREDERICK INC   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Complex disease; Human populations; Single nucleotide polymorphism

Indexed keywords

AFRICAN AMERICAN; ARTICLE; ASIAN AMERICAN; AUTOSOMAL INHERITANCE; CORRELATION ANALYSIS; EUROPEAN AMERICAN; GENE FREQUENCY; GENETIC DISTANCE; GENETIC MARKER; GENETIC VARIABILITY; GENOTYPE; HISPANIC; HISTORY; HUMAN; HUMAN GENOME; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

GENE FREQUENCY; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS;

EID: 45449100124     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2008.03.005     Document Type: Article

References (52)

1. Lillie-Blanton M., Parsons P.E., Gayle H., and Dievler A. Racial differences in health: not just black and white, but shades of gray. Annu. Rev. Public Health 17 (1996) 411-448
2. Whaley A.L. Ethnicity/race, ethics, and epidemiology. J. Natl. Med. Assoc. 95 (2006) 736-742
3. Shavers V.L. Racism and health inequity among Americans. J. Natl. Med. Assoc. 98 (2006) 386-396
4. Garte S. The racial genetics paradox in biomedical research and public health. Public Health Rep. 117 (2006) 421-425
5. Tishkoff S.A., and Williams S.M. Genetic analysis of African populations: human evolution and complex disease. Nat. Rev., Genet. 3 (2002) 611-621
6. Bamshad M. Genetic influences on health: does race matter?. JAMA 294 (2005) 937-946
7. Vigilant L., Stoneking M., Harpending H., Hawkes K., and Wilson A.C. African populations and the evolution of human mitochondrial DNA. Science 253 (1991) 1503-1507
8. Nei M., and Takezaki N. The root of the phylogenetic tree of human populations. Mol. Biol. Evol. 13 (1996) 170-177
9. Kidd K.K., Pakstis A.J., Speed W.C., and Kidd J.R. Understanding human DNA sequence variation. J. Heredity 95 (2004) 406-420
10. Nei M., and Roychoudhury A.K. Evolutionary relationships of human populations on a global scale. Mol. Biol. Evol. 10 (1993) 927-943
11. Jorde L.B., and Wooding S.P. Genetic variation, classification and 'race'. Nat. Genet. 36 (2004) 528-533
12. Hughes A.L., Packer B., Welch R., Bergen A.W., Chanock S.J., and Yeager M. Effects of natural selection on inter-population divergence at polymorphic sites in human protein-coding loci. Genetics 170 (2005) 1181-1187
13. Serre D., and Pääbo S. Evidence for gradients of human genetic diversity within and among continents. Genome Res. 14 (2004) 1679-1685
14. Barnes K.C. Genetic epidemiology of health disparities in allergy and clinical immunology. J. Allergy Clin. Immunol. 117 (2006) 243-254
15. Chen H., Hernandez W., Shriver M.D., Ahaghotu C.A., and Kittles R.A. ICAM gene cluster SNPs and prostate cancer risk in African Americans. Hum. Genet. 120 (2006) 69-76
16. Cross R.K., Jung C., Wasan S., Joshi G., Sawyer R., and Roghmannn M.C. Racial differences in disease phenotypes in patients with Crohn's disease. Inflamm. Bowel Dis. 12 (2006) 192-198
17. Dominick K.L., and Baker T.A. Racial and ethnic differences in osteoarthritis: prevalence, outcomes, and medical care. Ethn. Dis. 14 (2004) 558-566
18. Marshall Jr. M.C. Diabetes in African Americans. Postgrad. Med. J. 81 (2005) 734-740
19. Stansbury J.P., Jia H., Williams L.S., Vogel W.B., and Duncan P.W. Ethnic disparities in stroke: epidemiology, acute care, and postacute outcomes. Stroke 36 (2005) 374-386
20. Reich D.E., and Lander E.S. On the allelic spectrum of human disease. Trends Genet. 17 (2001) 502-510
21. Packer B., Yeager M., Staats B., Welch R., Crenshaw A., Kiley M., Eckert A., Beerman M., Miller E., Bergen A., Rothman N., Strausberg R., and Chanock S.J. SNP500 Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res. 32 (2004) D528-D532
22. International HapMap Consortium. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
23. Bamshad M., Wooding S., Salisbury B.A., and Stephens J.C. Deconstructing the relationship between genetics and race. Nat. Rev. Genet. 5 (2004) 598-609
24. Rosenberg N.A., Pritchard J.K., Weber J.L., Cann H.M., Kidd K.K., Zhivotovsky L.A., and Feldman M.W. Genetic structure of human populations. Science 298 (2002) 2381-2385
25. Hanis C.L., Hewett-Emmett D., Bertin T.K., and Schull W.J. Origins of U.S. Hispanics: implications for diabetes. Diabetes Care 14 (1991) 618-627
26. Barbosa M.D., Nguyen Q.A., Tchernev V.T., Ashley J.A., Detter J.C., Blaydes S.M., Brandt S.J., Chotai D., Hodgman C., Solari R.C., Lovett M., and Kingsmore S. Identification of the homologous beige and Chediak-Higashi syndrome genes. Nature 282 (1996) 262-265
27. Roessler E., Du Y.-Z., Mullot J.L., Casas E., Allen W.P., Gillessen-Kaesbach G., Roeder E.R., Ming J.E., Ruiz I., Altaba A., and Muenke M. Loss-of-function mutations in the human GLI2 gene are associated with pituitary anomalies and holoprosencephaly-like features. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 13424-13429
