A multilocus model for constructing a linkage disequilibrium map in human populations

Statistical Applications in Genetics and Molecular Biology

Volumn 8, Issue 1, 2009, Pages

  Li, Qin ^a   Wu, Rongling ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

EM algorithm; Human; Linkage; Linkage disequilibrium; Molecular markers

Indexed keywords

MOLECULAR MARKER;

ALGORITHM; ARTICLE; FAMILY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC PARAMETERS; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; MULTILOCUS SEQUENCE TYPING; POPULATION GENETICS; SEX DIFFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM; VERTICAL TRANSMISSION; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; FEMALE; GENETIC MARKER; HUMAN GENOME; MALE; STATISTICAL MODEL;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER SIMULATION; FEMALE; GENETIC MARKERS; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 64549086295     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1419     Document Type: Article

References (43)

1. Ardlie, K. G., Kruglyak, L. and Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics 3, 299-309.
2. Browning, S. R. (2008). Estimation of pairwise identity by descent from dense genetic marker data in a population sample of haplotypes. Genetics 178, 2123-2132.
3. Collins, A. R. (2007). Linkage Disequilibrium and Association Mapping: Anal- ysis and Applications. Humana Press, New York.
4. 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. Nature Genetics 29, 229-232.
5. Dawson, E., Abecasis, G. R., Bumpstead, S., Chen, Y. et al. (2002). A first- generation linkage disequilibrium map of human chromosome 22. Nature 418, 544-548.
6. De La Vega, F. M., Dailey, D., Ziegle, J., Williams, J., Madden, D. and Gilbert, D. A. (2002). New generation pharmacogenomic tools: a SNP linkage disequilibrium map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies. BioTechniques 32, 548-554.
7. Dupuis, J., Siegmund, D. and Yakir, B. (2007). A unified framework for linkage and association analysis of quantitative traits. Proceedings of the National Academy of Sciences of the United States of America 104, 20210-20215.
8. Farnir, F., Grisart, B., Coppieters, W., Riquet, J., Berzi, P. et al. (2002). Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: Revisiting the loca- tion of a quantitative trait locus with major effect on milk production on bovine Chromosome 14. Genetics 161, 275-287.
9. Farnir, F., Coppieters, W., Arranz, J. J., Berzi, P., Cambisano, N. et al. (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10, 220-227.
10. Fulker, D. W., Cherny, S. S., Sham, P. C. and Hewitt, J. K. (1999). Combined linkage and association sib-pair analysis for quantitative traits. American Journal of Human Genetics 64, 259-267.
11. Gabriel, S. B., S. F. Schaffner, H. Nyuyen, J. M. Moore et al. (2002) The structure of haplotype blocks in the human genome. Science 296: 2225- 2229.
12. Georges, M. (2007). Mapping, fine mapping, and molecular dissection of quan- titative trait loci in domestic animals. Annual Reviews of Genomics and Human Genetics 8, 131-162.
13. Hernandez, R. D., Hubisz, M. J., Wheeler, D. A., Smith, D. G., Ferguson, B. et al. (2007). Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science 316, 240-243.
14. Hill, W. G. and Hernandez-Sanchez, J. (2007). Prediction of multilocus identity- by-descent. Genetics 176, 2307-2315.
15. Hössjer, O. (2005). Combined association and linkage analysis for general pedigrees and genetic models. Statistical Applications in Genetics and Molecular Biology 4: Article 11.
16. Kurbasic, A. and Hössjer, O. (2008). A general method of linkage disequi- librium correction for multipoint linkage and association. Genetics Epi- demiology 32, S647-S657.
17. Lee, S. H. and Van der Werf, J. H. J. (2006). Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution. Genetics 174, 1009- 1016.
18. Liu, T., Todhunter, R. J., Lu, Q., Schoettinger, L., Li, H. Y., Littell, R. C. et al. (2006). Extent and distribution of zygotic linkage disequilibrium in canine. Genetics 174, 439-453.
19. Lou, X.-Y., Casella, G., Todhunter, R. J., Yang, M. K. C. and Wu, R. L. (2005). A general statistical framework for unifying interval and linkage disequilibrium mapping: Towards high-resolution mapping of quantitative traits. Journal of American Statistical Association 100, 158-171.
20. Lu, Q., Cui, Y. H. and Wu, R. L. (2004). A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genetics 5, 20.
21. Marques, E., Schnabel, R. D., Stothard, P., Kolbehdari, D., Wang, Z., Taylor, J. F. and Moore, S. S. (2008). High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genetics 9, 45.
22. McRae, A. F., MceWan, J. C., Dodds, K. G., Wilson, T., Crawford A. M. et al. (2002). Linkage disequilibrium in domestic sheep. Genetics 160, 1113-1122.
23. Meuwissen, T. H. E. and Goddard, M. E. (2000). Fine mapping of quantita- tive trait loci using linkage disequilibria with closely linked marker loci. Genetics 155, 421-430.
24. Morton, N. E. (2005). Linkage disequilibrium maps and association mapping. Journal of Clinical Investigation 115, 1425-1430.
25. Niu, T., Qin, Z. S., Xu, X. and Liu, J. S. (2002). Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. American Journal of Human Genetics 70, 157-169.
26. Perez-Enciso, M. (2003). Fine mapping of complex trait genes combining pedi- gree and linkage disequilibrium information: a Bayesian unified frame- work. Genetics 163, 1497-1510.
27. Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P. C., Richter, D. J. et al. (2001). Linkage disequilibrium in the human genome. Nature 411, 199-204.
28. Schork, N. J. (2002). Power calculations for genetic association studies using estimated probability distributions. American Journal of Human Genetics 70, 1480-1489.
29. Self, S. and Liang, K.-Y. (1987). Asymptotic properties of maximum likeli- hood estimators and likelihood ratio tests under non-standard conditions. Journal of American Statistical Association 82, 605-610.
30. Sham, P. C., Cherny, S. S., Purcell, S. and Hewitt, J. K. (2000). Power of linkage versus association analysis of quantitative traits, by use of vari- ance components models, for sibship data. American Journal of Human Genetics 66, 1616-1630.
31. Tapper, W., Gibson, J., Morton, N. W. and Collins, A. (2008). A comparison of methods to detect recombination hotspots. Human Heredity 66, 157- 169.
32. Terwilliger, J. D. and Goring, H. H. (2000). Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design. Human Biology 72, 63-132.
33. Thompson, E. A. (1984). Information gain in joint linkage analysis. IMA Journal of Mathematical Applications in Medicine and Biology 1, 31-50.
34. Tishkoff, S. A., Dietzsch, E., Speed, W., Pakstis, A. J., Kidd, J. R., Che- ung, K., Bonne-Tamir, B., Santachiara-Benerecetti, A. S., Moral, P. and Krings, M. (1996). Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271, 1380-1387.
35. Tishkoff, S. A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G. et al. (2001). Haplotype diversity and linkage disequi- librium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293, 455-462.
36. Tishkoff, S. A. and Williams, S. W. (2002). Genetic analysis of African popu- lations: Human evolution and complex disease. Nature Reviews Genetics 3, 611-621.
37. Tsunoda, T., Lathrop, G. M., Sekine, A., Yamada, R., Takahashi, A., Ohnishi, Y., Tanaka, T. and Nakamura, Y. (2004). Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Human Molec- ular Genetics 13, 1623-1632.
38. Weir, B. S. (1996). Genetic Data Analysis. Sinauer, Sunderland, MA.
39. Weir, B. S. (2008). Linkage disequilibrium and association mapping. Annual Reviews of Genomics and Human Genetics 9, 129-142.
40. Wu, R. L. and Zeng, Z.-B. (2001). Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157, 899-909.
41. Wu, R. L., Ma, C.-X. and Casella, G. (2002). Joint linkage and linkage disequi- librium mapping of quantitative trait loci in natural populations. Genetics 160, 779-792.
42. Wu, R. L., Ma, C.-X. and Casella, G. (2007). Statistical Genetics of Quanti- tative Traits: Linkage, Maps, and QTL. Springer-Verlag, New York.
43. Xiong, M. and Jin, L. (2000). Combined linkage and linkage disequilibrium mapping for genome screens. Genetics Epidemiology 19, 211-234.