Linkage disequilibrium structure of the 5q31-33 region in a Thai population
Pornlada Nuchnoi,Jun Ohashi,Izumi Naka,Duangporn Nacapunchai,Katsushi Tokunaga,Nao Nishida,Jintana Patarapotikul +6 more
TLDR
The results suggest that tagging SNPs from CHB + JPT (Northeast Asians) can efficiently capture common variants in Southeast Asians, and that the HapMap data are useful for association studies in Southeast Asian populations.Abstract:
A number of loci related to the immune response are located on human chromosomal region 5q31-33, and polymorphisms in this region have been reported to be associated with autoimmune and infectious diseases. In Southeast Asian populations, no systematic survey with dense SNP markers has been performed for the 5q31-33 region. In this study, the LD and haplotype structures for a 472-kb region on 5q31 were investigated in a Thai population to provide useful information for association studies. In addition, the LD structure in Thais was compared with that of the CHB and JPT HapMap populations (CHB + JPT) to evaluate the transferability of tagging SNPs from CHB + JPT for Thais. We show that the minor allele frequency, pattern of LD block, and genetic structure in the 5q31-33 region were highly concordant between Thais and CHB + JPT. A high transferability of tagging SNPs from CHB + JPT for Thais was observed. Our results suggest that tagging SNPs from CHB + JPT (Northeast Asians) can efficiently capture common variants in Southeast Asians, and that the HapMap data are useful for association studies in Southeast Asian populations.read more
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Genetic analysis systems and methods
TL;DR: In this paper, the authors present methods of determining a Genetic Composite Index score by assessing the association between an individual's genotype and at least one disease or condition, which is based on comparing the individual's genomic profile with a database of medically relevant genetic variations.
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Methods and systems for genomic analysis using ancestral data
TL;DR: In this paper, the authors provide methods and systems for assessing an individual's genotype correlations to a phenotype by analyzing the individual's genomic profile and using ancestral data to determine the correlations between genotypes and phenotypes.
Journal ArticleDOI
Are polymorphisms of the immunoregulatory factor CD40LG implicated in acute transfusion reactions
Chaker Aloui,Caroline Sut,Antoine Prigent,Jocelyne Fagan,Fabrice Cognasse,Viviana Granados-Herbepin,Renaud Touraine,Bruno Pozzetto,Mahjoub Aouni,Chedlia Fendri,Mohsen Hassine,Tahar Chakroun,Saloua Jemni-Yacoub,Olivier Garraud,Sandrine Laradi +14 more
TL;DR: Investigation of genetic diversity in the CD40LG using DHPLC and capillary electrophoresis for screening and genotyping found higher heterogeneity in the Tunisian, including three novel low frequency variants.
Journal ArticleDOI
Association analysis of susceptibility candidate region on chromosome 5q31 for tuberculosis.
Chutharut Ridruechai,Surakameth Mahasirimongkol,Jurairat Phromjai,Hidekatsu Yanai,Nao Nishida,Ikumi Matsushita,Jun Ohashi,N. Yamada,Saiyud Moolphate,Surin Summanapan,C Chuchottaworn,Weerawat Manosuthi,Pacharee Kantipong,S Kanitvittaya,Pathom Sawanpanyalert,Naoto Keicho,Srisin Khusmith,Katsushi Tokunaga +17 more
TL;DR: The results show that the variants carried by the haplotypes of SLC22A4, S LC22A5 and KIF3A region potentially contribute to tuberculosis susceptibility among the Thai population.
Journal ArticleDOI
Identification of a haplotype block in the 5q31 cytokine gene cluster associated with the susceptibility to severe malaria
Izumi Naka,Nao Nishida,Jintana Patarapotikul,Pornlada Nuchnoi,Katsushi Tokunaga,Hathairad Hananantachai,Naoyuki Tsuchiya,Jun Ohashi +7 more
TL;DR: A haplotype block in which a primary polymorphism associated with severe malaria is likely to be encoded was identified in Thai malaria patients.
References
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Inference of population structure using multilocus genotype data
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Journal ArticleDOI
Haploview: analysis and visualization of LD and haplotype maps
TL;DR: Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.
