Extensive and breed-specific linkage disequilibrium in Canis familiaris

Genome Research

Volumn 14, Issue 12, 2004, Pages 2388-2396

  Sutter, Nathan B ^a,e   Eberle, Michael A ^a   Parker, Heidi G ^a,b,e   Pullar, Barbara J ^a   Kirkness, Ewen F ^c   Kruglyak, Leonid ^a,d   Ostrander, Elaine A ^a,e  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c J CRAIG VENTER INSTITUTE   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^e NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL BEHAVIOR; ARTICLE; BREEDING; CHROMOSOME; CHROMOSOME 1; CHROMOSOME 2; CHROMOSOME 34; CHROMOSOME 37; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DISEASE PREDISPOSITION; DOG; FEASIBILITY STUDY; GENE CLUSTER; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; MARKER GENE; MORPHOLOGY; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE; UNITED STATES;

ANIMALS; DOGS; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SYNTENY; VARIATION (GENETICS);

CANIS; CANIS FAMILIARIS;

EID: 10944237840     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3147604     Document Type: Article

References (68)

1. Abecasis, G.R., Noguchi, E., Heinzmann, A., Traherne, J.A., Bhattacharyya, S., Leaves, N.I., Anderson, G.G., Zhang, Y., Lench, N.J., Carey, A., et al. 2001. Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68: 191-197.
2. Akey, J.M., Zhang, G., Zhang, K., Jin, L., and Shriver, M.D. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12: 1805-1814.
3. The American Kennel Club (AKC). 1998. The complete dog book. Howell Book House, New York.
4. Bonnen, P.E., Story, M.D., Ashorn, C.L., Buchholz, T.A., Weil, M.M., and Nelson, D.L. 2000. Haplotypes at ATM identify coding-sequence variation and indicate a region of extensive linkage disequilibrium. Am. J. Hum. Genet. 67: 1437-1451.
5. Breen, M., Thomas, R., Binns, M.M., Carter, N.P., and Langford, C.F. 1999. Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics 61: 145-155.
6. Breen, M., Jouquand, S., Renier, C., Mellersh, C.S., Hitte, C., Holmes, N.G., Cheron, A., Suter, N., Vignaux, F., Bristow, A.E., et al. 2001. Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res. 11: 1784-1795.
7. Breen, M., Hitte, C., Lorentzen, T.D., Thomas, R., Cadieu, E., Sabacan, L., Scott, A., Evanno, G., Parker, H.G., Kirkness, E., et al. 2004. An integrated 4249 marker FISH/RH map of the canine genome. BMC Genomics 5: 65.
8. Cambien, F., Poirier, O., Nicaud, V., Herrmann, S.M., Mallet, C., Ricard, S., Behague, I., Hallet, V., Blanc, H., Loukaci, V., et al. 1999. Sequence diversity in 36 candidate genes for cardiovascular disorders. Am. J. Hum. Genet. 65: 183-191.
9. Carlson, C.S., Eberle, M.A., Rieder, M.J., Smith, J.D., Kruglyak, L., and Nickerson, D.A. 2003. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33: 518-521.
10. Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.
11. Clark, A.G., Weiss, K.M., Nickerson, D.A., Taylor, S.L., Buchanan, A., Stengard, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., et al. 1998. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63: 595-612.
12. Clark, L.A., Tsai, K.L., Steiner, J.M., Williams, D.A., Guerra, T., Ostrander, E.A., Galibert, F., and Murphy, K.E. 2004. Chromosome-specific microsatellite multiplex sets for linkage studies in the domestic dog. Genomics 85: 550-554.
13. Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith, J.D., Eberle, M.A., Kruglyak, L., and Nickerson, D.A. 2004. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am. J. Hum. Genet. 74: 610-622.
14. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., and Lander, E.S. 2001. High-resolution haplotype structure in the human genome. Nat Genet. 29: 229-232.
15. Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., et al. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544-548.
16. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred, II: Error probabilities. Genome Res. 8: 186-194.
17. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequencer traces using phred, I: Accuracy assessment. Genome Res. 8: 175-185.
18. Fallin, D. and Schork, N.J. 2000. Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am. J. Hum. Genet. 67: 947-959.
