Power of variance component linkage analysis to detect quantitative trait loci

Annals of Human Genetics

Volumn 63, Issue 6, 1999, Pages 545-563

  Williams, Jeff T ^a   Blangero, J ^a  

^a SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC VARIABILITY; HERITABILITY; PEDIGREE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SAMPLE;

ANALYSIS OF VARIANCE; BIOMETRY; COMPUTER SIMULATION; FEMALE; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE (GENETICS); MALE; MODELS, GENETIC; NUCLEAR FAMILY; PARENTS; PEDIGREE; QUANTITATIVE TRAIT, HERITABLE; SAMPLE SIZE;

EID: 0033496277     PISSN: 00034800     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0003480099007848     Document Type: Article

References (77)

1. ALLISON, D. B., NEALE, M. C., ZANNOLLI, R., SCHORK, N. J., AMOS, C. I. & BLANGERO, J. (1999). Testing the robustness of the likelihood-ratio test in a variance-component quantitative-trait loci-mapping procedure. Am. J. Hum. Genet. 65, 531-544.
2. ALMASY, L. & BLANGERO, J. (1998). Multipoint quantitative trait linkage analysis in general pedigrees. Am. J. Hum. Genet. 62, 1198-1211.
3. ALMASY, L., HIXSON, J. E., RAINWATER, D. L., COLE, S., WILLAMS, J. T., MAHANEY, M. C., VANDEBERG, J. L., STERN, M. P., MACCLUER, J. W. & BLANGERO, J. (1999). Human pedigree-based quantitative-trait-locus mapping: Localization of two genes influencing HDL-cholesterol metabolism. Am. J. Hum. Genet. 64, 1686-1693.
4. AMOS, C. I. (1994). Robust variance-components approach for assessing genetic linkage in pedigrees. Am. J. Hum. Genet. 54, 535-543.
5. AMOS, C. I., ZHU, D. K. & BOERWINKLE, E. (1996). Assessing genetic linkage and association with robust components of variance approaches. Ann. Hum. Genet. 60, 143-160.
6. ANDREWS, D. F., GNANADESIKAN, R. & WARNER, J. L. (1971). Transformations of multivariate data. Biometrics 27, 825-840.
7. BEATY, T. H. & LIANG, K. Y. (1987). Robust inference for variance components models in families ascertained through probands: I. Conditioning on the proband's phenotype. Genet. Epidemiol. 4, 203-210.
8. BEATY, T. H., LIANG, K. Y., SEEREY, S. & COHEN, B. H. (1987). Robust inference for variance components models in families ascertained through probands: II. Analysis of spirometric measures, Genet. Epidemiol. 4, 211-221.
9. BEATY, T. H., SELF, S. G., LIANG, K. Y., CONNOLLY, M. A., CHASE, G. A. & KWITEROVICH, P. O. (1985). Use of robust variance components models to analyse triglyceride data in families. Ann. Hum. Genet. 49, 315-328.
10. BEGLEITER, H., PORJESZ, B., REICH, T. EDENBERG, H. J., GOATE, A., BLANGERO, J., ALMASY, L., FOROUD, T., VAN EERDEWEGH, P., POLICH, J., ROHRBAUGH, J., KUPERMAN, S., BAUER, L. O., O'CONNOR, S. J., CHORLIAN, D. B., LI, T. K., CONNELLY, P. M., HESSELBROCK, V., RICE, J. P., SCHUCKIT, M. A., CLONINGER, R., NURNBERGER, J. JR. CROWE, R. & BLOOM, F. E. (1998). Quantitative trait loci analysis of human event-related brain potentials: P3 voltage. Electroencephalogr. Clin. Neurophysiol. 108, 244-250.
11. BLACKWELDER, W. C. & ELSTON, R. C. (1974). Comment on Dr Robertson's communication. Behav. Genet. 4, 97-99.
12. BLANGERO, J., WILLIAMS, J. T. & ALMASY, L. (2000). Quantitative trait locus mapping using human pedigrees. Hum. Biol. 72, 35-62.
13. BLANGERO, J., ALMASY, L. & WILLIAMS, J. T. (1998). Tragedy of the commons: Common misconceptions about mapping genes for common diseases. Am. J. Hum. Genet. 63, A45.
14. BLANGERO, J. & ALMASY, L. (1997). Multipoint oligogenic linkage analysis of quantitative traits. Genet. Epidemiol. 14, 959-964.
15. BLANGERO, J., WILLIAMS-BLANGERO, S., KAMMERER, C. M., TOWNE, B. & KONIGSBERG, L. W. (1992). Multivariate genetic analysis of nevus measurements and melanoma. Cytogenet. Cell. Genet. 59, 170-181.