Journal ArticleDOI
The International HapMap Project
John W. Belmont,Paul Hardenbol,Thomas D. Willis,Fuli Yu,Huanming Yang,Lan Yang Ch'Ang,Wei Huang,Bin Liu,Yan Shen,Paul K.H. Tam,Lap-Chee Tsui,Mary M.Y. Waye,Jeffrey Tze Fei Wong,Changqing Zeng,Qingrun Zhang,Mark S. Chee,Luana Galver,Semyon Kruglyak,Sarah S. Murray,Arnold Oliphant,Alexandre Montpetit,Fanny Chagnon,Vincent Ferretti,Martin Leboeuf,Michael S. Phillips,Andrei Verner,Shenghui Duan,Denise L. Lind,Raymond D. Miller,John P. Rice,Nancy L. Saccone,Patricia Taillon-Miller,Ming Xiao,Akihiro Sekine,Koki Sorimachi,Yoichi Tanaka,Tatsuhiko Tsunoda,Eiji Yoshino,David R. Bentley,Sarah E. Hunt,Don Powell,Houcan Zhang,Ichiro Matsuda,Yoshimitsu Fukushima,Darryl Macer,Eiko Suda,Charles N. Rotimi,Clement Adebamowo,Toyin Aniagwu,Patricia A. Marshall,Olayemi Matthew,Chibuzor Nkwodimmah,Charmaine D.M. Royal,Mark Leppert,Missy Dixon,Fiona Cunningham,Ardavan Kanani,Gudmundur A. Thorisson,Peter E. Chen,David J. Cutler,Carl S. Kashuk,Peter Donnelly,Jonathan Marchini,Gilean McVean,Simon Myers,Lon R. Cardon,Andrew P. Morris,Bruce S. Weir,James C. Mullikin,Michael Feolo,Mark J. Daly,Renzong Qiu,Alastair Kent,Georgia M. Dunston,Kazuto Kato,Norio Niikawa,Jessica Watkin,Richard A. Gibbs,Erica Sodergren,George M. Weinstock,Richard K. Wilson,Lucinda Fulton,Jane Rogers,Bruce W. Birren,Hua Han,Hongguang Wang,Martin Godbout,John C. Wallenburg,Paul L'Archevêque,Guy Bellemare,Kazuo Todani,Takashi Fujita,Satoshi Tanaka,Arthur L. Holden,Francis S. Collins,Lisa D. Brooks,Jean E. McEwen,Mark S. Guyer,Elke Jordan,Jane Peterson,Jack Spiegel,Lawrence M. Sung,Lynn F. Zacharia,Karen Kennedy,Michael Dunn,Richard Seabrook,Mark Shillito,Barbara Skene,John Stewart,David Valle,Ellen Wright Clayton,Lynn B. Jorde,Aravinda Chakravarti,Mildred K. Cho,Troy Duster,Troy Duster,Morris W. Foster,Maria Jasperse,Bartha Maria Knoppers,Pui-Yan Kwok,Julio Licinio,Jeffrey C. Long,Pilar N. Ossorio,Vivian Ota Wang,Charles N. Rotimi,Patricia Spallone,Patricia Spallone,Sharon F. Terry,Eric S. Lander,Eric H. Lai,Deborah A. Nickerson,Gonçalo R. Abecasis,David Altshuler,Michael Boehnke,Panos Deloukas,Julie A. Douglas,Stacey Gabriel,Richard R. Hudson,Thomas J. Hudson,Leonid Kruglyak,Yusuke Nakamura,Robert L. Nussbaum,Stephen F. Schaffner,Stephen T. Sherry,Lincoln Stein,Toshihiro Tanaka +145 more
TL;DR: The HapMap will allow the discovery of sequence variants that affect common disease, will facilitate development of diagnostic tools, and will enhance the ability to choose targets for therapeutic intervention.
Journal ArticleDOI
The Structure of Haplotype Blocks in the Human Genome
Stacey Gabriel,Stephen F. Schaffner,Huy Nguyen,Jamie Moore,Jessica Roy,Brendan Blumenstiel,John M. Higgins,Matthew DeFelice,Amy L. Lochner,Maura Faggart,Shau Neen Liu-Cordero,Charles N. Rotimi,Adebowale Adeyemo,Richard S. Cooper,Ryk Ward,Eric S. Lander,Mark J. Daly,David Altshuler,David Altshuler +18 more
TL;DR: It is shown that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed.