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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Association of FKBP5 polymorphisms and childhood abuse with risk of posttraumatic stress disorder symptoms in adults.
Elisabeth B. Binder,Rebekah Bradley,Rebekah Bradley,Wei Liu,Michael P. Epstein,Todd C. Deveau,Kristina B. Mercer,Yi-Lang Tang,Charles F. Gillespie,Christine Heim,Charles B. Nemeroff,Ann C. Schwartz,Joseph F. Cubells,Kerry J. Ressler,Kerry J. Ressler +14 more
TL;DR: There were no main effects of the SNPs on PTSD symptoms and no significant genetic interactions with level of non-child abuse trauma as predictor of adult PTSD symptoms, suggesting a potential gene-childhood environment interaction for adult PTSD.
Journal ArticleDOI
Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease
Wataru Satake,Yuko Nakabayashi,Yuko Nakabayashi,Ikuko Mizuta,Ikuko Mizuta,Yushi Hirota,Yushi Hirota,Chiyomi Ito,Chiyomi Ito,Michiaki Kubo,Takahisa Kawaguchi,Tatsuhiko Tsunoda,Masahiko Watanabe,Atsushi Takeda,Hiroyuki Tomiyama,Kenji Nakashima,Kazuko Hasegawa,Fumiya Obata,Takeo Yoshikawa,Hideshi Kawakami,Saburo Sakoda,Mitsutoshi Yamamoto,Nobutaka Hattori,Miho Murata,Yusuke Nakamura,Tatsushi Toda,Tatsushi Toda +26 more
TL;DR: The results identify two new PD susceptibility loci, show involvement of autosomal dominant parkinsonism loci in typical PD and suggest that population differences contribute to genetic heterogeneity in PD.
Journal ArticleDOI
Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimertextquotesingles disease
Denise Harold,Richard Abraham,Paul Hollingworth,Rebecca Sims,Amy Gerrish,Marian L. Hamshere,Jaspreet Singh Pahwa,Valentina Moskvina,Kimberley Dowzell,Amy L. Williams,Nicola Jones,Charlene Thomas,Alexandra Stretton,Angharad R. Morgan,Simon Lovestone,John Powell,Petroula Proitsi,Michelle K. Lupton,Carol Brayne,David C. Rubinsztein,Michael Gill,Brian A. Lawlor,Aoibhinn Lynch,Kevin Morgan,Kristelle Brown,Peter Passmore,David Craig,Bernadette McGuinness,Stephen Todd,Clive Holmes,David G. Mann,A. David Smith,Seth Love,Patrick G. Kehoe,John Hardy,Simon Mead,Nick C. Fox,Martin N. Rossor,John Collinge,Wolfgang Maier,Frank Jessen,Britta Schürmann,Reinhard Heun,Hendrik van den Bussche,Isabella Heuser,Johannes Kornhuber,Jens Wiltfang,Martin Dichgans,Lutz Frölich,Harald Hampel,Michael Hüll,Dan Rujescu,Alison Goate,John S. K. Kauwe,Carlos Cruchaga,Petra Nowotny,John C. Morris,Kevin Mayo,Kristel Sleegers,Karolien Bettens,Sebastiaan Engelborghs,Peter Paul De Deyn,Christine Van Broeckhoven,Gill Livingston,Nicholas Bass,Hugh Gurling,Andrew McQuillin,Rhian Gwilliam,Panagiotis Deloukas,Ammar Al-Chalabi,Christopher Shaw,Magda Tsolaki,Andrew B. Singleton,Rita Guerreiro,Thomas W Mühleisen,Markus M Nöthen,Susanne Moebus,Karl-Heinz Jöckel,Norman Klopp,H-Erich Wichmann,Minerva M. Carrasquillo,V. Shane Pankratz,Steven G. Younkin,Peter Holmans,Michael OtextquotesingleDonovan,Michael John Owen,Julie Williams +86 more
TL;DR: A two-stage genome-wide association study of Alzheimer's disease involving over 16,000 individuals, the most powerful AD GWAS to date, produced compelling evidence for association with Alzheimer’s disease in the combined dataset.
