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Literature DB >> 21169219

Completely phased genome sequencing through chromosome sorting.

Abstract

The two haploid genome sequences that a person inherits from the two parents represent the most fundamentally useful type of genetic information for the study of heritable diseases and the development of personalized medicine. Because of the difficulty in obtaining long-range phase information, current sequencing methods are unable to provide this information. Here, we introduce and show feasibility of a scalable approach capable of generating genomic sequences completely phased across the entire chromosome.

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DNA Primers

Year: 2010 PMID： 21169219 PMCID： PMC3017199 DOI： 10.1073/pnas.1016725108

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

26 in total

1. Multiple personal genomes await.

Authors: J Craig Venter
Journal: Nature Date: 2010-04-01 Impact factor: 49.962

2. A haplotype map of the human genome.

Authors:
Journal: Nature Date: 2005-10-27 Impact factor: 49.962

Review 3. Next-generation DNA sequencing methods.

Authors: Elaine R Mardis
Journal: Annu Rev Genomics Hum Genet Date: 2008 Impact factor: 8.929

4. Human chromosome analysis and sorting.

Authors: J A Fantes; D K Green
Journal: Methods Mol Biol Date: 1990

5. Long-range linkage on chromosome 6p of VEGF, FKBP5, HLA and TNF alleles associated with transplant rejection.

Authors: Yan Chen; James Cicciarelli; Vera Pravica; Ian V Hutchinson
Journal: Mol Immunol Date: 2009-02-23 Impact factor: 4.407

6. 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

7. Detection of sharing by descent, long-range phasing and haplotype imputation.

Authors: Augustine Kong; Gisli Masson; Michael L Frigge; Arnaldur Gylfason; Pasha Zusmanovich; Gudmar Thorleifsson; Pall I Olason; Andres Ingason; Stacy Steinberg; Thorunn Rafnar; Patrick Sulem; Magali Mouy; Frosti Jonsson; Unnur Thorsteinsdottir; Daniel F Gudbjartsson; Hreinn Stefansson; Kari Stefansson
Journal: Nat Genet Date: 2008-09 Impact factor: 38.330

8. The diploid genome sequence of an individual human.

Authors: Samuel Levy; Granger Sutton; Pauline C Ng; Lars Feuk; Aaron L Halpern; Brian P Walenz; Nelson Axelrod; Jiaqi Huang; Ewen F Kirkness; Gennady Denisov; Yuan Lin; Jeffrey R MacDonald; Andy Wing Chun Pang; Mary Shago; Timothy B Stockwell; Alexia Tsiamouri; Vineet Bafna; Vikas Bansal; Saul A Kravitz; Dana A Busam; Karen Y Beeson; Tina C McIntosh; Karin A Remington; Josep F Abril; John Gill; Jon Borman; Yu-Hui Rogers; Marvin E Frazier; Stephen W Scherer; Robert L Strausberg; J Craig Venter
Journal: PLoS Biol Date: 2007-09-04 Impact factor: 8.029

9. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

Authors: Jonathan K Pritchard; Joseph K Pickrell; Graham Coop
Journal: Curr Biol Date: 2010-02-23 Impact factor: 10.834

Review 10. Long-range control of gene expression: emerging mechanisms and disruption in disease.

Authors: Dirk A Kleinjan; Veronica van Heyningen
Journal: Am J Hum Genet Date: 2004-11-17 Impact factor: 11.025

53 in total

1. A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs.

Authors: Li Ma; Wing Hung Wong; Art B Owen
Journal: Hum Hered Date: 2012-03-02 Impact factor: 0.444

2. Noninvasive whole-genome sequencing of a human fetus.

Authors: Jacob O Kitzman; Matthew W Snyder; Mario Ventura; Alexandra P Lewis; Ruolan Qiu; Lavone E Simmons; Hilary S Gammill; Craig E Rubens; Donna A Santillan; Jeffrey C Murray; Holly K Tabor; Michael J Bamshad; Evan E Eichler; Jay Shendure
Journal: Sci Transl Med Date: 2012-06-06 Impact factor: 17.956

Completely phased genome sequencing through chromosome sorting.

1. Multiple personal genomes await.

2. A haplotype map of the human genome.

Review 3. Next-generation DNA sequencing methods.

4. Human chromosome analysis and sorting.

5. Long-range linkage on chromosome 6p of VEGF, FKBP5, HLA and TNF alleles associated with transplant rejection.

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

7. Detection of sharing by descent, long-range phasing and haplotype imputation.

8. The diploid genome sequence of an individual human.

9. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

Review 10. Long-range control of gene expression: emerging mechanisms and disruption in disease.

1. A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs.

2. Noninvasive whole-genome sequencing of a human fetus.

3. GenomeLaser: fast and accurate haplotyping from pedigree genotypes.

Review 4. Haplotype-resolved genome sequencing: experimental methods and applications.

5. High-resolution whole-genome haplotyping using limited seed data.

6. GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

7. Chromosome-Range Whole-Genome High-Throughput Experimental Haplotyping by Single-Chromosome Microdissection.

8. Recursive organizer (ROR): an analytic framework for sequence-based association analysis.

9. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.

10. An accurate clone-based haplotyping method by overlapping pool sequencing.