LOD score exclusion analyses for candidate QTLs using random population samples

Genetica

Volumn 119, Issue 3, 2003, Pages 303-315

  Deng, Hong Wen ^a,b  

^a HUNAN NORMAL UNIVERSITY   (China)

^b CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Association studies; Candidate genes; Exclusion mapping; LOD scores; QTL; Quantitative traits

Indexed keywords

BONE DENSITY; COMPUTER SIMULATION; FEMALE; GENOTYPE; HUMANS; LOD SCORE; MALE; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE; RECEPTORS, CALCITRIOL; SAMPLE SIZE; SPINE;

EID: 0346146961     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:GENE.0000003827.86624.ac     Document Type: Article

References (35)

1. Amos. C.I., 1994. Robust variance-components approach for assessing genetic linkage in pedigrees. Am. J. Hum. Genet. 54: 535-543.
2. Boerwinkle, E., R. Chakraborty & C.F. Sing, 1986. The use of measured genotype information in the analysis of quantitative phenotypes in man. Ann. Hum. Genet. 50: 181-194.
3. Chakraborty, R. & P. Smouse, 1988. Recombination in haplotypes leads to biased estimates of admixture proportions in human populations. Proc. Natl. Acad. Sci. USA 85: 3071-3074.
4. Deng, H.-W., 2001. Population admixture may change, mask or reverse true genetic effects for complex traits. Genetics 159: 1319-1323.
5. Deng, H.-W. & W.-M. Chen, 2000a. Re: biased tests of association: comparison of allele frequencies when departing from Hardy-Weinberg proportions. Am. J. Epidemiol. 151: 335-357.
6. Deng, H.-W. & W.-M. Chen, 2000b. QTL fine mapping in extreme samples of finite populations for complex traits with familial correlation due to polygenes. Am. J. Hum. Genet. 67: 259-261.
7. Deng, H.-W. & J. Li, 2001. The effect of polygenes on transmission disequilibrium test of a QTL in nuclear families with multiple children. Genet. Epidemiol. 21: 243-256.
8. Deng, H.-W., J. Li, J.L. Li, M. Johnson, G. Gong & R.R. Recker, 1999. Association of VDR and estrogen receptor genotypes with bone mass in postmenopausal Caucasian women: different conclusions with different analyses and the implications. Osteoporosis Int. 9: 499-507.
9. Deng, H.-W., W.-M. Chen & R.R. Recker, 2000. QTL fine mapping by measuring and testing for Hardy-Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations. Am. J. Hum. Genet. 66: 1027-1045.
10. Deng, H.-W., W.-M. Chen, S. Recker, M.R. Stegman, J.L. Li, K.M. Davies, Y. Zhou, H.Y. Deng, R.R. Heaney & R.R. Recker, 2000a. Genetic determination of Colles' fractures and differential bone mass in women with and without Colles' fractures. J. Bone Miner. Res. 15: 1243-1252.
11. Deng, H.-W., W.-M. Chen, T. Conway, Y. Zhou, K.M. Davies. M.R. Stegman, H.Y. Deng & R.R. Recker, 2000b. Determination of bone mineral density of the hip and spine in human pedigrees by genetic and life-style factors. Genetic Epidemiol. 19: 160-177.
12. Deng, H.-W., W.-M. Chen & R.R. Recker, 2001. Population admixture: detection by Hardy-Weinberg test and its quantitative effects on linkage-disequilibrium methods for localizing genes underlying complex traits. Genetics 157: 885-897.
13. Deng, H.-W., J. Li & R.R. Recker, 2001. LOD score exclusion analyses of candidate genes with random population samples. Ann. Hum. Genet. 65: 313-329.
14. Deng, H.-W., F.H. Xu, T. Conway, X.T. Deng, J.L. Li, K.M. Davies, H.Y. Deng, M. Johnson & R.R. Recker, 2001. Is population BMD variation linked to the marker D11s987 on chromosome 11q12-13? J. Clin. Endocrinol. Metabolism 86: 3735-3741.
