Literature DB >> 22138821

A linear complexity phasing method for thousands of genomes.

Olivier Delaneau1, Jonathan Marchini, Jean-François Zagury.   

Abstract

Human-disease etiology can be better understood with phase information about diploid sequences. We present a method for estimating haplotypes, using genotype data from unrelated samples or small nuclear families, that leads to improved accuracy and speed compared to several widely used methods. The method, segmented haplotype estimation and imputation tool (SHAPEIT), scales linearly with the number of haplotypes used in each iteration and can be run efficiently on whole chromosomes.

Entities:  

Mesh：

Year:  2011        PMID： 22138821     DOI： 10.1038/nmeth.1785

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  12 in total

1.  A new statistical method for haplotype reconstruction from population data.

Authors:  M Stephens; N J Smith; P Donnelly
Journal:  Am J Hum Genet       Date:  2001-03-09       Impact factor: 11.025

2.  Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.

Authors:  Na Li; Matthew Stephens
Journal:  Genetics       Date:  2003-12       Impact factor: 4.562

Review 3.  Genotype imputation for genome-wide association studies.

Authors:  Jonathan Marchini; Bryan Howie
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242

4.  A new multipoint method for genome-wide association studies by imputation of genotypes.

Authors:  Jonathan Marchini; Bryan Howie; Simon Myers; Gil McVean; Peter Donnelly
Journal:  Nat Genet       Date:  2007-06-17       Impact factor: 38.330

5.  A comparison of phasing algorithms for trios and unrelated individuals.

Authors:  Jonathan Marchini; David Cutler; Nick Patterson; Matthew Stephens; Eleazar Eskin; Eran Halperin; Shin Lin; Zhaohui S Qin; Heather M Munro; Goncalo R Abecasis; Peter Donnelly
Journal:  Am J Hum Genet       Date:  2006-01-26       Impact factor: 11.025

6.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.

Authors:  Paul Scheet; Matthew Stephens
Journal:  Am J Hum Genet       Date:  2006-02-17       Impact factor: 11.025

7.  Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering.

Authors:  Sharon R Browning; Brian L Browning
Journal:  Am J Hum Genet       Date:  2007-09-21       Impact factor: 11.025

8.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.

Authors:  Yun Li; Cristen J Willer; Jun Ding; Paul Scheet; Gonçalo R Abecasis
Journal:  Genet Epidemiol       Date:  2010-12       Impact factor: 2.135

9.  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

10.  A flexible and accurate genotype imputation method for the next generation of genome-wide association studies.

Authors:  Bryan N Howie; Peter Donnelly; Jonathan Marchini
Journal:  PLoS Genet       Date:  2009-06-19       Impact factor: 5.917
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Journal:  Int J Behav Med       Date:  2017-12

2.  Blockwise HMM computation for large-scale population genomic inference.

Authors:  Joshua S Paul; Yun S Song
Journal:  Bioinformatics       Date:  2012-05-28       Impact factor: 6.937

3.  Whole-exome Sequence Analysis Implicates Rare Il17REL Variants in Familial and Sporadic Inflammatory Bowel Disease.

Authors:  Mark M Sasaki; Andrew D Skol; Eric A Hungate; Riyue Bao; Lei Huang; Stacy A Kahn; James M Allan; Steven R Brant; Dermot P B McGovern; Inga Peter; Mark S Silverberg; Judy H Cho; Barbara S Kirschner; Kenan Onel
Journal:  Inflamm Bowel Dis       Date:  2016-01       Impact factor: 5.325

4.  Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.

Authors:  Freyja Imsland; Kelly McGowan; Carl-Johan Rubin; Corneliu Henegar; Elisabeth Sundström; Jonas Berglund; Doreen Schwochow; Ulla Gustafson; Páll Imsland; Kerstin Lindblad-Toh; Gabriella Lindgren; Sofia Mikko; Lee Millon; Claire Wade; Mikkel Schubert; Ludovic Orlando; Maria Cecilia T Penedo; Gregory S Barsh; Leif Andersson
Journal:  Nat Genet       Date:  2015-12-21       Impact factor: 38.330

5.  Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure.

Authors:  Analabha Basu; Neeta Sarkar-Roy; Partha P Majumder
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-25       Impact factor: 11.205

Review 6.  Application of computational methods in genetic study of inflammatory bowel disease.

Authors:  Jin Li; Zhi Wei; Hakon Hakonarson
Journal:  World J Gastroenterol       Date:  2016-01-21       Impact factor: 5.742

7.  CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease.

Authors:  Lipika R Pal; Kunal Kundu; Yizhou Yin; John Moult
Journal:  Hum Mutat       Date:  2017-06-28       Impact factor: 4.878

8.  Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB.

Authors:  Mesude Bicak; Xing Wang; Xiaoni Gao; Xing Xu; Riina-Minna Väänänen; Pekka Taimen; Hans Lilja; Kim Pettersson; Robert J Klein
Journal:  Hum Mol Genet       Date:  2020-06-27       Impact factor: 6.150

9.  Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos.

Authors:  Maria Pino-Yanes; Christopher R Gignoux; Joshua M Galanter; Albert M Levin; Catarina D Campbell; Celeste Eng; Scott Huntsman; Katherine K Nishimura; Pierre-Antoine Gourraud; Kiana Mohajeri; Brian J O'Roak; Donglei Hu; Rasika A Mathias; Elizabeth A Nguyen; Lindsey A Roth; Badri Padhukasahasram; Andres Moreno-Estrada; Karla Sandoval; Cheryl A Winkler; Fred Lurmann; Adam Davis; Harold J Farber; Kelley Meade; Pedro C Avila; Denise Serebrisky; Rocio Chapela; Jean G Ford; Michael A Lenoir; Shannon M Thyne; Emerita Brigino-Buenaventura; Luisa N Borrell; William Rodriguez-Cintron; Saunak Sen; Rajesh Kumar; Jose R Rodriguez-Santana; Carlos D Bustamante; Fernando D Martinez; Benjamin A Raby; Scott T Weiss; Dan L Nicolae; Carole Ober; Deborah A Meyers; Eugene R Bleecker; Steven J Mack; Ryan D Hernandez; Evan E Eichler; Kathleen C Barnes; L Keoki Williams; Dara G Torgerson; Esteban G Burchard
Journal:  J Allergy Clin Immunol       Date:  2014-12-06       Impact factor: 10.793

10.  Next-generation genotype imputation service and methods.

Authors:  Sayantan Das; Lukas Forer; Sebastian Schönherr; Carlo Sidore; Adam E Locke; Alan Kwong; Scott I Vrieze; Emily Y Chew; Shawn Levy; Matt McGue; David Schlessinger; Dwight Stambolian; Po-Ru Loh; William G Iacono; Anand Swaroop; Laura J Scott; Francesco Cucca; Florian Kronenberg; Michael Boehnke; Gonçalo R Abecasis; Christian Fuchsberger
Journal:  Nat Genet       Date:  2016-08-29       Impact factor: 38.330
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