Methods for assessing gene content diversity of KIR with examples from a global set of populations

Immunogenetics

Volumn 60, Issue 12, 2008, Pages 711-725

  Single, Richard M ^a   Martin, Maureen P ^b   Meyer, Diogo ^c   Gao, Xiaojiang ^b   Carrington, Mary ^b  

^a Department of Mathematics and Statistics University of Vermont ^*  (United States)

^b SAIC FREDERICK INC   (United States)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Coevolution; HLA; KIR; Population genetics; Selection; Statistical methods

Indexed keywords

HLA ANTIGEN CLASS 1; KILLER CELL IMMUNOGLOBULIN LIKE RECEPTOR;

ALLELE; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME 19; COHORT ANALYSIS; COMPARATIVE STUDY; ETHNIC GROUP; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HAPLOTYPE; HUMAN; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PSEUDOGENE;

ALLELES; CHROMOSOMES, HUMAN, PAIR 19; COHORT STUDIES; ETHNIC GROUPS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOTYPE; HAPLOTYPES; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MULTIGENE FAMILY; POLYMORPHISM, GENETIC; PSEUDOGENES; RECEPTORS, KIR; SELECTION (GENETICS);

EID: 61449529327     PISSN: 00937711     EISSN: 14321211     Source Type: Journal    
DOI: 10.1007/s00251-008-0331-1     Document Type: Review

References (49)

