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Literature DB >> 19198595

Direct determination of haplotypes from single DNA molecules.

Ming Xiao¹, Eunice Wan, Catherine Chu, Wen-Chi Hsueh, Yang Cao, Pui-Yan Kwok.

Abstract

Determining the long-range haplotypes in a diploid individual is a major technical challenge. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual human DNA molecules simultaneously. We demonstrate the utility of this technology by accurately determining the haplotypes consisting of up to 16 single-nucleotide polymorphisms in genomic regions up to 50 kilobases.

Entities: CellLine Chemical Disease Gene Mutation Species

Mesh：

Substances：

Year: 2009 PMID： 19198595 PMCID： PMC3880790 DOI： 10.1038/nmeth.1301

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

15 in total

1. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies.

Authors: J A Douglas; M Boehnke; E Gillanders; J M Trent; S B Gruber
Journal: Nat Genet Date: 2001-08 Impact factor: 38.330

2. Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes.

Authors: Carola Burgtorf; Pamela Kepper; Margret Hoehe; Carsten Schmitt; Richard Reinhardt; Hans Lehrach; Sascha Sauer
Journal: Genome Res Date: 2003-12 Impact factor: 9.043

3. Digital genotyping and haplotyping with polymerase colonies.

Authors: Robi D Mitra; Vincent L Butty; Jay Shendure; Benjamin R Williams; David E Housman; George M Church
Journal: Proc Natl Acad Sci U S A Date: 2003-05-02 Impact factor: 11.205

4. Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers.

Authors: David Latorra; Krista Campbell; Andreas Wolter; J Michael Hurley
Journal: Hum Mutat Date: 2003-07 Impact factor: 4.878

5. Molecular haplotyping at high throughput.

Authors: Jörg Tost; Ole Brandt; Francis Boussicault; David Derbala; Christophe Caloustian; Doris Lechner; Ivo Glynne Gut
Journal: Nucleic Acids Res Date: 2002-10-01 Impact factor: 16.971

6. A vision for the future of genomics research.

Authors: Francis S Collins; Eric D Green; Alan E Guttmacher; Mark S Guyer
Journal: Nature Date: 2003-04-14 Impact factor: 49.962

Review 7. Single-molecule analysis for molecular haplotyping.

Authors: Pui-Yan Kwok; Ming Xiao
Journal: Hum Mutat Date: 2004-05 Impact factor: 4.878

8. Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization.

Authors: Ahmet Yildiz; Joseph N Forkey; Sean A McKinney; Taekjip Ha; Yale E Goldman; Paul R Selvin
Journal: Science Date: 2003-06-05 Impact factor: 47.728

9. A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis.

Authors: Cynthia Helms; Li Cao; James G Krueger; Ellen M Wijsman; Francesca Chamian; Derek Gordon; Michael Heffernan; Jil A Wright Daw; Jason Robarge; Jurg Ott; Pui-Yan Kwok; Alan Menter; Anne M Bowcock
Journal: Nat Genet Date: 2003-11-09 Impact factor: 38.330

10. 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

19 in total

Direct determination of haplotypes from single DNA molecules.

1. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies.

2. Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes.

3. Digital genotyping and haplotyping with polymerase colonies.

4. Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers.

5. Molecular haplotyping at high throughput.

6. A vision for the future of genomics research.

Review 7. Single-molecule analysis for molecular haplotyping.

8. Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization.

9. A putative RUNX1 binding site variant between SLC9A3R1 and NAT9 is associated with susceptibility to psoriasis.

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

Review 1. Allele-specific DNA methylation: beyond imprinting.

2. Completely phased genome sequencing through chromosome sorting.

Review 3. Haplotype-resolved genome sequencing: experimental methods and applications.

4. Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point.

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

6. Whole-genome molecular haplotyping of single cells.

7. Gold nanoparticles for high-throughput genotyping of long-range haplotypes.

8. Direct determination of molecular haplotypes by chromosome microdissection.

9. Experimental generation of SNP haplotype signatures in patients with sickle cell anaemia.

10. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA.