Note: Another list of references, which might be updated from this one, can be found on the SOLAR home page at http://solar.sfbrgenetics.org.
The main reference for SOLAR, including theoretical explanations of the variance component linkage method and the approximate multipoint IBD calculations in pedigrees, is:
Almasy L, Blangero J (1998) Multipoint quantitative trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
Bivariate Quantitative trait linkage is described in the following papers:
Almasy L, Dyer TD, Blangero J (1997) Bivariate quantitative trait linkage analysis: Pleiotropy versus co-incident linkages. Genet Epidemiol 14:953-958.Williams JT, Van Eerdewegh P, Almasy L, Blangero J (1999) Joint Multipoint Linkage Analysis of Multivariate Qualitative and Quantitative Traits. I. Likelihood Formulation and Simulation Results. Am J Hum Genet 65:1134-1147
The Liability Threshold model for discrete traits is described in the preceding paper as well as the following one:
Duggirala R, Williams JT, Williams-Blangero S, and Blangero J (1997) A variance component approach to dichotomous trait linkage analysis using a threshold model. Genet Epidemiol 14:987-992.
Gene By Environment Interaction is discussed in:
Towne B, Siervogel RM, Blangero J (1997) Effects of genotype-by-sex interaction on quantitative trait linkage analysis. Genet Epidemiol 14:1053-1058.Blangero J (1993) Statistical Genetic Approaches to Human Adaptability. Hum Biol 65:941-966.
An examination of LOD adjustment is given in:
Blangero J, Williams JT, Almasy L (2000) Robust LOD scores for variance component-based linkage analysis. Genet Epidemiol 19 Suppl 1:S8-14.Blangero J, Williams JT, Almasy L (2001) Variance component methods for detecting complex trait loci. Adv Genet 42:151-81.
For Bayesian QTN analysis or the QTLD procedure:
Blangero J, Goring HH, Kent JW Jr, Williams JT, Peterson CP, Almasy L, Dyer TD. Quantitative trait nucleotide analysis using Bayesian model selection. Hum Biol 2005 Oct; 77(5):541-549.
Additional references include:
Blangero J, Almasy L (1997) Multipoint oligogenic linkage analysis of quantitative traits. Genet Epidemiol 14:959-964.Mitchell BD, Ghosh S, Schneider JL, Birznieks G, Blangero J (1997) Power of variance component linkage analysis to detect epistasis. Genet Epidemiol 14:1017-1022.
Williams JT, Blangero J (1999) Power of variance component linkage analysis to detect quantitative trait loci. Ann Hum Genet 63(6):545-563.
Williams JT, Blangero J (1999) Comparison of variance components and sibpair-based approaches to quantitative trait linkage analysis in unselected samples. Genet Epidemiol 16(2):113-134.