Disequilibrium likelihoods for fine-scale mapping of a rare allele

American Journal of Human Genetics

Volumn 63, Issue 5, 1998, Pages 1517-1530

  Graham, Jinko ^a   Thompson, Elizabeth A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE MUTATION; GENETIC MARKER; HAPLOTYPE; HUMAN; MEIOSIS; PHYLOGENY; PRIORITY JOURNAL;

EID: 0032231634     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/302102     Document Type: Article

References (35)

1. Arnason A, Larsen B, Marshall WH, Edwards JH, MacIntosh P, Olaisen B, Teisberg P (1977) Very close linkage between HLA-B and Bf inferred from allelic association. Nature 268: 527-528
2. Benedict R (1989) The chrysanthemum and the sword. Houghton Mifflin, Boston
3. Boehnke M (1994) Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes. Am J Hum Genet 55:379-390
4. Cox T, Kerem B, Rommens J, Iannuzzi M, Drumm M, Collins F, Dean M, et al (1989) Mapping of the cystic fibrosis gene using putative ancestral recombinants. Am J Hum Genet Suppl 45:A136
5. Crow J, Kimura M (1970) An introduction to population genetics theory. Harper & Row, New York
6. Edwards J (1981) Allelic association in man. In: Eriksson AW (ed) Population structure and genetic disorders: proceedings of the 7th Sigfred Juselius Foundation Symposia. Academic Press, New York, pp 239-256
7. Felsenstein J (1971) The rate of loss of multiple alleles in finite haploid populations. Theor Popul Biol 2:391-403
8. Fisher R (1970) Statistical methods for research workers, 14th ed. Oliver & Boyd, Edinburgh
9. Goddard KA, Yu CE, Oshima J, Miki T, Nakura J, Piussan C, Martin GM, et al (1996) Toward localization of the Werner syndrome gene by linkage disequilibrium and ancestral haplotyping: lessons learned from analysis of 35 chromosome 8p11.1-21.1 markers. Am J Hum Genet 58: 1286-1302
10. Graham J (1998) Disequilibrium fine-mapping of a rare allele via coalescent models of gene ancestry. PhD thesis, Department of Biostatistics, University of Washington
11. Griffiths R, Tavaré S (1998) The age of a mutation in a general coalescent tree. Stoch Models 14:273-295
12. Hanihara K (1991) Dual structure model for the population history of the Japanese. Jpn Rev 2:1-33
13. Harding E (1971) The probabilities of rooted tree-shapes generated by random bifurcation. Adv Appl Prob 3:44-77
14. Hästbacka J, de la Chapelle A, Kaitila I, Sistonen P, Weaver A, Lander E (1992) Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat Genet 2:204-211
15. Hästbacka J, de la Chapelle A, Mahtani M, Clines G, Reeve-Daly MP, Daly M, Hamilton BA, et al (1994) The diastrophic dysplasia gene encodes a novel sulfate transporter: positional cloning by fine-structure linkage disequilibrium mapping. Cell 78:1073-1087
16. Hästbacka J, Kaitila I, Sistonen P, de la Chapelle A (1990) Diastrophic dysplasia gene maps to the distal long arm of chromosome 5. Proc Natl Acad Sci USA 87:8056-8059
17. International Society for Educational Information (ISEI) (1998) Teachers' and textbook writers' handbook on Japan, http://www.isei.or.jp/books/66/isei_66_contents.html
18. Japan Information Network (JIN) (1998) Census of Japan, http://www.jinjapan.org/stat/index-f.html
19. Kaplan NL, Hill WG, Weir BS (1995) Likelihood methods for locating disease genes in nonequilibrium populations. Am J Hum Genet 56:18-32
20. Kingman JFC (1982a) The coalescent. Stoch Process Appl 13: 235-248
21. _ (1982b) Exchangeability and the evolution of large populations. In: Koch G, Spizzichino F (eds) Exchangeability in probability and statistics. North-Holland, Amsterdam, pp 97-112
22. Koyama S (1979) Jomon subsistence and populations. Senri Ethnological Stud 2:1-65
23. Matsumoto T, Imamura O, Yamabe Y, Kuromitsu J, Tokutake Y, Shimamoto A, Suzuki N, et al (1997) Mutation and haplotype analyses of the Werner's syndrome gene based on its genomic structure: genetic epidemiology in the Japanese population. Hum Genet 100:123-130
24. Mehta CR, Patel NR (1983) A network algorithm for performing Fisher's exact test in r × c contingency tables. J Am Stat Assoc 78:427-434
25. Moran P (1962) The statistical processes of evolutionary theory. Clarendon Press, Oxford
26. Rannala B, Slatkin M (1998) Likelihood analysis of disequilibrium mapping, and related problems. Am J Hum Genet 62:459-473
27. Rose M (1996) The peopling of Japan. Archaeology 48:43
28. Snell R, Lazarou L, Youngman S, Quarrell O, Wasmuth J, Shaw D, Harper P (1989) Linkage disequilibrium in Huntington's disease: an improved localisation for the gene. J Med Genet 26:673-675
29. Theilmann J, Kanani S, Shiang R, Robbins C, Quarrell O, Huggins M, Hedrick A, et al (1989) Nonrandom association between alleles detected at D4S95 and D4S98 and the Huntington's disease gene. J Med Genet 26:676-681
30. Thompson EA (1978) The number of ancestral haplotypes contributing to a sample of B8 alleles. Nature 272:288
31. Thompson EA, Neel JV (1997) Allelic disequilibrium and allelel frequency distribution as a function of social and demographic history. Am J Hum Genet 60:197-204
32. Thompson EA, Neel JV, Smouse PE, Barrantes R (1992) Microevolution of the Chibcha-speaking peoples of lower Central America: rare genes in an Amerindian complex. Am J Hum Genet 51:609-626
33. Van der Meulen M, te Meerman GJ (1997) Association and haplotype sharing due to identity by descent, with an application to genetic mapping. In: Pawlowitzki I, Edwards J, Thompson E (eds) Genetic mapping of disease genes. Academic Press, London, pp 115-136
34. Xiong M, Guo SW (1997) Fine-scale genetic mapping based on linkage disequilibrium: theory and applications. Am J Hum Genet 60:1513-1531
35. Yu CE, Oshima J, Fu YH, Wijsman EM, Hisama F, Alisch R, Matthews S, et al (1996) Positional cloning of the Werner's syndrome gene. Science 272:258-262