Journal ArticleDOI
A chromosome conformation capture ordered sequence of the barley genome
Martin Mascher,Heidrun Gundlach,Axel Himmelbach,Sebastian Beier,Sven Twardziok,Thomas Wicker,Volodymyr Radchuk,Christoph Dockter,Pete E. Hedley,Joanne Russell,Micha Bayer,Luke Ramsay,Hui Liu,Georg Haberer,Xiao-Qi Zhang,Qisen Zhang,Roberto A. Barrero,Lin Li,Stefan Taudien,Marco Groth,Marius Felder,Alex Hastie,Hana Šimková,Helena Staňková,Jan Vrána,Saki Chan,María Muñoz-Amatriaín,Rachid Ounit,Steve Wanamaker,Dan Bolser,Christian Colmsee,Thomas Schmutzer,Lala Aliyeva-Schnorr,Stefano Grasso,Jaakko Tanskanen,Anna Chailyan,Dharanya Sampath,Darren Heavens,Leah Clissold,Sujie Cao,Brett Chapman,Fei Dai,Yong Han,Hua Li,Xuan Li,Chongyun Lin,John K. McCooke,Cong Tan,Penghao Wang,Songbo Wang,Shuya Yin,Gaofeng Zhou,Jesse Poland,Matthew I. Bellgard,Ljudmilla Borisjuk,Andreas Houben,Jaroslav Doležel,Sarah Ayling,Stefano Lonardi,Paul J. Kersey,Peter Langridge,Gary J. Muehlbauer,Matthew D. Clark,Matthew D. Clark,Mario Caccamo,Mario Caccamo,Alan H. Schulman,Klaus F. X. Mayer,Matthias Platzer,Timothy J. Close,Uwe Scholz,Mats Hansson,Guoping Zhang,Ilka Braumann,Manuel Spannagl,Chengdao Li,Chengdao Li,Chengdao Li,Robbie Waugh,Robbie Waugh,Nils Stein,Nils Stein +81 more
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Journal ArticleDOI
A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants
Lars G. Fritsche,Wilmar Igl,Jessica N. Cooke Bailey,Felix Grassmann,Sebanti Sengupta,Jennifer L. Bragg-Gresham,Kathryn P. Burdon,Scott J. Hebbring,Cindy Wen,Mathias Gorski,Ivana K. Kim,David Cho,Donald J. Zack,Donald J. Zack,Eric H. Souied,Hendrik P. N. Scholl,Hendrik P. N. Scholl,Elisa Bala,Kristine ELee,David J. Hunter,Rebecca J. Sardell,Paul Mitchell,Joanna E. Merriam,Valentina Cipriani,Valentina Cipriani,Joshua D. Hoffman,Tina Schick,Yara T. E. Lechanteur,Robyn H. Guymer,Matthew P. Johnson,Yingda Jiang,Chloe M. Stanton,Gabri'lle H.S. Buitendijk,Xiaowei Zhan,Xiaowei Zhan,Alan M. Kwong,Alexis Boleda,Matthew Brooks,Linn Gieser,Rinki Ratnapriya,Kari Branham,Johanna R. Foerster,John R. Heckenlively,Mohammad Othman,Brendan J. Vote,Helena Liang,Emmanuelle Souzeau,Ian L. McAllister,Timothy Isaacs,Janette Hall,Stewart Lake,David A. Mackey,David A. Mackey,David A. Mackey,Ian J. Constable,Jamie E Craig,Terrie Kitchner,Zhenglin Yang,Zhenglin Yang,Zhiguang Su,Hongrong Luo,Daniel Chen,Hong Ouyang,Ken Flagg,Danni Lin,Guanping Mao,Henry Ferreyra,Klaus Stark,Claudia N von Strachwitz,Armin Wolf,Caroline Brandl,G. Rudolph,Matthias Olden,Margaux A. Morrison,Denise J. Morgan,Matthew Schu,Jeeyun Ahn,Giuliana Silvestri,Evangelia E. Tsironi,Kyu Hyung Park,Lindsay A. Farrer,Anton Orlin,Alexander J. Brucker,Mingyao Li,Christine A. Curcio,Saddek Mohand-Sa'd,José-Alain Sahel,Isabelle Audo,Mustapha Benchaboune,Angela J. Cree,Christina A Rennie,S. V. Goverdhan,Michelle Grunin,Shira Hagbi-Levi,Peter A. Campochiaro,Nicholas Katsanis,Frank G. Holz,Frédéric Blond,Frédéric Blond,Frédéric Blond,Hél'ne Blanché,Jean Fran ois Deleuze,Robert P. Igo,Barbara Truitt,Neal S. Peachey,Neal S. Peachey,Stacy M. Meuer,Chelsea E. Myers,Emily L. Moore,Ronald Klein,Michael A. Hauser,Eric A. Postel,Monique D. Courtenay,Stephen G. Schwartz,Jaclyn L. Kovach,William K. Scott,Gerald Liew,Ava Grace Tan,Bamini Gopinath,John C. Merriam,R. Theodore Smith,R. Theodore Smith,Jane C. Khan,Jane C. Khan,Jane C. Khan,Humma Shahid,Humma Shahid,Anthony T. Moore,Anthony T. Moore,Anthony T. Moore,J Allie McGrath,Renee Laux,Milam A. Brantley,Anita Agarwal,Lebriz Ersoy,Albert Caramoy,Thomas Langmann,Nicole T.M. Saksens,Eiko Kde Jong,Carel B. Hoyng,Melinda Cain,Andrea J. Richardson,Tammy M. Martin,John Blangero,Daniel E. Weeks,Bal Dhillon,Cornelia M. van Duijn,Kimberly F. Doheny,Jane Romm,Caroline C W Klaver,Caroline Hayward,Michael B. Gorin,Michael L. Klein,Paul N. Baird,Anneke I. den Hollander,Sascha Fauser,John R. WYates,John R. WYates,John R. WYates,Rando Allikmets,Jie Jin Wang,Debra A. Schaumberg,Debra A. Schaumberg,Barbara E.K. Klein,Stephanie A. Hagstrom,Itay Chowers,Andrew J. Lotery,Thierry Léveillard,Thierry Léveillard,Thierry Léveillard,Kang Zhang,Kang Zhang,Murray H. Brilliant,Alex W. Hewitt,Alex W. Hewitt,Alex W. Hewitt,Anand Swaroop,Emily Y. Chew,Margaret A. Pericak-Vance,Margaret M. DeAngelis,Dwight Stambolian,Jonathan L. Haines,Sudha K. Iyengar,Bernhard H. F. Weber,Gon'alo R. Abecasis,Iris M. Heid +185 more
TL;DR: The results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.
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
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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