28. Pekarsky Y., Garrison P.N., Palamarchuk A., Zanesi N., Aqeilan R.I., Huebner K., Barnes L.D., and Croce C.M. Fhit is a physiological target of the protein kinase Src. Proc. Natl. Acad. Sci. U. S. A. 191 (2004) 3775-3779
29. Shiratsuchi T., Nishimori H., Ichise H., Nakamura Y., and Tokino T. Cloning and characterization of BAI2 and BAI3 novel genes homologous to brain-specific angiogenesis inhibitor 1 (BAI1). Cytogenet. Cell Genet. 79 (1997) 103-108
30. Targoff I.N. Autoantibodies in polymyositis. Rheum. Dis. Clin. North Am. 18 (1992) 455-482
31. Weihofen A., Binns K., Lemburg M.K., Ashmann K., and Martoglio B. Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 296 (2002) 2215-2218
32. Bennett B.D., Babu-Khan S., Loeloff R., Louis J.-C., Curran E., Citron M., and Vassar R. Expression analysis of BACE2 in brain and peripheral tissues. J. Biol. Chem. 275 (2000) 20647-20651
33. Hicar M.D., Liu Y., Allen C.E., and Wu L.-C. Structure of the human zinc finger protein HIVEP3: molecular cloning, expression, exon-intron structure, and comparison with paralogous genes HIVEP1 and HIVEP2. Genomics 71 (2001) 89-100
34. Nakanishi N., Kim Y.-S., Nakajima T., and Jetten A.M. Regulatory role for Krüppel-like zinc-finger protein Gli-similar 1 (Glis1) in PMA-treated and psoriatic epidermis. J. Invest. Dermatol. 126 (2006) 49-60
35. Pietropaolo M., Castaño L., Babu S., Buelow R., Kuo Y.-L., Martin S., Martin A., Powers A.C., Prochazka M., Naggert J., Leiter E.H., and Eisenbarth G.S. Islet cell autoantigen 69 kD (ICA69): molecular cloning and characterization of a novel diabetes-associated autoantigen. J. Clin. Invest. 92 (1993) 359-371
36. Smith C.A., Gruss H.J., Davis T., Anderson D., Farrah T., Baker E., Sutherland G.R., Brannan C.I., Copeland N.G., Jenkins N.A., Grabstein K.H., Gliniak B., McAlister I.B., Fanslow W., Alderson M., Falk B., Gimpel S., Gillis S., Din W.S., Goodwin R.G., and Armitage R.J. CD30 antigen, a marker for Hodgkin's lymphoma, is a receptor whose ligand defines an emerging family of cytokines with homology to TNF. Cell 73 (1993) 1349-1360
37. McLoughlin D.D., and Miller C.C. The intracellular cytoplasmic domain of the Alzheimer's disease amyloid precursor protein interacts with phosphotyrosine-binding domain proteins in the yeast two-hybrid system. FEBS Lett. 18 (1996) 197-200
38. Runkel F., Büssow H., Seburn K.L., Cox G.A., Ward D.M., Kaplan J., and Franz T. Grey, a novel mutation in the murine Lyst gene, causes the beige phenotype by skipping of exon 25. Mamm. Genome 17 (2006) 203-210
39. Izagirre N., García I., Junquera C., de la Rúa C., and Alonso S. A scan for signatures of positive selection in candidate loci for skin pigmentation in humans. Mol. Biol. Evol. 23 (2006) 1697-1706
40. Wang J.-W., Howson J., Haller E., and Kerr W.G. Identification of a novel lipopolysaccharide-inducible gene with key features of both kinase anchor proteins and chs1/beige proteins. J. Immunol. 166 (2001) 4586-4595
41. Gebauer D., Li J., Jogl G., Shen Y., Myszka D.G., and Tong L. Crystal structure of the PH-BEACH domains of human LRBA/BGL. Biochemistry 43 (2001) 14873-14880
42. Hughes A.L., Friedman R., and Glenn N.L. The future of data analysis in evolutionary genomics. Curr. Genomics 7 (2006) 227-234
43. Sabeti P.C., Schaffner S.K., Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen T.S., Altshuler D., and Lander E.S. Positive natural selection in the human lineage. Science 312 (2006) 1614-1620
44. Freudenberg-Hua Y., Freudenberg J., Kluck N., Cichon S., Propping P., and Nöthen M.M. Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. Genome Res. 13 (2003) 2271-2276
45. Hughes A.L., Packer B., Welch R., Bergen A.W., Chanock S.J., and Yeager M. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 15754-15757
46. Sunyaev S., Ramensky V., Koch I., Lathe III W.S., Kondrashov A.S., and Bork P. Prediction of deleterious human alleles. Hum. Mol. Genet. 10 (2001) 591-597
47. Zhao Z., Fu Y.-X., Hewett-Emmett D., and Boerwinkle E. Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312 (2003) 207-213
48. Hughes A.L., Packer B., Welch R., Chanock S.J., and Yeager M. High level of functional polymorphism indicates a unique role of natural selection at human immune system loci. Immunogenetics 57 (2005) 821-827
49. Mulligan C.J., Hunley K., Cole S., and Long J.C. Population genetics, history, and health patterns in Native Americans. Annu. Rev. Genomics Hum. Genet. 5 (2004) 295-315
50. Nei M. Molecular Evolutionary Genetics (1987), Columbia Univ. Press, New York
51. Dudewicz E.J., and Mishra S.N. Modern Mathematical Statistics (1988), Wiley, New York
52. Johnson R., and Wichern D. Applied Multivariate Statistical Methods. 3rd (1992), Prentice Hall, Englewood Cliffs, NJ