An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree

Genetics Selection Evolution

Volumn 38, Issue 1, 2006, Pages 25-43

  Lee, Sang Hong ^a   Van Der Werf, Julius H J ^a  

^a UNIVERSITY OF NEW ENGLAND   (Australia)

Author keywords

Average information; Fine mapping; Genotype relationships matrix; Linkage disequilibrium; Quantitative trait loci

Indexed keywords

GENETICS;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME MAP; GENOTYPE; PEDIGREE; STATISTICAL MODEL;

ALGORITHMS; CHROMOSOME MAPPING; GENOTYPE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PEDIGREE;

EID: 30444435351     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1051/gse:2005025     Document Type: Article

References (43)

1. Almasy L., Blangero J., Multipoint quantitative-trait linkage analysis in general pedigrees, Am. J. Hum. Genet. 62 (1998) 1198-1211.
2. Amestoy P.R., Davis T.A., Duff I.S., Amd version 1.1 user guide, 2004.
3. Amos C.I., Robust variance components approach for assessing genetic linkage in pedigrees, Am. J. Hum. Genet. 54 (1994) 535-543.
4. Churchill G.A., Doerge R.W., Empirical threshold values for quantitative trait mapping, Genetics 138 (1994) 963-971.
5. Dallas J.F., Estimation of microsatellite mutation rates in recombinant inbred strains of mouse, Mamm. Genome 3 (1992) 452-456.
6. Duff I.S., Erisman A.M., Reid J.K., Direct method for sparse matrix, Oxford, Clarendon Press, 1989.
7. Ellegren H., Mutation rates at porcine microsatellite loci, Mamm. Genome 6 (1995) 376-377.
8. Falconer D.S., Mackay T.F.C., Introduction to quantitative genetics, 4th edn., Longman, 1996.
9. Fernando R.L., Grossman M., Marker assisted selection using best linear unbiased prediction, Genet. Sel. Evol. 21 (1989) 467-477.
10. George A. W., Visscher P.M., Haley C.S., Mapping quantitative trait loci in complex pedigrees: A two-step variance component approach, Genetics 156 (2000) 2081-2092.
11. Gilmour A.R., Thompson R., Cullis B.R., Average information REML: An efficient algorithm for variance parameters estimation in linear mixed models, Biometrics 51 (1995) 1440-1450.
12. Gilmour A.R., Cullis B.R., Welham S.J., Thompson R., Asrem1 reference manual, Orange Agriculture Institute, New South Wales, Australia, 2004.
13. Goldgar D.E., Multipoint analysis of human quantitative genetic variation, Am. J. Hum. Genet. 47 (1990) 957-967.
14. Graser H.-U., Smith S.P., Tier B., A derivative-free approach for estimating variance components in animal models by restricted maximum likelihood, J. Anim. Sci. 64 (1987) 1362-1370.
15. Grignola F.E., Hoeschele I., Tier B., Mapping quantitative trait loci in outcross populations via residual maximum likelihood. I. Methodology, Genet. Sel. Evol. 28 (1996) 479-490.
16. Harville D.A., Maximum likelihood approaches to variance component estimation and to related problems, J. Am. Stat. Assoc. 72 (1977) 320-338.
17. Heath S.C., Markov chain Monte Carlo segregation and linkage analysis for oligogenic models, Am. J. Hum. Genet. 61 (1997) 748-760.
18. Jansen R.C., Interval mapping of multiple quantitative trait loci, Genetics 135 (1993) 205-211.
19. Johnson D.L., Thompson R., Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information, J. Dairy Sci. 78 (1995) 449-456.
20. Kao C.H., Zeng Z.B., Teasdale R.D., Multiple interval mapping for quantitative trait loci, Genetics 152 (1999) 1203-1216.
21. Lange K., Westlake J., Spence M.A., Extensions to pedigree analysis. Iii. Variance components by the scoring method, Ann. Hum. Genet. 39 (1976) 485-491.
