CYBB, an NADPH-oxidase gene: Restricted diversity in humans and evidence for differential long-terrn purifying selection on transmembrane and cytosolic domains

Human Mutation

Volumn 29, Issue 5, 2008, Pages 623-632

  Tarazona Santos, Eduardo ^a,b   Bernig, Toralf ^a   Burdett, Laurie ^a,c   Magalhaes, Wagner C S ^b   Fabbri, Cristina ^d   Liao, Jason ^a   Redondo, Rodrigo A F ^b   Welch, Robert ^a,c   Yeager, Meredith ^a,c   Chanock, Stephen J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c SAIC FREDERICK INC   (United States)

^d UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

CYBB; Haplotypes; Innate immunity; Linkage disequilibrium; Population genetics; Respiratory burst; Tag SNPs

Indexed keywords

GLYCOPROTEIN GP 91; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE OXIDASE;

AFRICAN AMERICAN; ARTICLE; AUTOIMMUNE DISEASE; CLADISTICS; CYTOSOL; ETHNICITY; GENETIC LINKAGE; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; INFECTION COMPLICATION; INTRON; MAMMAL; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME;

ANIMALS; CELL MEMBRANE; CHROMOSOMES, HUMAN, X; CYTOSOL; HAPLOTYPES; HUMANS; IMMUNITY, NATURAL; LINKAGE DISEQUILIBRIUM; MEMBRANE GLYCOPROTEINS; NADPH OXIDASE; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY;

MAMMALIA;

EID: 42949175052     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20667     Document Type: Article

References (54)

1. Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L. 2004. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2:e286.
2. Alonso S, Armour JA. 2004. Compound haplotypes at Xp11.23 and human population growth in Eurasia. Ann Hum Genet 68:428-437.
3. Anderson-Cohen M, Holland SM, Kuhns DB, Fleisher TA, Ding L, Brenner S, Malech HL, Roesler J. 2003. Severe phenotype of chronic granulomatous disease presenting in a female with a de novo mutation in gp91-phox and a non familial, extremely skewed X chromosome inactivation. Clin Immunol 109:308-317.
4. Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48.
5. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL. 1997. An apportionment of human DNA diversity. Proc Natl Acad Sci USA 94:4516-4519.
6. Barrett JC, Fry B, Mailer J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
7. Brandes RP, Kreuzer J. 2005. Vascular NADPH oxidases: molecular mechanisms of activation. Cardiovasc Res 6511:16-27.
8. Buckley RH. 2004. Pulmonary complications of primary immunodeficiencies. Paediatr Respir Rev 5(Suppl A):S225-S233.
9. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, Chen Z, Chu J, Carcassi C, Contu L, Du R, Excoffier L, Ferrara GB, Friedlaender JS, Groot H, Gurwitz D, Jenkins T, Herrera RJ, Huang X, Kidd J, Kidd KK, Langaney A, Lin AA, Mehdi SQ, Parham P, Piazza A, Pistillo MP, Qian Y, Shu Q, Xu J, Zhu S, Weber JL, Greely HT, Feldman MW, Thomas G, Dausset J, Cavalli-Sforza LL. 2002. A human genome diversity cell line panel. Science 296:261-262.
10. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 7411:106-120.
11. Cavalli-Sforza LL, Bodmer W. 1971. The genetics of human population. New York: Dover Publications.
12. Chanock SJ, el Benna J, Smith RM, Babior BM. 1994. The respiratory burst oxidase. J Biol Chem 269:24519-24522.
13. Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengard J, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF. 1998. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 63:595-612.
14. Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
15. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
16. Fullerton SM, Clark AG, Weiss KM, Nickerson DA, Taylor SL, Stengard JH, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF. 2000. Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Am J Hum Genet 67:881-900.
17. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
18. Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862-864.
19. Hammer MF, Garrigan D, Wood E, Wilder JA, Mobasher Z, Bigham A, Krenz JG, Nachman MW. 2004. Heterogeneous patterns of variation among multiple human X-linked loci: the possible role of diversity-reducing selection in non-Africans. Genetics 167:1841-1853.
20. Harris EE, Hey J. 2001. Human populations show reduced DNA sequence variation at the factor IX locus. Curr Biol 11:774-778.
21. Heyworth PG, Curnutte JT, Rae J, Noack D, Roos D, van Koppen E, Cross AR. 2001. Hematologically important mutations: X-linked chronic granulomatous disease (second update). Blood Cells Mol Dis 2711:16-26.
22. Heyworth PG, Cross AR, Curnutte JT. 2003. Chronic granulomatous disease. Curr Opin Immunol 15:578-584.
23. Hill WG, Robertson A. 1968. Linkage disequilibrium in finite populations. Theor Appl Genet 38:226-231.
24. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 1161:153-159.
25. Jirapongsananuruk O, Niemela JE, Malech HL, Fleisher TA. 2002. CYBB mutation analysis in X-linked chronic granulomatous disease. Clin Immunol 104:73-76.
26. Kaessmann H, Heissig F, von Haeseler A, Paabo S. 1999. DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat Genet 22:78-81.
27. Kitano T, Schwarz C, Nickel B, Paabo S. 2003. Gene diversity patterns at 10 X-chromosomal loci in humans and chimpanzees. Mol Biol Evol 20:1281-1289.
28. Li N, Stephens M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213-2233.
29. Miller MP, Kumar S. 2001. Understanding human disease mutations through the use of interspecific genetic variation. Hum Mol Genet 10:2319-2328.
30. Nachman MW, Crowell SL. 2000. Contrasting evolutionary histories of two introns of the Duchenne muscular dystrophy gene, Dmd, in humans. Genetics 155:1855-1864.
31. Nachman MW, D'Agostino SL, Tillquist CR, Mobasher Z, Hammer MF. 2004. Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans. Genetics 167:423-437.
32. Nei M. 1987. Molecular evolutionary genetics. New York: Princeton University Press.
33. Packer BR, Yeager M, Burdett L, Welch R, Beerman M, Qi L, Sicotte H, Staats B, Acharya M, Crenshaw A, Eckert A, Puri V, Gerhard DS, Chanock SJ. 2006. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res 34 (Database issue):D617-D621.
34. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
35. Roos D, van Bruggen R, Meischl C. 2003. Oxidative killing of microbes by neutrophils. Microbes Infect 5:1307-1315.
36. Rosenberg NA. 2006. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet 70:841-847.
37. Rozas J, Sanehez-DelBarrio JC, Messeguer X, Rozas R. 2003. DnaSP DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
38. Schneider S, Roessli D, Excoffier L. 2000. Arlequin v. 2.0: a software for population genetics data analysis. Genetics and Biometrics Laboratory. University of Geneva, Switzerland, p 111.
39. Staats B, Qi L, Beerman M, Sicotte H, Burdett LA, Packer B, Chanock SJ, Yeager M. 2005. Genewindow: an interactive tool for visualization of genomic variation. Nat Genet 37:109-110.
40. Stasia MJ, Bordigoni P, Floret D, Brion JP, Bost-Bru C, Michel G, Gatel P, Durant-Vital D, Voelckel MA, Li XJ, Guillot M, Maquet E, Martel C, Morel F. 2005. Characterization of six novel mutations in the CYBB gene leading to different sub-types of X-linked chronic granulomatous disease. Hum Genet 116:72-82.
41. Stephens M, Donnelly P. 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162-1169.
42. Tajima F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
43. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
44. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526.
45. Tarazona-Santos E, Tishkofif SA. 2005. Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus. Genes Immun 6:53-65.
46. Tishkoff SA, Verrelli BC. 2003. Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu Rev Genomics Hum Genet 4:293-340.
47. Uhlemann AC, Szlezak NA, Vonthein R, Tomiuk J, Emmer SA, Lell B, Kremsner PG, Kun JF. 2004. DNA phasing by TA dinucleotide microsatellite length determines in vitro and in vivo expression of the gp91phox subunit of NADPH oxidase and mediates protection against severe malaria. J Infect Dis 189:2227-2234.
48. Verrelli BC, Tishkoff SA. 2004. Signatures of selection and gene conversion associated with human color vision variation. Am J Hum Genet 75:363-375.
49. Wang JP, Rought SE, Corbeil J, Guiney DG. 2003. Gene expression profiling detects patterns of human macrophage responses following Mycobacterium tuberculosis infection. FEMS Immunol Med Microbiol 39:163-172.
50. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276.
51. Winkelstein JA, Marino MC, Johnston RB, Jr, Boyle J, Curnutte J, Gallin JI, Malech HL, Holland SM, Ochs H, Quie P, Buckley RH, Foster CB, Chanock SJ, Dickler H. 2000. Chronic granulomatous disease. Report on a national registry of 368 patients. Medicine (Baltimore) 79:155-169.
52. Wright SI, Charlesworth B. 2004. The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model. Genetics 168:1071-1076.
53. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556.
54. Yu N, Fu YX, Li WH. 2002. DNA polymorphism in a worldwide sample of human X chromosomes. Mol Biol Evol 19:2131-2141.