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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Journal ArticleDOI
Association analysis of genetic variants in IL23R , ATG16L1 and 5p13.1 loci with Crohn’s disease in Japanese patients
TL;DR: A distinct ethnic difference of genetic background of CD is revealed that was reported previously in other genes between Japanese and Caucasian populations and is now recognised as a robust tool for the identification of susceptibility genes for complex diseases.
Journal ArticleDOI
Genetic Polymorphisms of the Human PNPLA3 Gene Are Strongly Associated with Severity of Non-Alcoholic Fatty Liver Disease in Japanese
Takahisa Kawaguchi,Takahisa Kawaguchi,Yoshio Sumida,Atsushi Umemura,Keitaro Matsuo,Meiko Takahashi,Toshinari Takamura,Kohichiroh Yasui,Toshiji Saibara,Etsuko Hashimoto,Miwa Kawanaka,Sumio Watanabe,Sumio Kawata,Yasuharu Imai,Miki Kokubo,Toshihide Shima,Hyohun Park,Hideo Tanaka,Kazuo Tajima,Ryo Yamada,Fumihiko Matsuda,Fumihiko Matsuda +21 more
TL;DR: It is demonstrated that Matteoni type4 NAFLD is both a genetically and clinically different subset from the other spectrums of the disease and that the PNPLA3 gene is strongly associated with the progression of NASH in Japanese population.
Journal ArticleDOI
A degradation-sensitive anionic trypsinogen ( PRSS2 ) variant protects against chronic pancreatitis
Heiko Witt,Miklós Sahin-Tóth,Olfert Landt,Jian-Min Chen,Thilo Kähne,Joost P.H. Drenth,Zoltán Kukor,Edit Szepessy,Walter Halangk,Stefan Dahm,Klaus Rohde,Hans Ulrich Schulz,Cédric Le Maréchal,Nejat Akar,Rudolf W. Ammann,Kaspar Truninger,Mario Bargetzi,Eesh Bhatia,Carlo Castellani,Giulia Martina Cavestro,Milos Cerny,Giovanni Destro-Bisol,Gabriella Spedini,Hans Eiberg,Jan B.M.J. Jansen,Monika Koudova,Eva Rausova,Milan Macek,Núria Malats,Francisco X. Real,Hans Jürgen Menzel,Pedro Moral,Roberta Galavotti,Pier Franco Pignatti,Olga Rickards,Julius Spicak,Narcis O. Zarnescu,Wolfgang Böck,Thomas M. Gress,Helmut Friess,Johann Ockenga,Hartmut Schmidt,Roland H. Pfützer,Matthias Löhr,Peter Simon,Frank Ulrich Weiss,Markus M. Lerch,Niels Teich,Volker Keim,Thomas Berg,Bertram Wiedenmann,W Luck,David A. Groneberg,Michael Becker,Thomas Keil,Andreas Kage,Jana Bernardova,Markus Braun,Claudia Güldner,J. Halangk,Jonas Rosendahl,Ulrike Witt,Matthias Treiber,Renate Nickel,Claude Férec +64 more
TL;DR: The G191R variant of PRSS2 mitigates intrapancreatic trypsin activity and thereby protects against chronic pancreatitis.
Journal ArticleDOI
Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes
Maggie C.Y. Ng,Daniel Shriner,Brian H. Chen,Jiang Li,Wei-Min Chen,Xiuqing Guo,Jiankang Liu,Suzette J. Bielinski,Lisa R. Yanek,Mike A. Nalls,Mary E. Comeau,Laura J. Rasmussen-Torvik,Richard A. Jensen,Daniel S. Evans,Yan V. Sun,Ping An,Sanjay R. Patel,Yingchang Lu,Jirong Long,Loren L. Armstrong,Lynne E. Wagenknecht,Lingyao Yang,Beverly M. Snively,Nicholette D. Palmer,Poorva Mudgal,Carl D. Langefeld,Keith L. Keene,Barry I. Freedman,Josyf C. Mychaleckyj,Uma Nayak,Leslie J. Raffel,Mark O. Goodarzi,Y. D.I. Chen,Herman A. Taylor,Adolfo Correa,Mario Sims,David Couper,James S. Pankow,Eric Boerwinkle,Adebowale Adeyemo,Ayo P. Doumatey,Guanjie Chen,Rasika A. Mathias,Dhananjay Vaidya,Andrew B. Singleton,Alan B. Zonderman,Robert P. Igo,John R. Sedor,Edmond K. Kabagambe,David S. Siscovick,Barbara McKnight,Kenneth Rice,Yongmei Liu,Wen-Chi Hsueh,Wei Zhao,Lawrence F. Bielak,Aldi T. Kraja,Michael A. Province,Erwin P. Bottinger,Omri Gottesman,Qiuyin Cai,Wei Zheng,William J. Blot,William L. Lowe,Jennifer A. Pacheco,Dana C. Crawford,Elin Grundberg,Stephen S. Rich,M. Geoffrey Hayes,Xiao-Ou Shu,Ruth J. F. Loos,Ingrid B. Borecki,Patricia A. Peyser,Steven R. Cummings,Bruce M. Psaty,Myriam Fornage,Sudha K. Iyengar,Michele K. Evans,Diane M. Becker,W. H. Linda Kao,James G. Wilson,Jerome I. Rotter,Michèle M. Sale,Simin Liu,Charles N. Rotimi,Donald W. Bowden +85 more
TL;DR: A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.
Journal ArticleDOI
Interaction between a functional MAOA locus and childhood sexual abuse predicts alcoholism and antisocial personality disorder in adult women.
TL;DR: MAOA seems to moderate the impact of childhood trauma on adult psychopathology in female subjects in the same way as previously shown among male subjects.
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