Literature DB >> 19427271

Defining multiple common "completely" conserved major histocompatibility complex SNP haplotypes.

Erin E Baschal1, Theresa A Aly, Jean M Jasinski, Andrea K Steck, Janelle A Noble, Henry A Erlich, George S Eisenbarth.   

Abstract

The availability of both HLA data and genotypes for thousands of SNPs across the major histocompatibility complex (MHC) in 1240 complete families of the Type 1 Diabetes Genetics Consortium allowed us to analyze the occurrence and extent of megabase contiguous identity for founder chromosomes from unrelated individuals. We identified 82 HLA-defined haplotype groups, and within these groups, megabase regions of SNP identity were readily apparent. The conserved chromosomes within the 82 haplotype groups comprise approximately one third of the founder chromosomes. It is currently unknown whether such frequent conservation for groups of unrelated individuals is specific to the MHC, or if initial binning by highly polymorphic HLA alleles facilitated detection of a more general phenomenon within the MHC. Such common identity, specifically across the MHC, impacts type 1 diabetes susceptibility and may impact transplantation between unrelated individuals.

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Year:  2009        PMID： 19427271      PMCID： PMC3740523          DOI： 10.1016/j.clim.2009.03.530

Source DB:  PubMed          Journal:  Clin Immunol        ISSN： 1521-6616            Impact factor:   3.969


  33 in total

1.  Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex.

Authors:  A J Jeffreys; L Kauppi; R Neumann
Journal:  Nat Genet       Date:  2001-10       Impact factor: 38.330

2.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

Authors:  Koichiro Tamura; Joel Dudley; Masatoshi Nei; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2007-05-07       Impact factor: 16.240

3.  Runs of homozygosity in European populations.

Authors:  Ruth McQuillan; Anne-Louise Leutenegger; Rehab Abdel-Rahman; Christopher S Franklin; Marijana Pericic; Lovorka Barac-Lauc; Nina Smolej-Narancic; Branka Janicijevic; Ozren Polasek; Albert Tenesa; Andrew K Macleod; Susan M Farrington; Pavao Rudan; Caroline Hayward; Veronique Vitart; Igor Rudan; Sarah H Wild; Malcolm G Dunlop; Alan F Wright; Harry Campbell; James F Wilson
Journal:  Am J Hum Genet       Date:  2008-08-28       Impact factor: 11.025

4.  Conserved extended haplotypes discriminate HLA-DR3-homozygous Basque patients with type 1 diabetes mellitus and celiac disease.

Authors:  J R Bilbao; B Calvo; A M Aransay; A Martin-Pagola; G Perez de Nanclares; T A Aly; I Rica; J C Vitoria; S Gaztambide; J Noble; P R Fain; Z L Awdeh; C A Alper; L Castaño
Journal:  Genes Immun       Date:  2006-08-24       Impact factor: 2.676

5.  The haplotype structure of the human major histocompatibility complex.

Authors:  Chester A Alper; Charles E Larsen; Devendra P Dubey; Zuheir L Awdeh; Dolores A Fici; Edmond J Yunis
Journal:  Hum Immunol       Date:  2006-04-05       Impact factor: 2.850

6.  Analysis of single nucleotide polymorphisms identifies major type 1A diabetes locus telomeric of the major histocompatibility complex.

Authors:  Theresa A Aly; Erin E Baschal; Mohamed M Jahromi; Maria S Fernando; Sunanda R Babu; Tasha E Fingerlin; Adam Kretowski; Henry A Erlich; Pamela R Fain; Marian J Rewers; George S Eisenbarth
Journal:  Diabetes       Date:  2007-12-07       Impact factor: 9.461

