Literature DB >> 16131520

HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations.

Sheng Gu1, Andrew J Pakstis, Kenneth K Kidd.   

Abstract

UNLABELLED: Understanding of human variation relevant to association studies can benefit from population comparison, especially comparing populations in the same geographical region. Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern. We present here a win32 system based Perl/Tk application for visual comparisons of these variations in different populations. AVAILABILITY: The application package is available at http://info.med.yale.edu/genetics/kkidd/programs.html CONTACT: sheng.gu@yale.edu.

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Year:  2005        PMID： 16131520     DOI： 10.1093/bioinformatics/bti649

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


  15 in total

1.  Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation.

Authors:  Shigeki Nakagome; Shuhei Mano; Lukasz Kozlowski; Janusz M Bujnicki; Hiroki Shibata; Yasuaki Fukumaki; Judith R Kidd; Kenneth K Kidd; Shoji Kawamura; Hiroki Oota
Journal:  Mol Biol Evol       Date:  2012-01-12       Impact factor: 16.240

2.  Evidence of positive selection on a class I ADH locus.

Authors:  Yi Han; Sheng Gu; Hiroki Oota; Michael V Osier; Andrew J Pakstis; William C Speed; Judith R Kidd; Kenneth K Kidd
Journal:  Am J Hum Genet       Date:  2007-01-30       Impact factor: 11.025

3.  Behavioural genetic differences between Chinese and European pigs.

Authors:  Qingpo Chu; Tingting Liang; Lingling Fu; Huizhi Li; Bo Zhou
Journal:  J Genet       Date:  2017-09       Impact factor: 1.166

4.  Single nucleotide polymorphisms and haplotypes in Native American populations.

Authors:  Judith R Kidd; Françoise Friedlaender; Andrew J Pakstis; Manohar Furtado; Rixun Fang; Xudong Wang; Caroline M Nievergelt; Kenneth K Kidd
Journal:  Am J Phys Anthropol       Date:  2011-09-13       Impact factor: 2.868

5.  Haplotype structure and positive selection at TLR1.

Authors:  Christopher Heffelfinger; Andrew J Pakstis; William C Speed; Allison P Clark; Eva Haigh; Rixun Fang; Mahohar R Furtado; Kenneth K Kidd; Michael P Snyder
Journal:  Eur J Hum Genet       Date:  2013-09-04       Impact factor: 4.246

6.  Global patterns of variation in allele and haplotype frequencies and linkage disequilibrium across the CYP2E1 gene.

Authors:  M-Y Lee; N Mukherjee; A J Pakstis; S Khaliq; A Mohyuddin; S Q Mehdi; W C Speed; J R Kidd; K K Kidd
Journal:  Pharmacogenomics J       Date:  2008-07-29       Impact factor: 3.550

7.  The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase.

Authors:  N Mukherjee; K K Kidd; A J Pakstis; W C Speed; H Li; Z Tarnok; C Barta; S L B Kajuna; J R Kidd
Journal:  Mol Psychiatry       Date:  2008-06-24       Impact factor: 15.992

8.  Linkage disequilibrium decay and haplotype block structure in the pig.

Authors:  Andreia J Amaral; Hendrik-Jan Megens; Richard P M A Crooijmans; Henri C M Heuven; Martien A M Groenen
Journal:  Genetics       Date:  2008-05       Impact factor: 4.562

9.  A global view of the OCA2-HERC2 region and pigmentation.

Authors:  Michael P Donnelly; Peristera Paschou; Elena Grigorenko; David Gurwitz; Csaba Barta; Ru-Band Lu; Olga V Zhukova; Jong-Jin Kim; Marcello Siniscalco; Maria New; Hui Li; Sylvester L B Kajuna; Vangelis G Manolopoulos; William C Speed; Andrew J Pakstis; Judith R Kidd; Kenneth K Kidd
Journal:  Hum Genet       Date:  2011-11-08       Impact factor: 4.132

10.  Global variation in CYP2C8-CYP2C9 functional haplotypes.

Authors:  William C Speed; Soonmo Peter Kang; David P Tuck; Lyndsay N Harris; Kenneth K Kidd
Journal:  Pharmacogenomics J       Date:  2009-04-21       Impact factor: 3.550
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