Literature DB >> 19582764

Improved protocols for the illumina genome analyzer sequencing system.

Michael A Quail1, Harold Swerdlow, Daniel J Turner.   

Abstract

In this unit, we describe a set of improvements we have made to the standard Illumina Genome Analyzer protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and reliably obtain high yields of data.

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Year:  2009        PMID： 19582764      PMCID： PMC3849550          DOI： 10.1002/0471142905.hg1802s62

Source DB:  PubMed          Journal:  Curr Protoc Hum Genet        ISSN： 1934-8258


  19 in total

1.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

2.  A sequencing method based on real-time pyrophosphate.

Authors:  M Ronaghi; M Uhlén; P Nyrén
Journal:  Science       Date:  1998-07-17       Impact factor: 47.728

3.  A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones.

Authors:  J Riley; R Butler; D Ogilvie; R Finniear; D Jenner; S Powell; R Anand; J C Smith; A F Markham
Journal:  Nucleic Acids Res       Date:  1990-05-25       Impact factor: 16.971

4.  Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation.

Authors:  Michael A Quail; Yong Gu; Harold Swerdlow; Matthew Mayho
Journal:  Electrophoresis       Date:  2012-11-12       Impact factor: 3.535

5.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

6.  Solid-phase reversible immobilization for the isolation of PCR products.

Authors:  M M DeAngelis; D G Wang; T L Hawkins
Journal:  Nucleic Acids Res       Date:  1995-11-25       Impact factor: 16.971

7.  DNA purification and isolation using a solid-phase.

Authors:  T L Hawkins; T O'Connor-Morin; A Roy; C Santillan
Journal:  Nucleic Acids Res       Date:  1994-10-25       Impact factor: 16.971

8.  Finishing the euchromatic sequence of the human genome.

Authors: 
Journal:  Nature       Date:  2004-10-21       Impact factor: 49.962

9.  DNA sequencing with chain-terminating inhibitors.

Authors:  F Sanger; S Nicklen; A R Coulson
Journal:  Proc Natl Acad Sci U S A       Date:  1977-12       Impact factor: 11.205

10.  From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing.

Authors:  Matthias Meyer; Adrian W Briggs; Tomislav Maricic; Barbara Höber; Barbara Höffner; Johannes Krause; Antje Weihmann; Svante Pääbo; Michael Hofreiter
Journal:  Nucleic Acids Res       Date:  2007-12-15       Impact factor: 16.971
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  49 in total

Review 1.  Clinical implementation of comprehensive strategies to characterize cancer genomes: opportunities and challenges.

Authors:  Laura E MacConaill; Paul Van Hummelen; Matthew Meyerson; William C Hahn
Journal:  Cancer Discov       Date:  2011-09       Impact factor: 39.397

2.  Automated Gel Size Selection to Improve the Quality of Next-generation Sequencing Libraries Prepared from Environmental Water Samples.

Authors:  Miguel I Uyaguari-Diaz; Jared R Slobodan; Matthew J Nesbitt; Matthew A Croxen; Judith Isaac-Renton; Natalie A Prystajecky; Patrick Tang
Journal:  J Vis Exp       Date:  2015-04-17       Impact factor: 1.355

Review 3.  High-throughput sequencing in mutation detection: A new generation of genotoxicity tests?

Authors:  Alexander Y Maslov; Wilber Quispe-Tintaya; Tatyana Gorbacheva; Ryan R White; Jan Vijg
Journal:  Mutat Res       Date:  2015-04-20       Impact factor: 2.433

Review 4.  Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants.

Authors:  Michael Gundry; Jan Vijg
Journal:  Mutat Res       Date:  2011-10-12       Impact factor: 2.433

5.  High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome.

Authors:  Sam Alsford; Daniel J Turner; Samson O Obado; Alejandro Sanchez-Flores; Lucy Glover; Matthew Berriman; Christiane Hertz-Fowler; David Horn
Journal:  Genome Res       Date:  2011-03-01       Impact factor: 9.043

6.  Genome-wide chromatin immunoprecipitation-sequencing in Plasmodium.

Authors:  Jose-Juan Lopez-Rubio; T Nicolai Siegel; Artur Scherf
Journal:  Methods Mol Biol       Date:  2013

7.  Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

Authors:  Stephen S Gisselbrecht; Luis A Barrera; Martin Porsch; Anton Aboukhalil; Preston W Estep; Anastasia Vedenko; Alexandre Palagi; Yongsok Kim; Xianmin Zhu; Brian W Busser; Caitlin E Gamble; Antonina Iagovitina; Aditi Singhania; Alan M Michelson; Martha L Bulyk
Journal:  Nat Methods       Date:  2013-07-14       Impact factor: 28.547

8.  Increased CNV-region deletions in mild cognitive impairment (MCI) and Alzheimer's disease (AD) subjects in the ADNI sample.

Authors:  Guia Guffanti; Federica Torri; Jerod Rasmussen; Andrew P Clark; Anita Lakatos; Jessica A Turner; James H Fallon; Andrew J Saykin; Michael Weiner; Marquis P Vawter; James A Knowles; Steven G Potkin; Fabio Macciardi
Journal:  Genomics       Date:  2013-04-11       Impact factor: 5.736

Review 9.  Aging genomes: a necessary evil in the logic of life.

Authors:  Jan Vijg
Journal:  Bioessays       Date:  2014-01-25       Impact factor: 4.345

10.  Detection of EGFRvIII mutant DNA in the peripheral blood of brain tumor patients.

Authors:  Mohamad A Salkeni; Ahmad Zarzour; Tracy Y Ansay; Christopher M McPherson; Ronald E Warnick; Olivier Rixe; El Mustapha Bahassi
Journal:  J Neurooncol       Date:  2013-07-23       Impact factor: 4.130
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