16. BLAGERO, J., MACCLUER, J. W., KAMMERER, C. M., MOTT, G. E., DYER, T. E. & MCGILL, H. C. JR. (1990). Genetic analysis of apolipoprotein A-I in two dietary environments. Am. J. Hum. Genet. 47, 414-428.
17. BOEHNKE, M. & LANGE, K. (1984). Ascertainment and goodness of fit of variance component models for pedigree data. Prog. Clin. Biol. Res. 147, 173-192.
18. BOEHNKE, M., MOLL, P. P., LANGE, K., WEIDMAN, W. H. & KOTTKE, B. A. (1986). Univariate and bivariate analyses of cholesterol and triglyceride levels in pedigrees. Am. J. Med. Genet. 23, 775-792.
19. BOERWINKLE, E., CHAKRABORTY, R. & SING C. F. (1986). The use of measured genotype information in the analysis of quantitative phenotypes in man. I. Models and analytical methods. Ann. Hum. Genet. 50, 181-194.
20. CHERNOFF, H. (1954). On the distribution of the likelihood ratio. Ann. Math. Stat. 25, 573-578.
21. CLIFFORD, C. A., HOPPER, J. L., FULKER, D. W. & MURRAY, R. M. (1984). A genetic and environmental analysis of a twin family study of alcohol use, anxiety, and depression. Genet. Epidemiol. 1, 63-79.
22. CLONINGER, C. R., VAN EERDEWEGH, P., GOATE, A., EDENBERG, H. J., BLANGERO, J., HESSELBROCK, V., REICH, T., NURNBERGER, J., JR, SCHUCKIT, M., PORJESZ, B., CROWE, R., RICE, J. P., FOROUD, T., PRZYBECK, T. R., ALMASY, L., BUCHOLZ, K., WU, W., SHEARS, S., CARR, K., CROSE, C., WILLIG, C., ZHAO, J., TISCHFIELD, J. A., LI, T.-K., CONNEALLY, P. M. & BEGLEITER, H. (1998). Anxiety proneness linked to epistatic loci in genome scan of human personality traits. Am. J. Med. Genet. 81, 313-317.
23. COMUZZIE, A. G. & WILLIAMS, J. T. (1999). Correcting for ascertainment bias in the COGA data set. Genet. Epidemiol., 17 (Suppl 1), S109-S114.
24. COMUZZIE, A. G., HIXSON, J. E., ALMASY, L., MITCHELL, B. D., MAHANEY, M. C., DYER, T. D., STERN, M. P., MACCLUER, J. W. & BLANGERO, J. (1997). A major quantitative trait locus determining serum leptin levels and fat mass is located on human chromosome 2. Nature Genet. 15, 273-276.
25. CZERWINSKI, S. A., MAHANEY, M. C., WILLIAMS, J. T., ALMASY, L. & BLANGERO, J. (1999). Genetic analysis of personality traits and alcoholism using a mixed discrete-continuous trait variance component model, Genet. Epidemiol., 17 (Suppl 1), S121-S126.
26. DAVIES, R. B. (1977). Hypothesis testing when a nuisance parameter is present only under the alternative. Biometrika 64, 247-254.
27. DAVIES, R. B. (1987). Hypothesis testing when a nuisance parameter is present only under the alternative. Biometrika 74, 33-43.
28. DUGGIRALA, R., BLANGERO, J., ALMASY, L., DYER, T. D., WILLIAMS, K. L., LEACH, R. J., O'CONNELL, P. & STERN, M. P. (1999). Linkage of Type 2 diabetes mellitus and of age at onset to a genetic location on chromosome 10q in Mexican Americans. Am. J. Hum. Genet. 64, 1127-1140.
29. DUGGUIRALA, R., WILLIAMS, J. T., WILLIAMS-BLANGERO, S. & BLANGERO, J. (1997). A variance component approach to dichotomous trait linkage analysis using a threshold model. Genet. Epidemiol. 14, 987-992.
30. DUGGIRALA, R., STERN, M. P., MITCHELL, B. D., REINHART, L. J., SHIPMAN, P. A., URESANDI, O. C., CHUNG, W. K., LEIBEL, R. L., HALES, C. N., O'CONNELL, P. & BLANGERO, J. (1996). Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chomosome 7. Am. J. Hum. Genet. 59, 694-703.
31. EDWARDS, J. H. (1997). The sib-pair problem. I. Affected pairs with parents. Constant penetrance models. Ann. Hum. Genet. 61, 351-364.
32. EFRON, B. & HINKLEY, D. V. (1978). Assessing the accuracy of the maximum likelihood estimator: observed versus expected Fisher information. Biometrika 65, 457-487.
33. FALCONER, D. S. (1989). Introduction to quantitative genetic. Third edition. New York: Wiley.
34. FULKER, D. W., CHERNY, S. S. & CARDON, L. R. (1995). Multipoint interval mapping of quantitative trait loci, using sib pairs. Am. J. Hum. Genet. 56, 1224-1233.
