A method for detecting recent selection in the human genome from allele age estimates

Genetics

Volumn 165, Issue 1, 2003, Pages 287-297

  Toomajian, Christopher ^a,d   Ajioka, Richard S ^b   Jorde, Lynn B ^c   Kushner, James P ^b   Kreitman, Martin ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AGE; ALLELE; ARTICLE; GENE LOCUS; GENE MAPPING; GENE MUTATION; GENETIC LINKAGE; GENOME; HAPLOTYPE; HUMAN; HUMAN GENOME; NATURAL SELECTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENOME, HUMAN; HETEROZYGOTE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HUMANS; MEMBRANE PROTEINS; SELECTION (GENETICS);

EID: 0141455095     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. AJIOKA, R. S., L. B. JORDE, J. R. GRUEN, P. YU, D. DIMITROVA et al., 1997 Haplotype analysis of hemochromatosis: evaluation of different linkage-disequilibrium approaches and evolution of disease chromosomes. Am. J. Hum. Genet. 60: 1439-1447.
2. ANDOLFATTO, P., J. D. WALL and M. KREITMAN, 1999 Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
3. ARDLIE, K. G., L. KRUGLYAK and M. SEIELSTAD, 2002 Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3: 299-309.
4. BANDELT, H. J., P. FORSTER, B. C. SYKES and M. B. RICHARDS, 1995 Mitochondrial portraits of human populations using median networks. Genetics 141: 743-753.
5. BEUTLER, E., V. J. FELITTI, J. A. KOZIOL, N. J. HO and T. GELBART, 2002 Penetrance of 845G→A (C282Y) HFE hereditary haemochromatosis mutation in the USA. Lancet 359: 211-218.
6. BUGAWAN, T. L., W. KLITZ, A. BLAIR and H. A. ERLICH, 2000 High-resolution HLA class I typing in the CEPH families: analysis of linkage disequilibrium among HLA loci. Tissue Antigens 56: 392-404.
7. BULAJ, Z. J., L. M. GRIFFEN, L. B. JORDE, C. Q. EDWARDS and J. P. KUSHNER, 1996 Clinical and biochemical abnormalities in people heterozygous for hemochromatosis. New Engl. J. Med. 335: 1799-1805.
8. CARRINGTON, M., 1999 Recombination within the human MHC. Immunol. Rev. 167: 245-256.
9. EDWARDS, C. Q., L. M. GRIFFEN, D. GOLDGAR, C. DRUMMOND, M. H. SKOLNICK et al., 1988 Prevalence of hemochromatosis among 11,065 presumably healthy blood donors. N. Engl. J. Med. 318: 1355-1362.
10. FAIRBANKS, V. F., 2000 Hemochromatosis: population genetics, pp. 42-50 in Hemochromatosis: Genetics, Pathophysiology, Diagnosis and Treatment, edited by J. C. BARTON and C. Q. EDWARDS. Cambridge University Press, Cambridge, UK
11. FEDER, J. N., A. GNIRKE, W. THOMAS, Z. TSUCHIHASHI, D. A. RUDDY et al., 1996 A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat. Genet. 13: 399-408.
12. FEDER, J. N., D. M. PENNY, A. IRRINKI, V. K. LEE, J. A. LEBRÖN et al., 1998 The hemochromatosis gene product complexes with the transferrin receptor and lowers its affinity, for ligand binding. Proc. Natl. Acad. Sci. USA 95: 1472-1477.
13. GUO, S. W., and M. XIONG, 1997 Estimating the age of mutant disease alleles based on linkage disequilibrium. Hum. Hered. 47: 315-337.
14. HUDSON, R. R., 1990 Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7: 1-44.
15. HUDSON, R. R., K. BAILEY, D. SKARECKY, J. KWIATOWSKI and F. J. AYALA, 1994 Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329-1340.
16. JEFFREYS, A. J., L. KAUPPI and R. NEUMANN, 2001 Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
17. KIDD, K. K., 1987 Phenylketonuria: population genetics of a disease. Nature 327: 282-283.
18. KIMURA, M., and T. OHTA, 1973 The age of a neutral mutant persisting in a finite population. Genetics 75: 199-212.
19. KIRBY, D. A., and W. STEPHAN, 1999 Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics 141: 1483-1490.
20. Liu, J. S., C. SABATTI, J. TENG, B. J. B. KEATS and N. RISCH, 2001 Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 11: 1716-1724.
21. LUCOTTE, G., 2001 Frequency analysis and allele map in favor of the Celtic origin of the C282Y mutation of hemochromatosis. Blood Cells Mol. Dis. 27: 549-556.
22. MALFROY, L., M. P. ROTH, M. CARRINGTON, N. BOROT, A. VOLZ et al., 1997 Heterogeneity in rates of recombination in the 6-Mb region telomeric to the human major histocompatibility complex. Genomics 43: 226-231.
23. MARUYAMA, T., 1974 The age of an allele in a finite population. Genet. Res. 23: 137-143.
24. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
25. MCPEEK, M. S., and A. STRAHS, 1999 Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am. J. Hum. Genet. 65: 858-875.
26. MERRYWEATHER-CLARKE, A. T., J. J. POINTON, J. D. SHEARMAN and K. J. H. ROBSON, 1997 Global prevalence of putative haemochromatosis mutations. J. Med. Genet. 34: 275-278.
27. MOTULSKY, A. G., 1964 Hereditary red cell traits and malaria. Am. J. Trop. Med. Hyg. 13: 147-158.
28. NORDBORG, M., and S. TAVARÉ, 2002 Linkage disequilibrium: what history has to tell us. Trends Genet. 18: 83-90.
29. OHTA, T., and M. KIMURA, 1973 A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res. 22: 201-204.
30. PICHON, L., G. CARN, P. BOURIC, T. GIFFON, B. CHAUVEL et al., 1996 Structural analysis of the HLA-A/HLA-F subregion: precise localization of two new multigene families closely associated with the HLA class I sequences. Genomics 32: 236-244.
31. PRICE, P., C. WITT, R. ALLCOCK, D. SAYER, M. GARLEPP et al., 1999 The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunolopathological diseases. Immunol. Rev. 167: 257-274.
32. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
33. PRZEWORSKI, M., R. R. HUDSON and A. DI RIENZO, 2000 Adjusting the focus on human variation. Trends Genet. 16: 296-302.
34. RANNALA, B., and J. P. REEVE, 2001 High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. Am. J. Hum. Genet. 69: 159-178.
35. REICH, D. E., and D. B. GOLDSTEIN, 1999 Estimating the age of mutations using variation at linked markers, pp. 129-138 in Microsatellites. Evolution and Applications, edited by D. B. GOLDSTEIN and C. SCHLÖTTERER. Oxford University, Press, Oxford.
36. REICH, D. E., M. CARGILI, S. BOLK, J. IRELAND, P. C. SABETI et al., 2001 Linkage disequilibrium in the human genome. Nature 411:199-204.
37. REISCH, N., D. DE LEON, L. OZELIUS, P. KRAMER, L. ALMASY et al., 1995 Genetic analysis of idiopathic torsion dystonia in Ashkenazi Jews and their recent descent from a small founder population. Nat. Genet. 9: 152-159.
38. ROMEO, G., M. DEVOTO and L. J. V. GALIETTA, 1989 Why is the cystic fibrosis gene so frequent? Hum. Genet. 84: 1-5.
39. ROTTER, J. I., and J. M. DIAMOND, 1987 What maintains the frequencies of human genetic diseases? Nature 329: 289-290.
40. SABETI, P. C., D. E. REICH, J. M. HIGGINS, H. Z. P. LEVINE, D. J. RICHTER et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
41. SALTER-CID, L., A. BRUNMARK, Y. LI, D. LETURCQ, P. A. PETERSON et al., 1999 Transferrin receptor is negatively modulated by the hemochromatosis protein HFE: implications for cellular iron homeostasis. Proc. Natl. Acad. Sci. USA 96: 5434-5439.
42. SERRE, J. L., B. SIMON-BOUY, E. MORNET, B. JAUME-ROIG, A. BALASSOPOULOU et al., 1990 Studies of RFLP closely linked to the cystic fibrosis locus throughout Europe lead to new considerations in population genetics. Hum. Genet. 84: 449-454.
43. SLATKIN, M., 1994 Linkage disequlibrium in growing and stable populations. Genetics 137: 331-336.
44. SLATKIN, M., and G. BERTORELLE, 2001 The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics 158: 865-874.
45. SLATKIN, M., and B. RANNALA, 2000 Estimating allele age. Annu. Rev. Genomics Hum. Genet. 1: 225-249.
46. TERMIJTELEN, A., J. D'AMARO, J.J. VAN ROOD and G. M. T. SCHREUDER, 1995 Linkage disequilibrium in HLA cannot be explained by selective recombination. Tissue Antigens 46: 387-390.
47. TERWILLIGER, J. D., 1995 A powerful method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. Am. J. Hum. Genet. 56: 777-787.
48. THOMAS, W., A. FULLAN, D. B. LOEB, E. E. MCCLELLAND, B. R. BACON et al., 1998 A haplotype and linkage disequilibrium analysis of the hereditary hemochromatosis gene region. Hum. Genet. 102: 517-525.
49. TOOMAJIAN, C., and M. KREITMAN, 2002 Sequence variation and haplotype structure at the human HFE locus. Genetics 161: 1609-1623.
50. VALDES, A. M., M. SLATKIN and N. B. FREIMER, 1993 Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133: 737-749.
51. WORWOOD, M., R. RAHA CHOWDHURY, K. J. H. ROBSON, J. POINTON, J. D. SHEARMAN et al., 1997 The H-LA A1-B8 haplotype extends 6 Mb beyond HLA-A: associations between HLA-A, B, F and 15 microsatellite markers. Tissue Antigens 50: 521-526.