7.  A second generation human haplotype map of over 3.1 million SNPs.

Authors:  Kelly A Frazer; Dennis G Ballinger; David R Cox; David A Hinds; Laura L Stuve; Richard A Gibbs; John W Belmont; Andrew Boudreau; Paul Hardenbol; Suzanne M Leal; Shiran Pasternak; David A Wheeler; Thomas D Willis; Fuli Yu; Huanming Yang; Changqing Zeng; Yang Gao; Haoran Hu; Weitao Hu; Chaohua Li; Wei Lin; Siqi Liu; Hao Pan; Xiaoli Tang; Jian Wang; Wei Wang; Jun Yu; Bo Zhang; Qingrun Zhang; Hongbin Zhao; Hui Zhao; Jun Zhou; Stacey B Gabriel; Rachel Barry; Brendan Blumenstiel; Amy Camargo; Matthew Defelice; Maura Faggart; Mary Goyette; Supriya Gupta; Jamie Moore; Huy Nguyen; Robert C Onofrio; Melissa Parkin; Jessica Roy; Erich Stahl; Ellen Winchester; Liuda Ziaugra; David Altshuler; Yan Shen; Zhijian Yao; Wei Huang; Xun Chu; Yungang He; Li Jin; Yangfan Liu; Yayun Shen; Weiwei Sun; Haifeng Wang; Yi Wang; Ying Wang; Xiaoyan Xiong; Liang Xu; Mary M Y Waye; Stephen K W Tsui; Hong Xue; J Tze-Fei Wong; Luana M Galver; Jian-Bing Fan; Kevin Gunderson; Sarah S Murray; Arnold R Oliphant; Mark S Chee; Alexandre Montpetit; Fanny Chagnon; Vincent Ferretti; Martin Leboeuf; Jean-François Olivier; Michael S Phillips; Stéphanie Roumy; Clémentine Sallée; Andrei Verner; Thomas J Hudson; Pui-Yan Kwok; Dongmei Cai; Daniel C Koboldt; Raymond D Miller; Ludmila Pawlikowska; Patricia Taillon-Miller; Ming Xiao; Lap-Chee Tsui; William Mak; You Qiang Song; Paul K H Tam; Yusuke Nakamura; Takahisa Kawaguchi; Takuya Kitamoto; Takashi Morizono; Atsushi Nagashima; Yozo Ohnishi; Akihiro Sekine; Toshihiro Tanaka; Tatsuhiko Tsunoda; Panos Deloukas; Christine P Bird; Marcos Delgado; Emmanouil T Dermitzakis; Rhian Gwilliam; Sarah Hunt; Jonathan Morrison; Don Powell; Barbara E Stranger; Pamela Whittaker; David R Bentley; Mark J Daly; Paul I W de Bakker; Jeff Barrett; Yves R Chretien; Julian Maller; Steve McCarroll; Nick Patterson; Itsik Pe'er; Alkes Price; Shaun Purcell; Daniel J Richter; Pardis Sabeti; Richa Saxena; Stephen F Schaffner; Pak C Sham; Patrick Varilly; David Altshuler; Lincoln D Stein; Lalitha Krishnan; Albert Vernon Smith; Marcela K Tello-Ruiz; Gudmundur A Thorisson; Aravinda Chakravarti; Peter E Chen; David J Cutler; Carl S Kashuk; Shin Lin; Gonçalo R Abecasis; Weihua Guan; Yun Li; Heather M Munro; Zhaohui Steve Qin; Daryl J Thomas; Gilean McVean; Adam Auton; Leonardo Bottolo; Niall Cardin; Susana Eyheramendy; Colin Freeman; Jonathan Marchini; Simon Myers; Chris Spencer; Matthew Stephens; Peter Donnelly; Lon R Cardon; Geraldine Clarke; David M Evans; Andrew P Morris; Bruce S Weir; Tatsuhiko Tsunoda; James C Mullikin; Stephen T Sherry; Michael Feolo; Andrew Skol; Houcan Zhang; Changqing Zeng; Hui Zhao; Ichiro Matsuda; Yoshimitsu Fukushima; Darryl R Macer; Eiko Suda; Charles N Rotimi; Clement A Adebamowo; Ike Ajayi; Toyin Aniagwu; Patricia A Marshall; Chibuzor Nkwodimmah; Charmaine D M Royal; Mark F Leppert; Missy Dixon; Andy Peiffer; Renzong Qiu; Alastair Kent; Kazuto Kato; Norio Niikawa; Isaac F Adewole; Bartha M Knoppers; Morris W Foster; Ellen Wright Clayton; Jessica Watkin; Richard A Gibbs; John W Belmont; Donna Muzny; Lynne Nazareth; Erica Sodergren; George M Weinstock; David A Wheeler; Imtaz Yakub; Stacey B Gabriel; Robert C Onofrio; Daniel J Richter; Liuda Ziaugra; Bruce W Birren; Mark J Daly; David Altshuler; Richard K Wilson; Lucinda L Fulton; Jane Rogers; John Burton; Nigel P Carter; Christopher M Clee; Mark Griffiths; Matthew C Jones; Kirsten McLay; Robert W Plumb; Mark T Ross; Sarah K Sims; David L Willey; Zhu Chen; Hua Han; Le Kang; Martin Godbout; John C Wallenburg; Paul L'Archevêque; Guy Bellemare; Koji Saeki; Hongguang Wang; Daochang An; Hongbo Fu; Qing Li; Zhen Wang; Renwu Wang; Arthur L Holden; Lisa D Brooks; Jean E McEwen; Mark S Guyer; Vivian Ota Wang; Jane L Peterson; Michael Shi; Jack Spiegel; Lawrence M Sung; Lynn F Zacharia; Francis S Collins; Karen Kennedy; Ruth Jamieson; John Stewart
Journal:  Nature       Date:  2007-10-18       Impact factor: 49.962

8.  Genetic fixity in the human major histocompatibility complex and block size diversity in the class I region including HLA-E.