19. Farnir, F., Coppieters, W., Arranz, J.J., Berzi, P., Cambisano, N., Grisart, B., Karim, L., Marcq, F., Moreau, L., Mni, M., et al. 2000. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10: 220-227.
20. Fogel, B. 1995. The encyclopedia of the dog. DK Publishing, New York.
21. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
22. Galibert, F. and Andre, C. 2002. The canine genome: Alternative model for the functional analysis of mammalian genes. Bull. Acad. Natl. Med. 186: 1489-1499; discussion 1499-1502.
23. Galibert, F., Andre, C., Cheron, A., Chuat, J.C., Hitte, C., Jiang, Z., Jouquand, S., Priat, C., Renier, C., and Vignaux, F. 1998. The importance of the canine model in medical genetics. Bull. Acad. Natl. Med. 182: 811-821.
24. Gordon, D., Abajian, C., and Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
25. Guyon, R., Lorentzen, T.D., Hitte, C., Kim, L., Cadieu, E., Parker, H.G., Quignon, P., Lowe, J.K., Renier, C., Gelfenbeyn, B., et al. 2003. A 1 Mb resolution radiation hybrid map of the canine genome. Proc. Natl. Acad. Sci. 100: 5296-5301.
26. Guyon, R., Kirkness, E.F., Lorentzen, T.D., Hitte, C., Comstock, K.E., Quignon, P., Derrien, T., Andréa, C., Fraser, C.M., Galibert, F., et al. 2003. Building comparative maps using 1.5X sequence coverage: Human chromosome 1p and the canine genome. Cold Spring Harbor Symp. Quant. Biol. 68: 171-177.
27. Hall, D., Wijsman, E.M., Roos, J.L., Gogos, J.A., and Karayiorgou, M. 2002. Extended intermarker linkage disequilibrium in the Afrikaners. Genome Res. 12: 956-961.
28. HapMap Consortium. 2003. The International HapMap Project. Nature 426: 789-796.
29. Hardy, R. and Stevens, J. 1978. Chronic progressive hepatitis in Bedlington terriers. Proc. Am. Anim. Hosp. Assoc. (AAHA) 45: 187-190.
30. Hartl, D. and Clark, A. 1997. Principles of population genetics. Sinauer Associates, Sunderland, MA.
31. Hill, W.G. 1974. Estimation of linkage disequilibrium in randomly mating populations. Heredity 33: 229-239.
32. Hyun, C., Filippich, L.J., Lea, R.A., Shepherd, G., Hughes, I.P., and Griffiths, L.R. 2003. Prospects for whole genome linkage disequilibrium mapping in domestic dog breeds. Mamm. Genome 14: 640-649.
33. Johnson, G.C., Esposito, L., Barratt, B.J., Smith, A.N., Heward, J., Di Genova, G., Ueda, H., Cordell, H.J., Eaves, I.A., Dudbridge, F., et al. 2001. Haplotype tagging for the identification of common disease genes. Nat. Genet. 29: 233-237.
34. Ke, X., Hunt, S., Tapper, W., Lawrence, R., Stavrides, G., Ghori, J., Whittaker, P., Collins, A., Morris, A.P., Bentley, D., et al. 2004. The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum. Mol. Genet. 13: 577-588.
35. Kirkness, E.F., Bafna, V., Halpern, A.L., Levy, S., Remington, K., Rusch, D.B., Delcher, A.L., Pop, M., Wang, W., Fraser, C.M., et al. 2003. The dog genome: Survey sequencing and comparative analysis. Science 301: 1898-1903.
36. Kruglyak, L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
37. Lou, X.Y., Todhunter, R.J., Lin, M., Lu, Q., Liu, T., Wang, Z., Bliss, S.P., Casella, G., Acland, G.M., Lust, G., et al. 2003. The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree. Mamm. Genome 14: 555-564.
38. McRae, A.F., McEwan, J.C., Dodds, K.G., Wilson, T., Crawford, A.M., and Slate, J. 2002. Linkage disequilibrium in domestic sheep. Genetics 160: 1113-1122.
39. Mellersh, C.S., Langston, A.A., Acland, G.M., Fleming, M.A., Ray, K., Wiegand, N.A., Francisco, L.V., Gibbs, M., Aguirre, G.D., and Ostrander, E.A. 1997. A linkage map of the canine genome. Genomics 46: 326-336.
40. Moffatt, M.F., Traherne, J.A., Abecasis, G.R., and Cookson, W.O. 2000. Single nucleotide polymorphism and linkage disequilibrium within the TCR α/δ locus. Hum. Mol. Genet. 9: 1011-1019.
41. Mohlke, K.L., Lange, E.M., Valle, T.T., Ghosh, S., Magnuson, V.L., Silander, K., Watanabe, R.M., Chines, P.S., Bergman, R.N., Tuomilehto, J., et al. 2001. Linkage disequilibrium between microsatellite markers extends beyond 1 cM on chromosome 20 in Finns. Genome Res. 11: 1221-1226.
42. Nickerson, D.A., Tobe, V.O., and Taylor, S.L. 1997. PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25: 2745-2751.
43. Nomura, T., Honda, T., and Mukai, F. 2001. Inbreeding and effective population size of Japanese Black cattle. J. Anim. Sci. 79: 366-370.
44. Nsengimana, J., Baret, P., Haley, C.S., and Visscher, P.M. 2004. Linkage disequilibrium in the domesticated pig. Genetics 166: 1395-1404.
45. Ostrander, E.A. and Comstock, K.E. 2004. The domestic dog genome. Curr. Biol. 14: R98-R99.
46. Ostrander, E.A. and Giniger, E. 2001. Semper Fidelis: What man's best friend can teach us about human biology and disease. Am. J. Hum. Genet. 61: 475-480.
47. Ostrander, E.A. and Kruglyak, L. 2000. Unleashing the canine genome. Genome Res. 10: 1271-1274.
48. Ostrander, E.A., Jong, P.M., Rine, J., and Duyk, G. 1992. Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc. Natl. Acad. Sci. 89: 3419-3423.
49. Ostrander, E.A., Galibert, F., and Patterson, D.F. 2000. Canine genetics comes of age. Trends Genet. 16: 117-123.
50. Parker, H.G., Kim, L.V., Sutter, N.B., Carlson, S., Lorentzen, T.D., Malek, T.B., Johnson, G.S., DeFrance, H.B., Ostrander, E.A., and Kruglyak, L. 2004. Genetic structure of the purebred domestic dog. Science 304: 1160-1164.
51. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., et al. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719-1723.
52. Patterson, D.F. 1980. A catalogue of genetic disorders of the dog. In Current veterinary therapy, vol. VII. WB Saunders, Philadelphia, PA.
53. Patterson, D.F. 2000. Companion animal medicine in the age of medical genetics. J. Vet. Intern. Med. 14: 1-9.
54. Patterson, D.F., Haskins, M.E., and Jezyk, P.F. 1982. Models of human genetic disease in domestic animals. Adv. Hum. Genet. 12: 263-339.
55. Patterson, D.F., Haskins, M.E., Jezyk, P.F., Giger, U., Meyers-Wallen, V.N., Aguirre, G., Fyfe, J.C., and Wolfe, J.H. 1988. Research on genetic diseases: Reciprocal benefits to animals and man. J. Am. Vet. Med. Assoc. 193: 1131-1144.
56. Reich, D.E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R., et al. 2001. Linkage disequilibrium in the human genome. Nature 411: 199-204.
57. Rogers, C.A. and Brace, A.H. 1995. The international encyclopedia of dogs. Howell Book House, New York.
58. Sargan, D.R., Yang, F., Squire, M., Milne, B.S., O'Brien, P.C., and Ferguson-Smith, M.A. 2000. Use of flow-sorted canine chromosomes in the assignment of canine linkage, radiation hybrid, and syntenic groups to chromosomes: Refinement and verification of the comparative chromosome map for dog and human. Genomics 69: 182-195.
59. Service, S.K., Ophoff, R.A., and Freimer, N.B. 2001. The genome-wide distribution of background linkage disequilibrium in a population isolate. Hum. Mol. Genet. 10: 545-551.
60. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., Jiang, R., Messer, C.J., Chew, A., Han, J.H., et al. 2001a. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
61. Stephens, M., Smith, N.J., and Donnelly, P. 2001b. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
62. Tenesa, A., Knott, S.A., Ward, D., Smith, D., Williams, J.L., and Visscher, P.M. 2003. Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J. Anim. Sci. 81: 617-623.
63. Tenesa, A., Wright, A.F., Knott, S.A., Carothers, A.D., Hayward, C., Angius, A., Persico, I., Maestrale, G., Hastie, N.D., Pirastu, M., et al. 2004. Extent of linkage disequilibrium in a Sardinian sub-isolate: Sampling and methodological considerations. Hum. Mol. Genet. 13: 25-33.
64. Varilo, T., Paunio, T., Parker, A., Perola, M., Meyer, J., Terwilliger, J.D., and Peltonen, L. 2003. The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum. Mol. Genet. 12: 51-59.
65. Weiss, K.M. and Clark, A.G. 2002. Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18: 19-24.
66. Wilcox, B. and Walkowicz, C. 1995. Atlas of dog breeds of the world. T.F.H. Publications, Neptune City, NJ.
67. Yang, F., O'Brien, P.C., Milne, B.S., Graphodatsky, A.S., Solanky, N., Trifonov, V., Rens, W., Sargan, D., and Ferguson-Smith, M.A. 1999. A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps. Genomics 62: 189-202.
68. Yuzbasiyan-Gurkan, V., Blanton, S.H., Cao, V., Ferguson, P., Li, J., Venta, P.J., and Brewer, G.J. 1997. Linkage of a microsatellite marker to the canine copper toxicosis locus in Bedlington terriers. Am. J. Vet. Res. 58: 23-27.