Linkage Analysis Software

Abstract

Many methods exist to analyze the linkage of traits to genetic marker data, and various software packages are available to implement these methods.

Keywords: parametric; model‐free; binary trait; quantitative trait; LOD score

References

Abreu P, Greenberg D and Hodge S (1999) Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex disease. American Journal of Human Genetics 65: 847–857.

Bhat A, Heath SC and Ott J (1999) Heterogeneity for multiple disease loci in linkage analysis. Human Heredity 49: 229–231.

Blangero J, Williams JT and Almasy L (2001) Variance component methods for detecting complex trait loci. Advances in Genetics 42: 151–181.

Cox NJ, Frigge M, Nicolae DL, et al. (1999) Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans. Nature Genetics 21: 213–215.

Davis S and Weeks DE (1997) Comparison of nonparametric statistics for detection of linkage in nuclear families: single‐marker evaluation. American Journal of Human Genetics 61: 1431–1444.

Elston RC, Buxbaum S, Jacobs KB and Olson JM (2000) Haseman and Elston revisited. Genetic Epidemiology 19: 1–17.

Greenwood CMT and Bull SB (1999) Downweighting of multiple affected sib pairs leads to biased likelihood‐ratio tests, under the assumption of no linkage. American Journal of Human Genetics 64: 1248–1252.

Holmans P (2001) Likelihood‐ratio affected sib‐pair tests applied to multiply‐affected sibships: issues of power and type I error rate. Genetic Epidemiology 20: 44–56.

Knapp M, Seuchter SA and Baur MP (1994) Linkage analysis in nuclear families. II. Relationship between affected sib‐pair tests and lod score analysis. Human Heredity 44: 44–51.

Weeks DE and Lange K (1988) The affected‐pedigree‐member method of linkage analysis. American Journal of Human Genetics 42: 315–326.

Whittemore AS and Halpern J (1994) Probability of gene identity by descent: computation and applications. Biometrics 50: 109–117.

Further Reading

Blackwelder WC and Elston RC (1985) A comparison of sib‐pair linkage tests for disease susceptibility loci. Genetic Epidemiology 2: 85–97.

Haseman JK and Elston RC (1972) The investigation of linkage between a quantitative trait and a marker locus. Behavior Genetics 2: 3–19.

Ott J (1991) Analysis of Human Genetic Linkage, revised edn. Baltimore, MD: Johns Hopkins University Press.

Risch N (1990) Linkage strategies for genetically complex traits. II. The power of affected relative pairs. American Journal of Human Genetics 46: 229–241.

Risch N (1990) Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. American Journal of Human Genetics 46: 242–253.

Schork NJ, Boehnke M, Terwilliger JD and Ott J (1993) Two‐trait‐locus linkage analysis: a powerful strategy for mapping complex genetic traits. American Journal of Human Genetics 53: 1127–1136.

Strauch K, Fimmers R, Kurz T, et al. (2000) Parametric and non‐parametric multipoint linkage analysis with imprinting and two‐locus trait models: application to mite sensitization. American Journal of Human Genetics 66: 1945–1957.

Terwilliger JD and Ott J (1994) Handbook of Human Genetic Linkage. Baltimore, MD: Johns Hopkins University Press.

Web Links

Rockefeller University. Comprehensive list of linkage software packages, together with details of availability, and references http://linkage.rockefeller.edu

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How to Cite close
Holmans, Peter(Jan 2006) Linkage Analysis Software. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005406]