Literature DB >> 23940326

Isothermal amplification method for next-generation sequencing.

Zhaochun Ma1, Raymond W Lee, Bin Li, Paul Kenney, Yufang Wang, Jonathan Erikson, Swati Goyal, Kaiqin Lao.   

Abstract

We report an approach for generating immobilized monoclonal templates for next- generation sequencing applications. Our isothermal amplification method is based on a template walking mechanism using a pair of low-melting temperature (Tm) solid-surface homopolymer primers and a low-Tm solution phase primer. The method can generate more than one billion submicrometer-sized colonies in a single lane of a next-generation sequencing flowchip. An alternative paired-end sequencing method using interstrand DNA photo cross-linking to covalently link the complementary strands of the original templates to the solid surface is also demonstrated.

Keywords:  DNA breathing; forming colonies; genome; in situ PCR; polony

Mesh:

Year:  2013        PMID: 23940326      PMCID: PMC3761594          DOI: 10.1073/pnas.1311334110

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


  15 in total

1.  In situ localized amplification and contact replication of many individual DNA molecules.

Authors:  R D Mitra; G M Church
Journal:  Nucleic Acids Res       Date:  1999-12-15       Impact factor: 16.971

2.  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

3.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.

Authors:  Devin Dressman; Hai Yan; Giovanni Traverso; Kenneth W Kinzler; Bert Vogelstein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-11       Impact factor: 11.205

4.  Accurate multiplex polony sequencing of an evolved bacterial genome.

Authors:  Jay Shendure; Gregory J Porreca; Nikos B Reppas; Xiaoxia Lin; John P McCutcheon; Abraham M Rosenbaum; Michael D Wang; Kun Zhang; Robi D Mitra; George M Church
Journal:  Science       Date:  2005-08-04       Impact factor: 47.728

5.  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

6.  Ultrafast reversible photo-cross-linking reaction: toward in situ DNA manipulation.

Authors:  Yoshinaga Yoshimura; Kenzo Fujimoto
Journal:  Org Lett       Date:  2008-06-27       Impact factor: 6.005

7.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Authors:  Anton Valouev; Jeffrey Ichikawa; Thaisan Tonthat; Jeremy Stuart; Swati Ranade; Heather Peckham; Kathy Zeng; Joel A Malek; Gina Costa; Kevin McKernan; Arend Sidow; Andrew Fire; Steven M Johnson
Journal:  Genome Res       Date:  2008-05-13       Impact factor: 9.043

Review 8.  Comparison of next-generation sequencing systems.

Authors:  Lin Liu; Yinhu Li; Siliang Li; Ni Hu; Yimin He; Ray Pong; Danni Lin; Lihua Lu; Maggie Law
Journal:  J Biomed Biotechnol       Date:  2012-07-05

9.  BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies.

Authors:  Milan Fedurco; Anthony Romieu; Scott Williams; Isabelle Lawrence; Gerardo Turcatti
Journal:  Nucleic Acids Res       Date:  2006-02-09       Impact factor: 16.971