1. Abi-Rached L, Parham P (2005) Natural selection drives recurrent formation of activating killer cell immunoglobulin-like receptor and Ly49 from inhibitory homologues. J Exp Med 201:1319-1332. doi:10.1084/jem.20042558 (Pubitemid 40629074)
2. Bamshad M, Wooding SP (2003) Signatures of natural selection in the human genome. Nat Rev Genet 4:99-111. doi:10.1038/nrg999 (Pubitemid 36150682)
3. Carrington M, Cullen M (2004) Justified chauvinism: advances in defining meiotic recombination through sperm typing. Trends Genet 20:196-205. doi:10.1016/j.tig.2004.02.006 (Pubitemid 38369191)
4. Cramer H (1946) Mathematical methods of statistics. Princeton University Press, Princeton
5. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser A Stat Soc 39:1-38
6. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927
7. Garrigan D, Hedrick PW (2003) Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution 57:1707-1722 (Pubitemid 37096389)
8. Gendzekhadze K, Norman PJ, Abi-Rached L, Layrisse Z, Parham P (2006) High KIR diversity in Amerindians is maintained using few gene-content haplotypes. Immunogenetics 58:474-480. doi:10.1007/s00251-006-0108-3 (Pubitemid 43830112)
9. Gomez-Lozano N, Gardiner CM, Parham P, Vilches C (2002) Some human KIR haplotypes contain two KIR2DL5 genes: KIR2-DL5A and KIR2DL5B. Immunogenetics 54:314-319. doi:10.1007/s00251-002-0476-2 (Pubitemid 34983949)
10. Gourraud P-A, Barnetche T, Vidan-Jeras B, Cambon-Thomsen A (2005) Introduction to statistical analysis of population data in immunogenetics. Transpl Immunol 14:245-253. doi:10.1016/j.trim.2005.03.016 (Pubitemid 40848531)
11. Gourraud PA, Gagne K, Bignon JD, Cambon-Thomsen A, Middleton D (2007) Preliminary analysis of a KIR haplotype estimation algorithm: a simulation study. Tissue Antigens 69(Suppl 1):96-100. doi:10.1111/j.1399-0039.2006.762-4.x (Pubitemid 46625864)
12. Hao L, Nei M (2005) Rapid expansion of killer cell immunoglobulin-like receptor genes in primates and their coevolution with MHC Class I genes. Gene 347:149-159. doi:10.1016/j.gene.2004.12.012 (Pubitemid 40403755)
13. Hedrick PW (1987) Gametic disequilibrium measures: proceed with caution. Genetics 117:331-341
14. Hiby SE, Walker JJ, O'shaughnessy KM, Redman CW, Carrington M, Trowsdale J, Moffett A (2004) Combinations of maternal KIR and fetal HLA-C genes influence the risk of preeclampsia and reproductive success. J Exp Med 200:957-965. doi:10.1084/jem.20041214 (Pubitemid 39431121)
15. Hsu KC, Liu XR, Selvakumar A, Mickelson E, O'Reilly RJ, Dupont B (2002) Killer Ig-like receptor haplotype analysis by gene content: evidence for genomic diversity with a minimum of six basic framework haplotypes, each with multiple subsets. J Immunol 169:5118-5129 (Pubitemid 35217181)
16. Hughes AL (2002) Evolution of the human killer cell inhibitory receptor family. Mol Phylogenet Evol 25:330-340. doi:10.1016/S1055-7903(02)00255-5
17. Jones DC, Hiby SE, Moffett A, Trowsdale J, Young NT (2006) Nature of allelic sequence polymorphism at the KIR3DL3 locus. Immunogenetics 58:614-627. doi:10.1007/s00251-006-0130-5 (Pubitemid 44100410)
18. Khakoo SI, Carrington M (2006) KIR and disease: a model system or system of models? Immunol Rev 214:186-201. doi:10.1111/j.1600-065X.2006.00459.x (Pubitemid 44707911)
19. Khakoo SI, Rajalingam R, Shum BP, Weidenbach K, Flodin L, Muir DG et al (2000) Rapid evolution of NK cell receptor systems demonstrated by comparison of chimpanzees and humans. Immunity 12:687-698. doi:10.1016/S1074-7613(00)80219-8
20. Kulkarni S, Martin MP, Carrington M (2008) The Yin and Yang of HLA and KIR in Human Disease. Semin Immunol (in press)
21. Lewontin RC (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49-67
22. Martin AM, Kulski JK, Gaudieri S, Witt CS, Freitas EM, Trowsdale J et al (2004) Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B. Gene 335:121-131. doi:10.1016/j.gene.2004.03.018 (Pubitemid 38759758)
23. Mattiuz PL, Ihde D, Piazza A, Ceppellini R, Bodmer WF (1971) New approaches to the population genetic and segregation analysis of the HLA system. In: Terasaki PI (ed) Histocompatibility testing 1970. Munskaard, Copenhagen, p 193
24. Maxwell LD, Wallace A, Middleton D, Curran MD (2002) A common KIR2DS4 deletion variant in the human that predicts a soluble KIR molecule analogous to the KIR1D molecule observed in the rhesus monkey. Tissue Antigens 60:254-258. doi:10.1034/j.1399-0039.2002.600307.x (Pubitemid 35398828)
25. Meyer D, Single RM, Mack SJ, Erlich HA, Thomson G (2006) Signatures of demographic history and natural selection in the human major histocompatibility complex Loci. Genetics 173:2121-2142. doi:10.1534/genetics.105.052837 (Pubitemid 44285690)
