PSYCH OpenIR  > 中国科学院心理健康重点实验室
Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees
Schaeffer, Alejandro A.1; Lemire, Mathieu2; Ott, Jurg3,4; Lathrop, G. Mark5,6; Weeks, Daniel E.7,8; Schaffer, AA (reprint author), NIH, Natl Ctr Biotechnol Informat, DHHS, Bldg 38A,Room 6S605,8600 Rockville Pike, Bethesda, MD 20894 USA.
2011
Source PublicationHUMAN HEREDITY
ISSN0001-5652
SubtypeArticle
Volume71Issue:2Pages:126-134
Contribution Rank3
AbstractSimulation of genotypes in pedigrees is an important tool to evaluate the power of a linkage or an association study and to assess the empirical significance of results. SLINK is a widely-used package for pedigree simulations, but its implementation has not previously been described in a published paper. SLINK was initially derived from the LINKAGE programs. Over the 20 years since its release, SLINK has been modified to incorporate faster algorithms, notably from the linkage analysis package FASTLINK, also derived from LINKAGE. While SLINK can simulate genotypes on pedigrees of high complexity, one limitation of SLINK, as with most methods based on peeling algorithms to evaluate pedigree likelihoods, is the small number of linked markers that can be generated. The software package SUP includes an elegant wrapper for SLINK that circumvents the limitation on number of markers by using descent markers generated by SLINK to simulate a much larger number of markers on the same chromosome, linked and possibly associated with a trait locus. We have released new coordinated versions of SLINK (3.0; available from http://watson.hgen.pitt.edu) and SUP (v090804; available from http://mlemire.freeshell.org/software or http://watson.hgen.pitt.edu) that integrate the two software packages. Thereby, we have removed some of the previous limitations on the joint functionality of the programs, such as the number of founders in a pedigree. We review the history of SLINK and describe how SLINK and SUP are now coordinated to permit the simulation of large numbers of markers linked and possibly associated with a trait in large pedigrees. Copyright (C) 2011 S. Karger AG, Basel
KeywordCoordinated conditional simulation SLINK SUP Linkage study Association study Pedigree, large Pedigree, complex
Subject AreaMedical Psychology
URL查看原文
Indexed BySCI
Language英语
Funding OrganizationUniversity of Pittsburgh ; National Institutes of Health, NLM
Project Intro.This research was supported in part by the University of Pittsburgh and the Intramural Research Program of the National Institutes of Health, NLM.
WOS IDWOS:000292500000006
Citation statistics
Document Type期刊论文
Identifierhttp://ir.psych.ac.cn/handle/311026/11454
Collection中国科学院心理健康重点实验室
Corresponding AuthorSchaffer, AA (reprint author), NIH, Natl Ctr Biotechnol Informat, DHHS, Bldg 38A,Room 6S605,8600 Rockville Pike, Bethesda, MD 20894 USA.
Affiliation1.NIH, Natl Ctr Biotechnol Informat, DHHS, Bethesda, MD 20894 USA
2.Ontario Inst Canc Res, Toronto, ON, Canada
3.Chinese Acad Sci, Inst Psychol, Beijing 100101, Peoples R China
4.Rockefeller Univ, Lab Stat Genet, New York, NY 10021 USA
5.CEA, Inst Genom, Ctr Natl Genotypage, Evry, France
6.Fdn Jean Dausset CEPH, Paris, France
7.Univ Pittsburgh, Grad Sch Publ Hlth, Dept Human Genet, Pittsburgh, PA 15261 USA
8.Univ Pittsburgh, Grad Sch Publ Hlth, Dept Biostat, Pittsburgh, PA 15261 USA
Recommended Citation
GB/T 7714
Schaeffer, Alejandro A.,Lemire, Mathieu,Ott, Jurg,et al. Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees[J]. HUMAN HEREDITY,2011,71(2):126-134.
APA Schaeffer, Alejandro A.,Lemire, Mathieu,Ott, Jurg,Lathrop, G. Mark,Weeks, Daniel E.,&Schaffer, AA .(2011).Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees.HUMAN HEREDITY,71(2),126-134.
MLA Schaeffer, Alejandro A.,et al."Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees".HUMAN HEREDITY 71.2(2011):126-134.
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