Haploview: analysis and visualization of LD and haplotype maps
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TLDR
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.Abstract:
Summary: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. 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.
Availability: http://www.broad.mit.edu/mpg/haploview/
Contact: jcbarret@broad.mit.eduread more
Citations
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Genome-wide scan revealed that polymorphisms in the PNPLA3, SAMM50, and PARVB genes are associated with development and progression of nonalcoholic fatty liver disease in Japan.
Takuya Kitamoto,Aya Kitamoto,Masato Yoneda,Hideyuki Hyogo,Hidenori Ochi,Takahiro Nakamura,Hajime Teranishi,Seiho Mizusawa,Takato Ueno,Kazuaki Chayama,Atsushi Nakajima,Kazuwa Nakao,Akihiro Sekine,Kikuko Hotta +13 more
TL;DR: Polymorphisms in the SAMM50 and PARVB genes in addition to those in the PNPLA3 gene were observed to be associated with the development and progression of NAFLD.
Journal ArticleDOI
Evidence for two independent prostate cancer risk-associated loci in the HNF1B gene at 17q12.
Jielin Sun,Siqun Lilly Zheng,Fredrik Wiklund,Sarah D. Isaacs,Lina Purcell,Zhengrong Gao,Fang-Chi Hsu,Seong Tae Kim,Wennuan Liu,Yi Zhu,Pär Stattin,Hans-Olov Adami,Hans-Olov Adami,Kathleen E. Wiley,Latchezar Dimitrov,Jishan Sun,Tao Li,Aubrey R. Turner,Tamara S. Adams,Jan Adolfsson,Jan-Erik Johansson,James Lowey,Bruce J. Trock,Alan W. Partin,Patrick C. Walsh,Jeffrey M. Trent,David Duggan,John D. Carpten,Bao Li Chang,Henrik Grönberg,William B. Isaacs,Jianfeng Xu +31 more
TL;DR: A fine-mapping study in the HNF1B gene at 17q12 in two study populations identified a second locus associated with prostate cancer risk, ∼26 kb centromeric to the first known locus (rs4430796); these loci are separated by a recombination hot spot.
Journal ArticleDOI
SNCA variant associated with Parkinson disease and plasma α-synuclein level
Ignacio F. Mata,Min Shi,Pinky Agarwal,Kathryn A. Chung,Karen L. Edwards,Stewart A. Factor,Douglas Galasko,Carmen Ginghina,Alida Griffith,Donald S. Higgins,Denise M. Kay,Hojoong Kim,James B. Leverenz,Joseph F. Quinn,John W. Roberts,Ali Samii,Katherine W. Snapinn,Debby W. Tsuang,Dora Yearout,Jing Zhang,Haydeh Payami,Cyrus P. Zabetian +21 more
TL;DR: The data suggest that 1 or more unidentified functional SNCA variants modify risk for PD and that the effect is larger than and independent of REP1.
Journal ArticleDOI
Association of the Trp719Arg Polymorphism in Kinesin-Like Protein 6 With Myocardial Infarction and Coronary Heart Disease in 2 Prospective Trials: The CARE and WOSCOPS Trials
Olga Iakoubova,Carmen H. Tong,Charles M. Rowland,Todd G. Kirchgessner,Bradford A. Young,Andre R. Arellano,Dov Shiffman,Marc S. Sabatine,Hannia Campos,Chris J. Packard,Marc A. Pfeffer,Thomas J. White,Eugene Braunwald,James Shepherd,James J. Devlin,Frank M. Sacks,Frank M. Sacks +16 more
TL;DR: In both the CARE and the WOSCOPS trials, carriers of the KIF6 719Arg allele had an increased risk of coronary events, and pravastatin treatment substantially reduced that risk.
Journal ArticleDOI
Association of the Anxiogenic and Alerting Effects of Caffeine with ADORA2A and ADORA1 Polymorphisms and Habitual Level of Caffeine Consumption
Peter J. Rogers,Christa Hohoff,Susan V. Heatherley,EL Mullings,Peter Maxfield,Richard P. Evershed,Jürgen Deckert,David J. Nutt +7 more
TL;DR: Results showed greater susceptibility to caffeine-induced anxiety, but not lower habitual caffeine intake (indeed coffee intake was higher), in the rs5751876 TT genotype group, and a reduced anxiety response in MH vs NL participants irrespective of genotype.
References
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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.
Journal ArticleDOI
High-resolution haplotype structure in the human genome.
Mark J. Daly,John D. Rioux,Stephen F. Schaffner,Thomas J. Hudson,Thomas J. Hudson,Eric S. Lander +5 more
TL;DR: A high-resolution analysis of the haplotype structure across 500 kilobases on chromosome 5q31 using 103 single-nucleotide polymorphisms (SNPs) in a European-derived population offers a coherent framework for creating a haplotype map of the human genome.
Journal ArticleDOI
Linkage disequilibrium in the human genome
David Reich,Michele Cargill,Michele Cargill,Stacey Bolk,James S. Ireland,Pardis C. Sabeti,Daniel J. Richter,Thomas Lavery,Rose Kouyoumjian,Shelli F. Farhadian,Ryk Ward,Eric S. Lander +11 more
TL;DR: The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000–53,000 years ago, implying that LD mapping is likely to be practical in this population.
Journal ArticleDOI
Association of the adam33 gene with asthma and bronchial hyperresponsiveness
TL;DR: The identification and characterization of ADAM33, a putative asthma susceptibility gene identified by positional cloning in an outbred population, should provide insights into the pathogenesis and natural history of this common disease.
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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
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