A scan for linkage disequilibrium across the human genome

Genetics

Volumn 152, Issue 4, 1999, Pages 1711-1722

  Huttley, Gavin A ^a,c   Smith, Michael W ^b   Carrington, Mary ^b   O'Brien, Stephen J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC DRIFT; GENETIC HETEROGENEITY; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENOME; HAPLOTYPE; HUMAN; HUMAN CELL; PRIORITY JOURNAL; TANDEM REPEAT;

ALLELES; CHROMOSOME MAPPING; EUROPE; FEMALE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; PEDIGREE; PROBABILITY;

MARTES PENNANTI;

EID: 0344500841     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. AYALA, F. J., 1995 The myth of Eve: molecular biology and human origins. Science 270: 1930-1936.
2. AYALA, F. J., and A. A. ESCALANTE, 1996 The evolution of human populations: a molecular perspective. Mol. Phylogenet. Evol. 5: 188-201.
3. BEGOVICH, A. B., G. R. MCCLURE, V. C. SURAJ, R. C. HELMUTH, N. FILDES et al., 1992 Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. J. Immunol. 148: 249-258.
4. BENNETT, B. M., and P. HSU, 1960 On the power function of the exact test for the 2 × 2 contingency table. Biometrika 47: 393-398.
5. BODMER, W. F., 1986 Human genetics: the molecular challenge. Cold Spring Harbor Symp. Quant. Biol. 51: 1-13.
6. BRISCOE, D., J. C. STEPHENS and S. J. O'BRIEN, 1994 Linkage disequilibrium in admixed populations: applications in gene mapping. J. Hered. 85: 59-63.
7. BROMAN, K. W., J. C. MURRAY, V. C. SHEFFIELD, R. L. WHITE and J. L. WEBER, 1998 Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63: 861-869.
8. BRZUSTOWICZ, L. M., C. MERETTE, X. XIE, L. TOWNSEND, T. C. GILLIAM et al., 1993 Molecular and statistical approaches to the detection and correction of errors in genotype databases. Am. J. Hum. Genet. 53: 1137-1145.
9. CARRINGTON, M., D. MARTI, J. WADE, W. KLITZ, L. BARCELLOS et al., 1999 Microsatellite markers in complex disease: mapping disease-associated regions within the human Major Histocompatibility Complex, pp. in Microsatellites: Evolution and Applications, edited by D. B. GOLDSTEIN and C. SCHLÖTTERER. Oxford University Press, Oxford.
10. CHAKRABORTY, R., and K. M. WEISS, 1988 Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc. Natl. Acad. Sci. USA 85: 9119-9123.
11. DELOUKAS, P., G. D. SCHULER, G. GYAPAY, E. M. BEASLEY, C. SODERLUND et al., 1998 A physical map of 30,000 human genes. Science 282: 744-746.
12. DIB, C., S. FAURE, C. FIZAMES, D. SAMSON, N. DROUOT et al., 1996 A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380: 152-154.
13. EWENS, W. J., 1979 Mathematical Population Genetics. Springer-Verlag, New York.
14. EWENS, W. J., and R. S. SPIELMAN, 1995 The transmission/disequilibrium test: history, subdivision, and admixture. Am. J. Hum. Genet. 57: 455-464.
15. FOISSAC, A., B. CROUAU-ROY, S. FAURÉ, M. THOMSEN and A. CAMBON-THOMSEN, 1997 Microsatellites in the HLA region: an overview. Tissue Antigens 49: 197-214.
16. GUO, S. W., and E. A. THOMPSON, 1992 Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
17. GYAPAY, G., J. MORISSETTE, A. VIGNAL, C. DIB, C. FIZAMES et al., 1994 The 1993-94 Généthon human genetic linkage map. Nat. Genet. 7: 246-339.
18. HARTL, D. L., and A. G. CLARK, 1990 Principles of Population Genetics. Sinauer Associates, Sunderland, MA.
19. HASTBACKA, J., A. DE LA CHAPELLE, I. KAITILA, P. SISTONEN, A. WEAVER et al., 1992 Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat. Genet. 2: 204-211.
20. HENDRICK, P. W., 1987 Gametic disequilibrium measures: proceed with caution. Genetics 117: 331-341.
21. HEDRICK, P., 1994 Evolutionary genetics of the major histocompatibility complex. Am. Nat. 143: 945-964.
22. HILL, W. G., and A. ROBERTSON, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
23. HUDSON, R. R., 1985 The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
24. HUDSON, T. J., L. D. STEIN, S. S. GERETY, J. MA, A. B. CASTLE et al., 1995 An STS-based map of the human genome. Science 270: 1945-1954.
25. JORDE, L. B., 1995 Linkage disequilibrium as a gene-mapping tool. Am. J. Hum. Genet. 56: 11-14.
26. KAPLAN, N. L., P. O. LEWIS and B. S. WEIR, 1994 Age of the delta F508 cystic fibrosis mutation. Nat. Genet. 8: 216-218.
27. KAPLAN, N. L., W. G. HILL and B. S. WEIR, 1995 Likelihood methods for locating disease genes in nonequilibrium populations. Am. J. Hum. Genet. 56: 18-32.
28. KLEIN, J. (Editor), 1986 Natural History of the Major Histocompatibility Complex. John Wiley and Sons, New York.
29. KLITZ, W., J. C. STEPHENS, M. GROTE and M. CARRINGTON, 1995 Discordant patterns of linkage disequilibrium of the peptide-transporter loci within the HLA class II region. Am. J. Hum. Genet. 57: 1436-1444.
30. LAAN, M., and S. PAABO, 1997 Demographic history and linkage disequilibrium in human populations. Nat. Genet. 17: 435-438.
31. LEWONTIN, R. C., 1964 The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67.
32. LEWONTIN, R. C., and K. KOJIMA, 1960 The evolutionary dynamics of complex polymorphisms. Evolution 14: 458-472.
33. MANTEL, N., 1967 The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
34. MARTIN, M. P., A. HARDING, R. CHADWICK, M. KRONICK, M. CULLEN et al., 1998 Characterization of 12 microsatellite loci of the human MHC in a panel of reference cell lines. Immunogenetics 47: 503.
35. MCLELLAN, T., L. B. JORDE and M. H. SKOLNICK, 1984 Genetic distances between the Utah Mormons and related populations. Am. J. Hum. Genet. 36: 836-857.
36. MEHTA, C. R., and N. R. PATEL, 1983 A network algorithm for performing Fisher's exact test in r × c contingency tables. J. Am. Stat. Assoc. 78: 427-434.
37. MOONSAMY, P. V., W. KLITZ, M. G. TILANUS and A. B. BEGOVICH, 1997 Genetic variability and linkage disequilibrium within the DP region in the CEPH families. Hum. Immunol. 58: 112-121.
38. OHTA, T., and M. KIMURA, 1969 Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics 63: 229-238.
39. PETERSON, A. C., A. DI RIENZO, A. E. LEHESJOKI, A. DE LA CHAPELLE, M. SLATKIN et al., 1995 The distribution of linkage disequilibrium over anonymous genome regions. Hum. Mol. Genet. 4: 887-894.
40. PRESS, W. H., S. A. TEUKOVSKY, W. T. VETTERING and B. P. FLANNERY, 1992 Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge, United Kingdom.
41. RAYMOND, M., and F. ROUSSET, 1995 An exact test for population differentiation. Evolution 49: 1280-1283.
42. RICE, W. R., 1989 Analyzing tables of statistical tests. Evolution 43: 223-225.
43. ROTHMAN, K.J., 1990 No adjustments are needed for multiple comparisons. Epidemiology 1: 43-46.
44. SLATKIN, M., 1994 Linkage disequilibrium in growing and stable populations. Genetics 137: 331-336.
45. SOKAL, R. R., and F. J. ROHLE, 1995 Biometry. W. H. Freeman and Company, New York.
46. STEPHENS, J. C., D. BRISCOE and S. J. O'BRIEN, 1994 Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. Am. J. Hum. Genet. 55: 809-824.
47. STEPHENS, J. C., D. E. REICH, D. B. GOLDSTEIN, H. D. SHIN, M. W. SMITH et al., 1998 Dating the origin of the CCR5-Δ32 AIDS resistance allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62: 1507-1515.
48. STEWART, E. A., K. B. MCKUSICK, A. AGGARWAL, E. BAJOREK, S. BRADY et al., 1997 An STS-based radiation hybrid map of the human genome. Genome Res. 7: 422-433.
49. TAKAHATA, N., 1993 Allelic genealogy and human evolution. Mol. Biol. Evol. 10: 2-22.
50. TAKAHATA, N., Y. SATTA and J. KLEIN, 1992 Polymorphism and balancing selection at the major histocompatibility complex loci. Genetics 130: 925-938.
51. TISHKOFF, S. A., E. DIETZSCH, W. SPEED, A. J. PAKSTIS, J. R. KIDD et al., 1996 Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1387.
52. TROWSDALE, J., 1995 "Both man and bird and beast": comparative organization of MHC genes. Immunogenetics 41: 1-17.
53. VON HAESELER, A., A. SAJANTILA and S. PAABO, 1996 The genetical archaeology of the human genome. Nat. Genet. 14: 135-140.
54. WEISSENBACH, J., G. GYAPAY, C. DIB, A. VIGNAL, J. MORISETTE et al., 1992 A second-generation linkage map of the human genome. Nature 359: 794-801.
55. WIEHE, T., and M. SLATKIN, 1998 Epistatic selection in a multilocus Levene model and implications for linkage disequilibrium. Theor. Popul. Biol. 53: 75-84.