26. Middleton D, Williams F, Halfpenny IA (2005) KIR genes. Transpl Immunol 14:135-142. doi:10.1016/j.trim.2005.03.002 (Pubitemid 40848518)
27. Middleton D, Meenagh A, Gourraud PA (2007) KIR haplotype content at the allele level in 77 Northern Irish families. Immunogenetics 59:145-158. doi:10.1007/s00251-006-0181-7 (Pubitemid 46130793)
28. Mueller JC (2004) Linkage disequilibrium for different scales and applications. Brief Bioinform 5:1-10. doi:10.1093/bib/5.4.355
29. Norman PJ, Carrington CV, Byng M, Maxwell LD, Curran MD, Stephens HA et al (2002) Natural killer cell immunoglobulin-like receptor (KIR) locus profiles in African and South Asian populations. Genes Immun 3:86-95. doi:10.1038/sj.gene.6363836 (Pubitemid 38961114)
30. Norman PJ, CookMA, Carey BS, Carrington CV, Verity DH, Hameed K et al (2004) SNP haplotypes and allele frequencies show evidence for disruptive and balancing selection in the human leukocyte receptor complex. Immunogenetics 56:225-237. doi:10.1007/s00251-004-0674-1 (Pubitemid 39119277)
31. Norman PJ, Abi-Rached L, Gendzekhadze K, Korbel D, Gleimer M, Rowley D et al (2007) Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans. Nat Genet 39:1092-1099. doi:10.1038/ng2111 (Pubitemid 47340657)
32. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60:227-237. doi:10.1006/tpbi.2001.1543 (Pubitemid 34235093)
33. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170-181. doi:10.1086/302959 (Pubitemid 30481554)
34. Sasieni P (1997) From genotypes to genes: doubling the sample size. Biometrics 53:1253-1261. doi:10.2307/2533494
35. Schipper RF, D'Amaro J, de Lange P, Schreuder GM, van Rood JJ, Oudshoorn M (1998) Validation of haplotype frequency estimation methods. Hum Immunol 59:518-523. doi:10.1016/S0198-8859(98)00054-8 (Pubitemid 28354972)
36. Shilling HG, Guethlein LA, Cheng NW, Gardiner CM, Rodriguez R, Tyan D et al (2002) Allelic polymorphism synergizes with variable gene content to individualize human KIR genotype. J Immunol 168:2307-2315 (Pubitemid 34171832)
37. Single RM, Martin MP, Gao X, Meyer D, Yeager M, Kidd JR et al (2007) Global diversity and evidence for coevolution of KIR and HLA. Nat Genet 39:1114-1119. doi:10.1038/ng2077 (Pubitemid 47342436)
38. Slatkin M (2008) Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9:477-485. doi:10.1038/nrg2361
39. Slatkin M, Excoffier L (1996) Testing for linkage disequilibrium in genotypic data using the expectation-maximization algorithm. Heredity 76:377-383. doi:10.1038/hdy.1996.55
40. Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18:74-82. doi:10.1016/S0168-9525(02)02592-1 (Pubitemid 34127806)
41. Tishkoff SA, Kidd KK (2004) Implications of biogeography of human populations for 'race' and medicine. Nat Genet 36:S21-S27. doi:10.1038/ng1438 (Pubitemid 41103834)
42. Toneva M, Lepage V, Lafay G, Dulphy N, Busson M, Lester S et al (2001) Genomic diversity of natural killer cell receptor genes in three populations. Tissue Antigens 57:358-362. doi:10.1034/j.1399-0039.2001.057004358.x (Pubitemid 32511307)
43. Uhrberg M, Valiante NM, Shum BP, Shilling HG, Lienert-Weidenbach K, Corliss B et al (1997) Human diversity in killer cell inhibitory receptor genes. Immunity 7:753-763. doi:10.1016/S1074-7613(00)80394-5 (Pubitemid 28064889)
44. Watterson GA (1978) The homozygosity test of neutrality. Genetics 88:405-417
45. Weiss KM, Clark AG (2002) Linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19. doi:10.1016/S0168-9525(01)02550-1
46. Williams RC, Steinberg AG, Knowler WC, Pettitt DJ (1986) Gm 3;5,13,14 and stated-admixture: independent estimates of admixture in American Indians. Am J Hum Genet 39:409-413 (Pubitemid 17170844)
47. Yawata M, Yawata N, McQueen KL, Cheng NW, Guethlein LA, Rajalingam R et al (2002) Predominance of group A KIR haplotypes in Japanese associated with diverse NK cell repertoires of KIR expression. Immunogenetics 54:543-550. doi:10.1007/s00251-002-0497-x (Pubitemid 35435512)
48. Yawata M, Yawata N, Draghi M, Little AM, Partheniou F, Parham P (2006) Roles for HLA and KIR polymorphisms in natural killer cell repertoire selection and modulation of effector function. J Exp Med 203:633-645. doi:10.1084/jem. 20051884
49. Yoo Y, Kaslow R, Tang J, Zhang K (2007) Haplotype inference for present-absent genotype data for clustered genes using identified haplotypes and haplotype patterns. Bioinformatics 23:2399-2406. doi:10.1093/bioinformatics/ btm371 (Pubitemid 47423837)