35. GOLDGAR, D. E. (1990). Multipoint analysis of human quantitative genetic variation. Am. J. Hum. Genet. 47, 957-967.
36. GNANADESIKAN, R. (1977). Methods for statistical data analysis of multivariate observations. New York: Wiley.
37. HOPPER, J. L. & CULROSS, P. R. (1983). Covariation between family members as a function of cohabitation history. Behavior Genetics 13, 459-471.
38. HOPPER, J. L. & MATHEWS, J. D. (1982). Extensions to multivariate normal models for pedigree analysis. Ann. Hum. Genet. 46, 373-383.
39. HOPPER, J. L., TAIT, B. D., PROPERT, D. N. & MATHEWS, J. D. (1982). Genetic analysis of systolic blood pressure in Melbourne families. Clinical and Experimental Pharmacology & Physiology 9, 247-252.
40. ITURRIA, S. J., WILLIAMS, J. T., ALMASY, L., DYER, T. D. & BLANGERO, J. (1999). An empirical test of the significance of an observed quantitative trait locus effect that preserves additive genetic variation, Genet. Epidemiol. 17 (Suppl 1), S169-S173.
41. JACQURD, A. (1972). Genetic information given by a relative, Biometrics 28, 1101-1114.
42. JENNRICH, R. I. & SAMPSON, P. F. (1976). Newton-Raphson and related algorithms for maximum likelihood variance component estimation. Technometrics 18, 11-17.
43. KEMPTHORNE, O. (1957). An introduction to genetic statitics. New York: Wiley.
44. KENDALL, M. G. & STUART, A. (1967). The advanced theory of statistics. Vol. 2. Inference and relationship. Second edition. New York: Hafner.
45. LANGE, K. (1997). Mathematical and statistical methods for genetic analysis. New York: Springer-Verlag.
46. LANGE, K. (1986). Cohabitation, convergence, and environmental covariances. Am. J. Med. Genet. 24, 483-491.
47. LANGE, K. (1978). Central limit theorems for pedigrees. J. Math, Biology 6, 59-66.
48. LANGE, K. L., LITTLE, R. J. A. & TAYLOR, J. M. G. (1989). Robust statistical modeling using the t distribution. J. Am. Stat. Assoc. 84, 881-896.
49. LANGE, K., WESTLAKE, J. & SPENCE, M. A. (1976). Extensions to pedigree analysis. III. Variance components by the scoring method. Ann. Hum. Genet. 39, 485-491.
50. LIANG, K.-Y., RATHOUZ, P. J. & BEATY, T. H. (1996). Determining linkage and mode of inheritance: mod scores and other methods, Genet. Epidemiol. 13, 575-593.
51. MACCLUER, J. W., STERN, M. P., ALMASY, L., ATWOOD, L. A., BLANGERO, J., COMUZZIE, A. G., DYKE, B., HAFFNER, S. M., HENKEL, R. D., HIXSON, J. E., KAMMERER, C. M., MAHANEY, M. C., MITCHELL, B. D., RAINWATER, D. L., SAMOLLOW, P. B., SHARP, R. M., VANDEBERG, J. L. & WILLIAMS, J. T. (1999). Genetics of atherosclerosis risk factors in Mexican Americans. Nutrition Reviews 57, S59-65.
52. MITCHELL, B. D., GHOSH, S., SCHNEIDER, J. L., BIRZNIEKS, G. & BLANGERO, J. (1997). Power of variance component linkage analysis to detect epistasis. Genet. Epidemiol. 14, 1017-1022.
53. MITCHELL, B. D., KAMMERER, C. M., BLANGERO, J., MAHANEY, M. C., RAINWATER, D. L., DYKE, B., HIXSON, J. E., HENKEL, R. D., SHARP, R. M., COMUZZIE, A. G., VANDEBERG, J. L., STERN, M. P. & MACCLUER, J. W. (1996). Genetic and environmental contributions to cardiovascular risk factors in Mexican Americans: The San Antonio Family Heart Study. Circulation 94, 2159-2170.
54. MOOD, A. M., GRAYBILL, F. A. & BOES, D. C. (1974). Introduction to the theory of statistic. New York: MCGraw-Hill.
55. OTT, J. (1991). Analysis of human genetic linkage. Revised edition. Baltimore, MD: The Johns Hopkins University Press.
56. PAGE, G. P. (1997). 'The QLOD score: a sequential method for linkage and exclusion of quantitative traits in humans and the power of exclusion analysis.' Master's Thesis. Graduate School of Biomedical Sciences. Universitv of Texas Health Science Center. Houston. TX.
57. PAGE, G. P., AMOS, C. I. & BOERWINKLE, E. (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.
