Literature DB >> 17586827

HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies.

Jason M Laramie1, Jemma B Wilk, Anita L DeStefano, Richard H Myers.   

Abstract

UNLABELLED: We have created a program that searches densely genotyped regions for associated non-contiguous haplotypes using a standard family based haplotype association test. This program was designed to expand upon the 'sliding window' methodologies commonly used for haplotype construction by allowing the association of subsets of single nucleotide polymorphisms (SNPs) to drive the construction of the haplotype. This strategy permits HaploBuild to construct more biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation. AVAILABILITY: http://snp.bumc.bu.edu.

Mesh：

Year:  2007        PMID： 17586827      PMCID： PMC2665175          DOI： 10.1093/bioinformatics/btm316

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


  10 in total

1.  Score tests for association between traits and haplotypes when linkage phase is ambiguous.

Authors:  Daniel J Schaid; Charles M Rowland; David E Tines; Robert M Jacobson; Gregory A Poland
Journal:  Am J Hum Genet       Date:  2001-12-27       Impact factor: 11.025

2.  Family-based tests for associating haplotypes with general phenotype data: application to asthma genetics.

Authors:  Steve Horvath; Xin Xu; Stephen L Lake; Edwin K Silverman; Scott T Weiss; Nan M Laird
Journal:  Genet Epidemiol       Date:  2004-01       Impact factor: 2.135

3.  Statistical significance for genomewide studies.

Authors:  John D Storey; Robert Tibshirani
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-25       Impact factor: 11.205

4.  Graphical modeling of the joint distribution of alleles at associated loci.

Authors:  Alun Thomas; Nicola J Camp
Journal:  Am J Hum Genet       Date:  2004-04-26       Impact factor: 11.025

5.  Haploview: analysis and visualization of LD and haplotype maps.

Authors:  J C Barrett; B Fry; J Maller; M J Daly
Journal:  Bioinformatics       Date:  2004-08-05       Impact factor: 6.937

6.  Characterizing allelic associations from unphased diploid data by graphical modeling.

Authors:  Alun Thomas
Journal:  Genet Epidemiol       Date:  2005-07       Impact factor: 2.135

7.  Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies.

Authors:  Shin Lin; Aravinda Chakravarti; David J Cutler
Journal:  Nat Genet       Date:  2004-10-24       Impact factor: 38.330

8.  Bayesian graphical models for genomewide association studies.

Authors:  Claudio J Verzilli; Nigel Stallard; John C Whittaker
Journal:  Am J Hum Genet       Date:  2006-05-30       Impact factor: 11.025

9.  Multipoint quantitative-trait linkage analysis in general pedigrees.

Authors:  L Almasy; J Blangero
Journal:  Am J Hum Genet       Date:  1998-05       Impact factor: 11.025

10.  The family based association test method: strategies for studying general genotype--phenotype associations.

Authors:  S Horvath; X Xu; N M Laird
Journal:  Eur J Hum Genet       Date:  2001-04       Impact factor: 4.246
  10 in total
  9 in total

1.  Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae.

Authors:  Eimear E Kenny; Alexander Gusev; Kaitlin Riegel; Dieter Lütjohann; Jennifer K Lowe; Jacqueline Salit; Julian B Maller; Markus Stoffel; Mark J Daly; David M Altshuler; Jeffrey M Friedman; Jan L Breslow; Itsik Pe'er; Ephraim Sehayek
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-10       Impact factor: 11.205

2.  A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies.

Authors:  Raphaël Mourad; Christine Sinoquet; Philippe Leray
Journal:  BMC Bioinformatics       Date:  2011-01-12       Impact factor: 3.169

3.  Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor.

Authors:  Karen Curtin; Roger K Wolff; Jennifer S Herrick; Ryan Abo; Martha L Slattery
Journal:  BMC Med Genet       Date:  2010-12-03       Impact factor: 2.103

4.  Rule-based induction method for haplotype comparison and identification of candidate disease loci.

Authors:  Sirkku Karinen; Silva Saarinen; Rainer Lehtonen; Pasi Rastas; Pia Vahteristo; Lauri A Aaltonen; Sampsa Hautaniemi
Journal:  Genome Med       Date:  2012-03-19       Impact factor: 11.117

5.  Automated construction and testing of multi-locus gene-gene associations.

Authors:  Ryan Abo; Stacey Knight; Alun Thomas; Nicola J Camp
Journal:  Bioinformatics       Date:  2010-11-13       Impact factor: 6.937

6.  Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis.

Authors:  Sven Knüppel; Jorge Esparza-Gordillo; Ingo Marenholz; Hermann-Georg Holzhütter; Anja Bauerfeind; Andreas Ruether; Stephan Weidinger; Young-Ae Lee; Klaus Rohde
Journal:  BMC Med Genet       Date:  2012-01-27       Impact factor: 2.103

7.  hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework.

Authors:  Ryan Abo; Stacey Knight; Jathine Wong; Angela Cox; Nicola J Camp
Journal:  Bioinformatics       Date:  2008-07-23       Impact factor: 6.937

8.  Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping.

Authors:  Fang Liu; Renate H Schmidt; Jochen C Reif; Yong Jiang
Journal:  G3 (Bethesda)       Date:  2019-12-03       Impact factor: 3.154

Review 9.  Features and applications of haplotypes in crop breeding.

Authors:  Javaid Akhter Bhat; Deyue Yu; Abhishek Bohra; Showkat Ahmad Ganie; Rajeev K Varshney
Journal:  Commun Biol       Date:  2021-11-04
  9 in total

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