Login to MyKarger

New to MyKarger? Click here to sign up.

Login with Facebook

Forgot Password? Reset your password

Authors, Editors, Reviewers

For Manuscript Submission, Check or Review Login please go to Submission Websites List.

Submission Websites List

Institutional Login (Shibboleth)

For the academic login, please select your country in the dropdown list. You will be redirected to verify your credentials.

Table of Contents
Vol. 71, No. 2, 2011
Issue release date: July 2011
Section title: Paper
Open Access Gateway
Hum Hered 2011;71:126–134

Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees

Schäffer A.A.a · Lemire M.b · Ott J.c, d · Lathrop G.M.e, f · Weeks D.E.g
aNational Center for Biotechnology Information, National Institutes of Health, DHHS, Bethesda, Md., USA; bOntario Institute for Cancer Research, Toronto, Ont., Canada; cInstitute of Psychology, Chinese Academy of Sciences, Beijing, China; dLaboratory of Statistical Genetics, Rockefeller University, New York, N.Y., USA; eCommissariat à l’Energie Atomique, Institut Genomique, Centre National de Genotypage, Evry, fFondation Jean Dausset-CEPH, Paris, France; gDepartments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa., USA
email Corresponding Author

Alejandro A. Schäffer

National Center for Biotechnology Information, NIH, Bldg. 38A, Room 6S605

8600 Rockville Pike

Bethesda, MD 20894 (USA)

E-Mail schaffer@helix.nih.gov


  1. MacCluer JW, VandeBerg JL, Read B, Ryder OA: Pedigree analysis by computer simulation. Zoo Biol 1986;5:147–160.
    External Resources
  2. Lathrop GM, Lalouel JM, Julier C, Ott J: Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 1984;81:3443–3446.
  3. Weeks DE, Ott J, Lathrop GM: SLINK: A general simulation program for linkage analysis. Am J Hum Genet 1990;47:A204.
  4. Ott J: Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci USA 1989;86:4175–4178.
  5. Lemire M: SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values. BMC Genet 2006;7:40.
    External Resources
  6. Cottingham RW Jr, Idury RM, Schäffer AA: Faster sequential genetic linkage computations. Am J Hum Genet 1993;53:252–263.
  7. Ott J: Analysis of Human Genetic Linkage, ed 3. Baltimore, Johns Hopkins University Press, 1999.
  8. Terwilliger JD, Speer M, Ott J: Chromosome-based method for rapid computer simulation in human genetic linkage analysis. Genet Epidemiol 1993;10:217–224.
  9. Zuppan P, Hall JM, Lee MK, Ponglikitmongkol M, Kong M-C: Possible linkage of the estrogen receptor gene to breast cancer in a family with late-onset disease. Am J Hum Genet 1991;48:1065–1068.
  10. Martinez M, Khlat M, Leboyer M, Clerget-Darpoux F: Performance of linkage analysis under misclassification error when the genetic model is unknown. Genet Epidemiol 1989;6:253–258.
  11. Greenberg DA, Abreu P, Hodge SE: The power to detect linkage in complex disease by means of simple LOD-score analyses. Am J Hum Genet 1998;63:870–879.
  12. Ploughman LM and Boehnke M: Estimating the power of a proposed linkage study for a complex genetic trait. Am J Hum Genet 1989;44:543–551.
  13. Zhou J-Y, Ding J, Fung WK, Lin S: Detection of parent-of-origin effects using general pedigree data. Genet Epidemiol 2010;34:151–158.
    External Resources
  14. Buyske S, Yang G, Matise TC, Gordon D: When a case is not a case: effects of phenotype misclassification on power and sample size requirements for the transmission disequilibrium test with affected child trios. Hum Hered 2009;67:287–292.
  15. Mendoza MCB, Burns TL, Jones MP: Case-deletion diagnostics for maximum likelihood multipoint quantitative trait locus linkage analysis. Hum Hered 2009;67:276–286.
  16. Hanson RL, Knowler WC: Design and analysis of genetic association studies to finely map a locus identified by linkage analysis: assessment of the extent to which an association can account for the linkage. Ann Hum Genet 2007;72:126–139.
    External Resources
  17. Elston RC, Stewart JM: A general model for the genetic analysis of pedigree data. Hum Hered 1971;21:523–542.
  18. Finck A, Van der Meer JWM, Schäffer AA, Pfannstiel J, Fieschi C, Plebani A, Webster ADB, Hammarström L, Grimbacher B: Linkage of autosomal-dominant common variable immunodeficiency to chromosome 4q. Eur J Hum Genet 2006;14:867–875.
  19. Leal SM, Yan K, Müller-Myhsok B: SimPed: a simulation program to generate haplotype and genotype data for pedigree structures. Hum Hered 2005;60:119–122.
  20. Lemire M, Roslin NM, Laprise C, Hudson TJ, Morgan K: Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3. Am J Hum Genet 2004;75:571–586.
  21. Schmidt M, Hauser ER, Martin ER, Schmidt S: Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: environmental covariates, gene-gene and gene-environment interaction. Stat Appl Genet Mol Biol. 2005;4:15.
  22. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A: Allegro, a new computer program for multipoint linkage analysis. Nat Genet 2000;25:12–13.
  23. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2001;30:97–101.
  24. Fishelson M, Geiger D: Exact genetic linkage computations for general pedigrees. Bioinformatics 2002;18(suppl 1):S189–S198.