58. RISCH, N. (1990). Linkage strategies for genetically complex traits. II. The power of affected relative pairs. Am. J. Hum. Genet. 46, 229-241.
59. SCHORK, N. J. (1993a). The design and use of variance component models in the analysis of human quantitative pedigree data, Biom. J. 35, 387-405.
60. SCHORK, N. J. (1993b). Extended multipoint identity-by-deseent analysis of human quantitative traits: efficiency, power, and modeling considerations. Am. J. Hum. Genet. 53, 1306-1319.
61. SCHORK, N. J. & SCHORK, M. A. (1993). The relative efficiency and power of small-pedigree studies of the heritability of a quantitative trait. Hum. Hered. 43, 1-11.
62. SEARLE, S. R., CASELLA, G. & MCCULLOCH, C. E. (1992). Variance components. New York: John Wiley and Sons.
63. SELF, S. G. & LIANG, K.-Y. (1987). Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82, 605-610.
64. SPENCE, M. A., WESTLAKE, J. & LANGE, K. (1977). Estimation of the variance components for dermal ridge count. Ann. Hum. Genet. 41, 111-115.
65. STERN, M. P., DUGGIRALA, R., MITCHELL, B. D., REINHART, L. J., SHIVAKUMAR. S., SHIPMAN, P. A., URESANDI, O. C., BENAVIDES, E., BLANGERO, J. & O'CONNELL, P. (1996). Evidence for linkage of regions on chromosomes 6 and 11 to plasma glucose concentrations in Mexican Americans, Genome. Res. 6, 724-734.
66. STRAM, D. O. & LEE, J. W. (1994). Variance components testing in the longitudinal mixed effect model, Biometrics 50, 1171-1177.
67. THOMPSON, E. A. (1974). Gene identities and multiple relationships. Biometrics 30, 667-680.
68. TOWNE, B., SHERVOGEL, R. M. & BLANGERO, J. (1997). Effects of genotype-by-sex interaction on quantitative trait linkage analysis, Genet. Epidemiol, 14, 1053-1058.
69. WALD, A. (1943). Tests of statistical hypotheses concerning several parameters when the number of observations is large. Trans. Amer. Math. Soc. 54, 426-482.
70. WANG, X. L., MAHANEY, M. C., SIM, A. S., WANG, J., WANG, J., BLANGERO, J., ALMASY, L., BADENHOP, R. B. & WILCKEN, D. E. L. (1997). Genetic contribution of the endothelial constitutive nitric oxide synthase gene to plasma nitric oxide levels. Asterioscler. Thromb. Vasc. Biol. 17, 3147-3153.
71. WHITTEMORE, A. S. & HALPERN, J. (1994). Probability of gene identity by descent: computation and applications. Biometrics 50, 109-117.
72. WILLIAMS, J. T., DUGGIRALA, R. & BLANGERO, (1997). Statistical properties of a variance components method for quantitative trait linkage analysis in nuclear families and extended pedigrees. Genet. Epidemiol. 14, 1065-1070.
73. WILLIAMS, J. T. & BLANGERO, J. (1999a). Comparison of variance components and sibpair-based approaches to quantitative trait linkage analysis in unselected samples, Genetic Epidemiol. 16, 113-134.
74. WILLIAMS, J. T. & BLANGERO, J. (1999b). Asymptotic power of likelihood-ratio tests for detecting quantitative trait loci using the COGA data, Genet. Epidemiol. 17 (Suppl 1), S397-S402.
75. WILLIAMS. J. T., VAN EERDEWEGH, P., ALMASY, L. & BLANGERO, J. (1999a). Joint multipoint linkage analysis of multivariate qualitative and quantitative traits. I. Likelihood formulation and simulation results. Am. J. Hum. Genet. 65, 1134-1147.
76. WILLIAMS, J. T., BEGLEITER, H., PORJESZ, B., EDENBERG, H. J., FOROUD, T., REICH, T., GOATE, A., VAN EERDEWEGH, P., ALMASY, L. & BLANGERO, J. (1999b). Joint multipoint linkage analysis of multivariate qualitative and quantitative traits. II. Alcoholism and event-related potentials. Am. J. Hum. Genet. 65, 1148-1160.
77. WILLIAMS-BLANGERO, S., SUBEDI, J., UPAHAYAY, R. P., MANRAL, D. B., RAI, D. R., JHA, B., ROBINSON, E. S. & BLANGERO, J. (1999). Genetic analysis of susceptibility to infection with Ascaris lumbricoides. Am. J. Trop. Med. Hyg. 60, 921-926.