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Literature DB >> 12097348

Single nucleotide polymorphism mapping using genome-wide unique sequences.

Leslie Y Y Chen¹, Szu-Hsien Lu, Edward S C Shih, Ming-Jing Hwang.

Abstract

As more and more genomic DNAs are sequenced to characterize human genetic variations, the demand for a very fast and accurate method to genomically position these DNA sequences is high. We have developed a new mapping method that does not require sequence alignment. In this method, we first identified DNA fragments of 15 bp in length that are unique in the human genome and then used them to position single nucleotide polymorphism (SNP) sequences. By use of four desktop personal computers with AMD K7 (1 GHz) processors, our new method mapped more than 1.6 million SNP sequences in 20 hr and achieved a very good agreement with mapping results from alignment-based methods.

Entities: Disease Species

Mesh：

Substances：
Genetic Markers

Year: 2002 PMID： 12097348 PMCID： PMC186620 DOI： 10.1101/gr.224502

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

26 in total

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Journal: Nat Genet Date: 1999-12 Impact factor: 38.330

2. MaskerAid: a performance enhancement to RepeatMasker.

Authors: J A Bedell; I Korf; W Gish
Journal: Bioinformatics Date: 2000-11 Impact factor: 6.937

3. Single-nucleotide polymorphisms in the public domain: how useful are they?

Authors: G Marth; R Yeh; M Minton; R Donaldson; Q Li; S Duan; R Davenport; R D Miller; P Y Kwok
Journal: Nat Genet Date: 2001-04 Impact factor: 38.330

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Journal: Nature Date: 2001-02-15 Impact factor: 49.962

5. Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries.

Authors: C Gemünd; C Ramu; B Altenberg-Greulich; T J Gibson
Journal: Nucleic Acids Res Date: 2001-03-15 Impact factor: 16.971

6. An SNP map of human chromosome 22.

Authors: J C Mullikin; S E Hunt; C G Cole; B J Mortimore; C M Rice; J Burton; L H Matthews; R Pavitt; R W Plumb; S K Sims; R M Ainscough; J Attwood; J M Bailey; K Barlow; R M Bruskiewich; P N Butcher; N P Carter; Y Chen; C M Clee; P C Coggill; J Davies; R M Davies; E Dawson; M D Francis; A A Joy; R G Lamble; C F Langford; J Macarthy; V Mall; A Moreland; E K Overton-Larty; M T Ross; L C Smith; C A Steward; J E Sulston; E J Tinsley; K J Turney; D L Willey; G D Wilson; A A McMurray; I Dunham; J Rogers; D R Bentley
Journal: Nature Date: 2000-09-28 Impact factor: 49.962

7. An SNP map of the human genome generated by reduced representation shotgun sequencing.

Authors: D Altshuler; V J Pollara; C R Cowles; W J Van Etten; J Baldwin; L Linton; E S Lander
Journal: Nature Date: 2000-09-28 Impact factor: 49.962

8. A DNA polymorphism discovery resource for research on human genetic variation.

Authors: F S Collins; L D Brooks; A Chakravarti
Journal: Genome Res Date: 1998-12 Impact factor: 9.043

9. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

Authors: R Sachidanandam; D Weissman; S C Schmidt; J M Kakol; L D Stein; G Marth; S Sherry; J C Mullikin; B J Mortimore; D L Willey; S E Hunt; C G Cole; P C Coggill; C M Rice; Z Ning; J Rogers; D R Bentley; P Y Kwok; E R Mardis; R T Yeh; B Schultz; L Cook; R Davenport; M Dante; L Fulton; L Hillier; R H Waterston; J D McPherson; B Gilman; S Schaffner; W J Van Etten; D Reich; J Higgins; M J Daly; B Blumenstiel; J Baldwin; N Stange-Thomann; M C Zody; L Linton; E S Lander; D Altshuler
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

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Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

3 in total