15. Devlin, B., K. Roeder & S.-A. Bacanu, 2001. Unbiased methods for population-based association studies. Genetic Epidemiol. 21: 273-284.
16. Edwards, J.H., 1980. Exclusion mapping. J. Med. Genet. 24: 539-543.
17. Eisman. J.A., 1995. Vitamin D receptor gene alleles and osteoporosis: An affirmative view. J. Bone Miner. Res. 10: 1289-1293.
18. Feder, J.N., A. Gnirke, W. Thomas & Z. Tsuchihasi, 1996. A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat. Genet. 13: 399-408.
19. Gong, G., S. Stern, S.C. Cheng, F. Fong, N. Mordeson, H.-W. Deng & R.R. Recker, 1999. On the association of bone mass density and Vitamin-D genotype polymorphisms. Osteoporosis Int. 9: 55-64.
20. Hanis. C.L., E. Boerwinkle, R. Chakraborty, D.L. Ellsworth & G.I. Bell, 1996. A genome-wide search for human non-insulin-dependent (type 2) diabetes genes reveals a major susceptibility locus on chromosome 2. Nat. Genet. 13: 161-166.
21. Kruglyak, L. & E.S. Lander, 1995. Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am. J. Hum. Genet. 57: 439-454.
22. Lander. E. & L. Kruglyak, 1995. Genetic dissection of complex traits: guidelines for interpreting the reporting results. Nat. Genet. 11: 241-247.
23. Liu, Y.-Z., Y.-J. Liu, R.R. Recker & H.-W. Deng. 2003. Molecular genetic studies of gene identification for osteoporosis: the 2002 update. J. Endocrinol. 177: 147-196.
24. Morton, N.E. & A. Collins, 1999. Tests and estimates of allelic association in complex inheritance. Proc. Natl. Acad. Sci. USA 95: 11389-11393.
25. Nielsen, D.M., M.G. Ehm & B.S. Weir, 1998. Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus. Am. J. Hum. Genet. 63: 1531-1540.
26. Ott, J., 1999. Analysis of Human Genetic Linkage. Johns Hopkins University Press, Baltimore, MD, 3rd edn.
27. Page, G.P. & C.I. Amos, 1999. Comparison of linkage-disequilibrium methods for localization of genes influencing quantitative traits in humans. Am. J. Hum. Genet. 64: 1194-1205.
28. Page, O.P., C.I. Amos & E. Boerwinkle, 1998. The quantitative LOD score: test statistic and sample size for exclusion and linkage of quantitative traits in human sibships. Am. J. Hum. Genet. 62: 962-968.
29. Recker, R.R. & H.-W. Deng, 2002. Role of genetics in osteoporosis. Endocrine 17: 55-66.
30. Risch, N. & J. Teng, 1998. The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. I. DNA polling. Genome Res. 8: 1273-1288.
31. Salamone, L.M., R. Ferrell, D.M. Black, L. Palermo, R.S. Epstein, N. Petro, N. Steadman, L.H. Kuller & J.A. Cauley, 1996. The association between Vitamin D receptor gene polymorphisms and bone mineral density at the spine, hip and whole-body in premenopausal women. Osteoporos Int. 6: 63-68.
32. Spielman, R.S., R.E. Mcginnis & W.J. Ewens, 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52: 506-516.
33. Tsai, K.S., S.H. Hsu, W.C. Cheng, C.K. Chen, P.U. Chieng & W.H. Pan, 1996. Bone mineral density and bone markers in relation to Vitamin D receptor gene polymorphisms in Chinese men and women. Bone 19: 513-518.
34. Weir, B.S., 1996. Genetic Data Analysis II. Sinauer, Sunderland, MA.
35. Yamagata, Z., T. Miyamura, S. Iijima, A. Asaka, M. Sasaki, J. Kato & K. Koizumi, 1994. Vitamin D receptor gene polymorphism and bone mineral density in healthy Japanese women. Lancet 344: 1027 (letter). 315