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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Genetics is a major determinant of expression of the human hepatic uptake transporter OATP1B1, but not of OATP1B3 and OATP2B1.
Anne T. Nies,Mikko Niemi,Oliver Burk,Stefan Winter,Ulrich M. Zanger,Bruno Stieger,Matthias Schwab,Elke Schaeffeler +7 more
TL;DR: This work systematically elucidated the contribution of SLCO variants on expression of the three hepatic OATPs under consideration of additional important covariates and showed that expression of OATP1B1, but not of O ATP 1B1B3 and OATp2B 1, is significantly affected by genetic variants.
Journal ArticleDOI
SDHAF2 mutations in familial and sporadic paraganglioma and phaeochromocytoma
Jean-Pierre Bayley,Henricus P. M. Kunst,Alberto Cascón,M. L. Sampietro,José Gaal,Esther Korpershoek,Adolfo Hinojar-Gutierrez,Henri J L M Timmers,Lies H. Hoefsloot,Mario Hermsen,Carlos Suárez,A. Karim Hussain,Annette H. J. T. Vriends,Frederik J. Hes,Jeroen C. Jansen,Carli M. J. Tops,Eleonora P M Corssmit,Peter de Knijff,Jacques W.M. Lenders,Cor W. R. J. Cremers,Peter Devilee,Winand N.M. Dinjens,Ronald R. de Krijger,Mercedes Robledo +23 more
TL;DR: It is concluded that SDHAF2 mutation analysis is justified in very young patients with isolated head and neck paraganglioma without mutations in SDHD, SDHC, or SDHB, and in individuals with familial antecedents who are negative for mutations in all other risk genes.
Journal ArticleDOI
Modeling recent human evolution in mice by expression of a selected EDAR variant
Yana G. Kamberov,Sijia Wang,Sijia Wang,Jingze Tan,Pascale Gerbault,Abigail R. Wark,Longzhi Tan,Yajun Yang,Shilin Li,Kun Tang,Hua Chen,Adam Powell,Yuval Itan,Dorian Q. Fuller,Jason Lohmueller,Junhao Mao,Asa Schachar,Asa Schachar,Madeline Paymer,Madeline Paymer,Elizabeth Hostetter,Elizabeth H. Byrne,Melissa Burnett,Andrew P. McMahon,Mark G. Thomas,Daniel E. Lieberman,Li Jin,Li Jin,Clifford J. Tabin,Bruce A. Morgan,Pardis C. Sabeti,Pardis C. Sabeti +31 more
TL;DR: It is found that EDAR370A is associated with an increased number of active eccrine glands in the Han Chinese, and this interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.
Journal ArticleDOI
Out of southern East Asia: the natural history of domestic dogs across the world.
Guo-Dong Wang,Weiwei Zhai,He-Chuan Yang,He-Chuan Yang,He-Chuan Yang,Lu Wang,Li Zhong,Yan-Hu Liu,Ruo-xi Fan,Ting-Ting Yin,Ting-Ting Yin,Chun-Ling Zhu,Andrei D. Poyarkov,David M. Irwin,Marjo K. Hytönen,Hannes Lohi,Chung-I Wu,Peter Savolainen,Ya-Ping Zhang,Ya-Ping Zhang +19 more
TL;DR: It is found that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern EastAsia 33 000 years ago.
Journal ArticleDOI
The genetics of monarch butterfly migration and warning colouration
Shuai Zhan,Shuai Zhan,Shuai Zhan,Wei Zhang,Kristjan Niitepõld,Kristjan Niitepõld,Jeremy L. Hsu,Juan Fernández Haeger,Myron P. Zalucki,Sonia Altizer,Jacobus C. de Roode,Steven M. Reppert,Marcus R. Kronforst +12 more
TL;DR: The history of the monarch's evolutionary origin and global dispersal is uncovered, the strongest signatures of selection associated with migration centre on flight muscle function, resulting in greater flight efficiency among migratory monarchs, and that variation in monarch warning colouration is controlled by a single myosin gene not previously implicated in insect pigmentation.
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