Authors:  Viviana Romero; Charles E Larsen; Jonathan S Duke-Cohan; Edward A Fox; Tatiana Romero; Olga P Clavijo; Dolores A Fici; Zaheed Husain; Ingrid Almeciga; Dennis R Alford; Zuheir L Awdeh; Joaquin Zuñiga; Lama El-Dahdah; Chester A Alper; Edmond J Yunis
Journal:  BMC Genet       Date:  2007-04-12       Impact factor: 2.797

9.  Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A.

Authors:  Sergey Nejentsev; Joanna M M Howson; Neil M Walker; Jeffrey Szeszko; Sarah F Field; Helen E Stevens; Pamela Reynolds; Matthew Hardy; Erna King; Jennifer Masters; John Hulme; Lisa M Maier; Deborah Smyth; Rebecca Bailey; Jason D Cooper; Gloria Ribas; R Duncan Campbell; David G Clayton; John A Todd
Journal:  Nature       Date:  2007-11-14       Impact factor: 49.962

10.  Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations.

Authors:  D Curtis; A E Vine; J Knight
Journal:  Ann Hum Genet       Date:  2008-01-20       Impact factor: 1.670
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  19 in total

1.  Genotyping of single nucleotide polymorphisms by 5' nuclease allelic discrimination.

Authors:  Mari Malkki; Effie W Petersdorf
Journal:  Methods Mol Biol       Date:  2012

2.  The next big idea.

Authors:  Marian Rewers
Journal:  Diabetes Technol Ther       Date:  2013-06       Impact factor: 6.118

Review 3.  Genetics of graft-versus-host disease: the major histocompatibility complex.

Authors:  Effie W Petersdorf
Journal:  Blood Rev       Date:  2012-11-20       Impact factor: 8.250

4.  Protective effect of HLA-DQB1 alleles against alloimmunization in patients with sickle cell disease.

Authors:  Zohreh Tatari-Calderone; Heather Gordish-Dressman; Ross Fasano; Michael Riggs; Catherine Fortier; Andrew D Campbell; Dominique Charron; Victor R Gordeuk; Naomi L C Luban; Stanislav Vukmanovic; Ryad Tamouza
Journal:  Hum Immunol       Date:  2015-10-22       Impact factor: 2.850

5.  Dominant suppression of Addison's disease associated with HLA-B15.

Authors:  Peter R Baker; Erin E Baschal; Pam R Fain; Priyaanka Nanduri; Taylor M Triolo; Janet C Siebert; Taylor K Armstrong; Sunanda R Babu; Marian J Rewers; Peter A Gottlieb; Jennifer M Barker; George S Eisenbarth
Journal:  J Clin Endocrinol Metab       Date:  2011-05-11       Impact factor: 5.958

6.  Significance of ethnicity in the risk of acute graft-versus-host disease and leukemia relapse after unrelated donor hematopoietic stem cell transplantation.

Authors:  Yasuo Morishima; Takakazu Kawase; Mari Malkki; Satoko Morishima; Stephen Spellman; Koichi Kashiwase; Shunichi Kato; Anne Cesbron; Jean-Marie Tiercy; David Senitzer; Andrea Velardi; Effie W Petersdorf
Journal:  Biol Blood Marrow Transplant       Date:  2013-06-06       Impact factor: 5.742

Review 7.  The MHC in the era of next-generation sequencing: Implications for bridging structure with function.

Authors:  Effie W Petersdorf; Colm O'hUigin
Journal:  Hum Immunol       Date:  2018-10-12       Impact factor: 2.850

8.  Haplotype analysis discriminates genetic risk for DR3-associated endocrine autoimmunity and helps define extreme risk for Addison's disease.

Authors:  Peter R Baker; Erin E Baschal; Pam R Fain; Taylor M Triolo; Priyaanka Nanduri; Janet C Siebert; Taylor K Armstrong; Sunanda R Babu; Marian J Rewers; Peter A Gottlieb; Jennifer M Barker; George S Eisenbarth
Journal:  J Clin Endocrinol Metab       Date:  2010-07-14       Impact factor: 5.958

9.  Banting Lecture 2009: An unfinished journey: molecular pathogenesis to prevention of type 1A diabetes.

Authors:  George S Eisenbarth
Journal:  Diabetes       Date:  2010-04       Impact factor: 9.461

10.  HLA and celiac disease susceptibility: new genetic factors bring open questions about the HLA influence and gene-dosage effects.

Authors:  Luz María Medrano; Bárbara Dema; Arturo López-Larios; Carlos Maluenda; Andrés Bodas; Natalia López-Palacios; M Ángeles Figueredo; Miguel Fernández-Arquero; Concepción Núñez
Journal:  PLoS One       Date:  2012-10-31       Impact factor: 3.240
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