Literature DB >> 15840706

SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.

Emily L Webb1, Gabrielle S Sellick, Richard S Houlston.   

Abstract

SUMMARY: SNPLINK is a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets. The presence of linkage disequilibrium (LD) between closely spaced SNP markers can falsely inflate linkage statistics. SNPLINK removes LD from the marker sets in an automated fashion before carrying out linkage analysis. SNPLINK can compute both parametric and non-parametric statistics, utilizing the freely available Allegro and Merlin software. Graphical outputs of whole genome multipoint linkage statistics are provided allowing comparison of results before and after the removal of LD.

Entities:  

Mesh：

Year:  2005        PMID： 15840706     DOI： 10.1093/bioinformatics/bti449

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  27 in total

1.  PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.

Authors:  Alejandro Q Nato; Nicola H Chapman; Harkirat K Sohi; Hiep D Nguyen; Zoran Brkanac; Ellen M Wijsman
Journal:  Bioinformatics       Date:  2015-07-30       Impact factor: 6.937

2.  The affected-/discordant-sib-pair design can guarantee validity of multipoint model-free linkage analysis of incomplete pedigrees when there is marker-marker disequilibrium.

Authors:  Chao Xing; Ritwik Sinha; Guan Xing; Qing Lu; Robert C Elston
Journal:  Am J Hum Genet       Date:  2006-06-26       Impact factor: 11.025

3.  Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees.

Authors:  Ellen M Wijsman; Joseph H Rothstein; Elizabeth A Thompson
Journal:  Am J Hum Genet       Date:  2006-09-20       Impact factor: 11.025

4.  A genome-wide scan for genes involved in primary vesicoureteric reflux.

Authors:  H Kelly; C M Molony; J M Darlow; M E Pirker; A Yoneda; A J Green; P Puri; D E Barton
Journal:  J Med Genet       Date:  2007-07-27       Impact factor: 6.318

5.  Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data.

Authors:  Yoonhee Kim; Priya Duggal; Elizabeth M Gillanders; Ho Kim; Joan E Bailey-Wilson
Journal:  Genet Epidemiol       Date:  2008-01       Impact factor: 2.135

6.  Linkage analysis with dense SNP maps in isolated populations.

Authors:  Céline Bellenguez; Carole Ober; Catherine Bourgain
Journal:  Hum Hered       Date:  2009-04-09       Impact factor: 0.444

7.  Autosomal dominant nonsyndromic cleft lip and palate: significant evidence of linkage at 18q21.1.

Authors:  Soraya Beiraghi; Swapan K Nath; Matthew Gaines; Desh D Mandhyan; David Hutchings; Uppala Ratnamala; Ken McElreavey; Lucia Bartoloni; Gregory S Antonarakis; Stylianos E Antonarakis; Uppala Radhakrishna
Journal:  Am J Hum Genet       Date:  2007-05-18       Impact factor: 11.025

8.  Finding disease genes: a fast and flexible approach for analyzing high-throughput data.

Authors:  William C L Stewart; Esther N Drill; David A Greenberg
Journal:  Eur J Hum Genet       Date:  2011-05-25       Impact factor: 4.246

9.  Evaluation of approaches to identify associated SNPs that explain the linkage evidence in nuclear families with affected siblings.

Authors:  Ming-Huei Chen; Paul Van Eerdewegh; Quentin B Vincent; Alexandre Alcais; Laurent Abel; Josée Dupuis
Journal:  Hum Hered       Date:  2009-12-04       Impact factor: 0.444

10.  Handling linkage disequilibrium in qualitative trait linkage analysis using dense SNPs: a two-step strategy.

Authors:  Kelly Cho; Josée Dupuis
Journal:  BMC Genet       Date:  2009-08-10       Impact factor: 2.797
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