22. Lee S.H., van der Werf J.H.J., Efficient designs for fine-mapping of quantitative trait loci using linkage disequilibrium and linkage, Proceedings, of the Association for the Advancement of Animal Breeding and Genetics 15 (2003) 9-13.
23. Lee S.H., van der Werf J.H.J., The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage, Genet. Sel. Evol. 36 (2004) 145-161.
24. Lee S.H., van der Werf J.H.J., The role of pedigree information in combined linkage disequilibrium and linkage mapping of quantitative trait loci in a general complex pedigree, Genetics 169 (2005) 455-466.
25. Lynch M., Walsh B., Genetics and analysis of quantitative traits, 1st edn., Sinauer Associates, Sunderland, 1998.
26. MacCluer J.W, VanderBerg J.L., Raed B., Ryder O.A., Pedigree analysis by computer simulation, Zoo Biol. 5 (1986) 147-160.
27. Meuwissen T.H.E., Goddard M.E., Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci, Genetics 155 (2000) 421-430.
28. Meuwissen T.H.E., Goddard M.E., Prediction of identity by descent probabilities from marker-haplotypes, Genet. Sel. Evol. 33 (2001) 605-634.
29. Meuwissen T.H.E., Goddard M.E., Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data, Genet. Sel. Evol. 36 (2004) 261-279.
30. Meuwissen T.H.E., Karlsen A., Lien S., Olsaker I., Goddard M.E., Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping, Genetics 161 (2002) 373-379.
31. Meyer K., Restricted maximum likelihood to estimate variance components for animal models with several random effects using a derivative-free algorithm, Genet. Sel. Evol. 21 (1989) 317-340.
32. Pong-Wong R., George A.W., Woolliams J.A., Haley C.S., A simple and rapid method for calculating identity-by-descent matrices using multiple markers, Genet. Sel. Evol. 33 (2001) 453-471.
33. Searle S.R., Casella G., McCulloch C.E., Variance components, John Wiley & Sons, New York, NY, 1992.
34. Sobel E., Lange K., Descent graphs in pedigree analysis: Applications to haplotyping, location scores, and marker-sharing statistics, Am. J. Hum. Genet. 58 (1996) 1323-1337.
35. Sorensen A.C., Pong-Wong R., Windig J.J., Woolliams J.A., Precision of methods for calculating identity-by-descent matrices using multiple markers, Genet. Sel. Evol. 34 (2002) 557-579.
36. Thompson E.A., Heath S.C., Estimation of conditional multilocus gene identity among relatives, in: Seller-Moiseiwitsch (Ed.), Statistics in molecular biology and genetics, ims lecture notes, Institute of Mathematical Statistics, American Mathematical Society, Providence, RI, 1999, pp. 95-113.
37. Tier B., Solkner J., Analysing gametic variation with an animal model, Theor. Appl. Genet. 85 (1993) 868-872.
38. Van Arendonk J.A., Tier B., Bink M.C., Bovenhuis H., Restricted maximum likelihood analysis of linkage between genetic markers and quantitative trait loci for a granddaughter design, J. Dairy Sci. 81 Suppl. 2 (1998) 76-84.
39. Van Arendonk J.A., Tier B., Kinghorn B.P., Use of multiple genetic markers in prediction of breeding values, Genetics 137 (1994) 319-329.
40. Wang T., Fernando R.L., van der Beek S., Grossman M., van Arendonk J.A.M., Covariance between relatives for a marked quantitative trait locus, Genet. Sel. Evol. 27 (1995) 251-274.
41. Weber J.L., Wong C., Mutation of human short tandem repeats, Hum. Mol. Genet. 2 (1993) 1123-1128.
42. Zeng Z.B., Precision mapping of quantitative trait loci, Genetics 136 (1993) 1456-1468.
43. Zeng Z.B., Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci, Proc. Natl. Acad. Sci. USA 90 (1993) 10972-10976.