Literature DB >> 16169928

Simple, robust methods for high-throughput nanoliter-scale DNA sequencing.

Duane E Smailus1, Andre Marziali, Philip Dextras, Marco A Marra, Robert A Holt.   

Abstract

We have developed high-throughput DNA sequencing methods that generate high quality data from reactions as small as 400 nL, providing an approximate order of magnitude reduction in reagent use relative to standard protocols. Sequencing of clones from plasmid, fosmid, and BAC libraries yielded read lengths (PHRED20 bases) of 765 +/- 172 (n = 10,272), 621 +/- 201 (n = 1824), and 647 +/- 189 (n = 568), respectively. Implementation of these procedures at high-throughput genome centers could have a substantial impact on the amount of data that can be generated per unit cost.

Mesh:

Year:  2005        PMID: 16169928      PMCID: PMC1240088          DOI: 10.1101/gr.4221805

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


  12 in total

1.  Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.

Authors:  S Brenner; M Johnson; J Bridgham; G Golda; D H Lloyd; D Johnson; S Luo; S McCurdy; M Foy; M Ewan; R Roth; D George; S Eletr; G Albrecht; E Vermaas; S R Williams; K Moon; T Burcham; M Pallas; R B DuBridge; J Kirchner; K Fearon; J Mao; K Corcoran
Journal:  Nat Biotechnol       Date:  2000-06       Impact factor: 54.908

2.  An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones.

Authors:  Yaron S N Butterfield; Marco A Marra; Jennifer K Asano; Susanna Y Chan; Ranabir Guin; Martin I Krzywinski; Soo Sen Lee; Kim W K MacDonald; Carrie A Mathewson; Teika E Olson; Pawan K Pandoh; Anna-Liisa Prabhu; Angelique Schnerch; Ursula Skalska; Duane E Smailus; Jeff M Stott; Miranda I Tsai; George S Yang; Scott D Zuyderduyn; Jacqueline E Schein; Steven J M Jones
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

3.  Sequence information can be obtained from single DNA molecules.

Authors:  Ido Braslavsky; Benedict Hebert; Emil Kartalov; Stephen R Quake
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-21       Impact factor: 11.205

4.  Zero-mode waveguides for single-molecule analysis at high concentrations.

Authors:  M J Levene; J Korlach; S W Turner; M Foquet; H G Craighead; W W Webb
Journal:  Science       Date:  2003-01-31       Impact factor: 47.728

5.  Fluorescent in situ sequencing on polymerase colonies.

Authors:  Robi D Mitra; Jay Shendure; Jerzy Olejnik; George M Church
Journal:  Anal Biochem       Date:  2003-09-01       Impact factor: 3.365

Review 6.  DNA sequencing by capillary electrophoresis.

Authors:  N J Dovichi
Journal:  Electrophoresis       Date:  1997-11       Impact factor: 3.535

7.  Fluorescence detection in automated DNA sequence analysis.

Authors:  L M Smith; J Z Sanders; R J Kaiser; P Hughes; C Dodd; C R Connell; C Heiner; S B Kent; L E Hood
Journal:  Nature       Date:  1986 Jun 12-18       Impact factor: 49.962

8.  The synthesis of oligonucleotides containing an aliphatic amino group at the 5' terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis.

Authors:  L M Smith; S Fung; M W Hunkapiller; T J Hunkapiller; L E Hood
Journal:  Nucleic Acids Res       Date:  1985-04-11       Impact factor: 16.971

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.  High-throughput sequencing: a failure mode analysis.

Authors:  George S Yang; Jeffery M Stott; Duane Smailus; Sarah A Barber; Miruna Balasundaram; Marco A Marra; Robert A Holt
Journal:  BMC Genomics       Date:  2005-01-04       Impact factor: 3.969

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  4 in total

1.  Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines.

Authors:  Jaswinder Khattra; Allen D Delaney; Yongjun Zhao; Asim Siddiqui; Jennifer Asano; Helen McDonald; Pawan Pandoh; Noreen Dhalla; Anna-Liisa Prabhu; Kevin Ma; Stephanie Lee; Adrian Ally; Angela Tam; Danne Sa; Sean Rogers; David Charest; Jeff Stott; Scott Zuyderduyn; Richard Varhol; Connie Eaves; Steven Jones; Robert Holt; Martin Hirst; Pamela A Hoodless; Marco A Marra
Journal:  Genome Res       Date:  2006-11-29       Impact factor: 9.043

2.  Gene discovery and annotation using LCM-454 transcriptome sequencing.

Authors:  Scott J Emrich; W Brad Barbazuk; Li Li; Patrick S Schnable
Journal:  Genome Res       Date:  2006-11-09       Impact factor: 9.043

3.  A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination.

Authors:  Perseus I Missirlis; Duane E Smailus; Robert A Holt
Journal:  BMC Genomics       Date:  2006-04-04       Impact factor: 3.969

4.  Constructing large DNA segments by iterative clone recombination.

Authors:  Duane E Smailus; Rene L Warren; Robert A Holt
Journal:  Syst Synth Biol       Date:  2008-01-24
  4 in total

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