10.  Accurate whole human genome sequencing using reversible terminator chemistry.

Authors:  David R Bentley; Shankar Balasubramanian; Harold P Swerdlow; Geoffrey P Smith; John Milton; Clive G Brown; Kevin P Hall; Dirk J Evers; Colin L Barnes; Helen R Bignell; Jonathan M Boutell; Jason Bryant; Richard J Carter; R Keira Cheetham; Anthony J Cox; Darren J Ellis; Michael R Flatbush; Niall A Gormley; Sean J Humphray; Leslie J Irving; Mirian S Karbelashvili; Scott M Kirk; Heng Li; Xiaohai Liu; Klaus S Maisinger; Lisa J Murray; Bojan Obradovic; Tobias Ost; Michael L Parkinson; Mark R Pratt; Isabelle M J Rasolonjatovo; Mark T Reed; Roberto Rigatti; Chiara Rodighiero; Mark T Ross; Andrea Sabot; Subramanian V Sankar; Aylwyn Scally; Gary P Schroth; Mark E Smith; Vincent P Smith; Anastassia Spiridou; Peta E Torrance; Svilen S Tzonev; Eric H Vermaas; Klaudia Walter; Xiaolin Wu; Lu Zhang; Mohammed D Alam; Carole Anastasi; Ify C Aniebo; David M D Bailey; Iain R Bancarz; Saibal Banerjee; Selena G Barbour; Primo A Baybayan; Vincent A Benoit; Kevin F Benson; Claire Bevis; Phillip J Black; Asha Boodhun; Joe S Brennan; John A Bridgham; Rob C Brown; Andrew A Brown; Dale H Buermann; Abass A Bundu; James C Burrows; Nigel P Carter; Nestor Castillo; Maria Chiara E Catenazzi; Simon Chang; R Neil Cooley; Natasha R Crake; Olubunmi O Dada; Konstantinos D Diakoumakos; Belen Dominguez-Fernandez; David J Earnshaw; Ugonna C Egbujor; David W Elmore; Sergey S Etchin; Mark R Ewan; Milan Fedurco; Louise J Fraser; Karin V Fuentes Fajardo; W Scott Furey; David George; Kimberley J Gietzen; Colin P Goddard; George S Golda; Philip A Granieri; David E Green; David L Gustafson; Nancy F Hansen; Kevin Harnish; Christian D Haudenschild; Narinder I Heyer; Matthew M Hims; Johnny T Ho; Adrian M Horgan; Katya Hoschler; Steve Hurwitz; Denis V Ivanov; Maria Q Johnson; Terena James; T A Huw Jones; Gyoung-Dong Kang; Tzvetana H Kerelska; Alan D Kersey; Irina Khrebtukova; Alex P Kindwall; Zoya Kingsbury; Paula I Kokko-Gonzales; Anil Kumar; Marc A Laurent; Cynthia T Lawley; Sarah E Lee; Xavier Lee; Arnold K Liao; Jennifer A Loch; Mitch Lok; Shujun Luo; Radhika M Mammen; John W Martin; Patrick G McCauley; Paul McNitt; Parul Mehta; Keith W Moon; Joe W Mullens; Taksina Newington; Zemin Ning; Bee Ling Ng; Sonia M Novo; Michael J O'Neill; Mark A Osborne; Andrew Osnowski; Omead Ostadan; Lambros L Paraschos; Lea Pickering; Andrew C Pike; Alger C Pike; D Chris Pinkard; Daniel P Pliskin; Joe Podhasky; Victor J Quijano; Come Raczy; Vicki H Rae; Stephen R Rawlings; Ana Chiva Rodriguez; Phyllida M Roe; John Rogers; Maria C Rogert Bacigalupo; Nikolai Romanov; Anthony Romieu; Rithy K Roth; Natalie J Rourke; Silke T Ruediger; Eli Rusman; Raquel M Sanches-Kuiper; Martin R Schenker; Josefina M Seoane; Richard J Shaw; Mitch K Shiver; Steven W Short; Ning L Sizto; Johannes P Sluis; Melanie A Smith; Jean Ernest Sohna Sohna; Eric J Spence; Kim Stevens; Neil Sutton; Lukasz Szajkowski; Carolyn L Tregidgo; Gerardo Turcatti; Stephanie Vandevondele; Yuli Verhovsky; Selene M Virk; Suzanne Wakelin; Gregory C Walcott; Jingwen Wang; Graham J Worsley; Juying Yan; Ling Yau; Mike Zuerlein; Jane Rogers; James C Mullikin; Matthew E Hurles; Nick J McCooke; John S West; Frank L Oaks; Peter L Lundberg; David Klenerman; Richard Durbin; Anthony J Smith
Journal:  Nature       Date:  2008-11-06       Impact factor: 49.962

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  5 in total

1.  A computational framework for DNA sequencing microscopy.

Authors:  Ian T Hoffecker; Yunshi Yang; Giulio Bernardinelli; Pekka Orponen; Björn Högberg
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-04       Impact factor: 11.205

2.  Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.

Authors:  Diana Zhang; Terry Huang; Philip S Lukeman; Paul J Paukstelis
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 16.971

3.  Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome.

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Journal:  Biol Direct       Date:  2016-01-12       Impact factor: 4.540

Review 4.  Methods and novel technology for microRNA quantification in colorectal cancer screening.

Authors:  Laura Moody; Hongshan He; Yuan-Xiang Pan; Hong Chen
Journal:  Clin Epigenetics       Date:  2017-10-24       Impact factor: 6.551

5.  Clonal rolling circle amplification for on-chip DNA cluster generation.

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Journal:  Biol Methods Protoc       Date:  2017-05-12
  5 in total

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