Literature DB >> 14973330

Unlocking hidden genomic sequence.

Jonathan M Keith1, Duncan A E Cochran, Gita H Lala, Peter Adams, Darryn Bryant, Keith R Mitchelson.   

Abstract

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs.

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Year:  2004        PMID: 14973330      PMCID: PMC373418          DOI: 10.1093/nar/gnh022

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  43 in total

1.  Regions of genomic instability on 22q11 and 11q23 as the etiology for the recurrent constitutional t(11;22).

Authors:  H Kurahashi; T H Shaikh; P Hu; B A Roe; B S Emanuel; M L Budarf
Journal:  Hum Mol Genet       Date:  2000-07-01       Impact factor: 6.150

Review 2.  Survey and summary: The applications of universal DNA base analogues.

Authors:  D Loakes
Journal:  Nucleic Acids Res       Date:  2001-06-15       Impact factor: 16.971

3.  A simulated annealing algorithm for finding consensus sequences.

Authors:  Jonathan M Keith; Peter Adams; Darryn Bryant; Dirk P Kroese; Keith R Mitchelson; Duncan A E Cochran; Gita H Lala
Journal:  Bioinformatics       Date:  2002-11       Impact factor: 6.937

4.  Slippage synthesis of simple sequence DNA.

Authors:  C Schlötterer; D Tautz
Journal:  Nucleic Acids Res       Date:  1992-01-25       Impact factor: 16.971

5.  DNA compression caused by an upstream point mutation.

Authors:  B G Weinshenker; D D Hebrink; A M Gacy; C T McMurray
Journal:  Biotechniques       Date:  1998-07       Impact factor: 1.993

6.  In vitro expansion of GGC:GCC repeats: identification of the preferred strand of expansion.

Authors:  J Ji; N J Clegg; K R Peterson; A L Jackson; C D Laird; L A Loeb
Journal:  Nucleic Acids Res       Date:  1996-07-15       Impact factor: 16.971

7.  Comparative mutagenicities of N6-methoxy-2,6-diaminopurine and N6-methoxyaminopurine 2'-deoxyribonucleosides and their 5'-triphosphates.

Authors:  F Hill; D M Williams; D Loakes; D M Brown
Journal:  Nucleic Acids Res       Date:  1998-03-01       Impact factor: 16.971

8.  Mutants affecting nucleotide recognition by T7 DNA polymerase.

Authors:  M J Donlin; K A Johnson
Journal:  Biochemistry       Date:  1994-12-13       Impact factor: 3.162

9.  An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues.

Authors:  M Zaccolo; D M Williams; D M Brown; E Gherardi
Journal:  J Mol Biol       Date:  1996-02-02       Impact factor: 5.469

10.  A methylated human 9-kb repetitive sequence on acrocentric chromosomes is homologous to a subtelomeric repeat in chimpanzees.

Authors:  D Thoraval; J Asakawa; M Kodaira; C Chang; E Radany; R Kuick; B Lamb; B Richardson; J V Neel; T Glover; S Hanash
Journal:  Proc Natl Acad Sci U S A       Date:  1996-04-30       Impact factor: 11.205

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  9 in total

1.  An intermediate grade of finished genomic sequence suitable for comparative analyses.

Authors:  Robert W Blakesley; Nancy F Hansen; James C Mullikin; Pamela J Thomas; Jennifer C McDowell; Baishali Maskeri; Alice C Young; Beatrice Benjamin; Shelise Y Brooks; Bradley I Coleman; Jyoti Gupta; Shi-Ling Ho; Eric M Karlins; Quino L Maduro; Sirintorn Stantripop; Cyrus Tsurgeon; Jennifer L Vogt; Michelle A Walker; Catherine A Masiello; Xiaobin Guan; Gerard G Bouffard; Eric D Green
Journal:  Genome Res       Date:  2004-10-12       Impact factor: 9.043

2.  Genome assembly quality: assessment and improvement using the neutral indel model.

Authors:  Stephen Meader; LaDeana W Hillier; Devin Locke; Chris P Ponting; Gerton Lunter
Journal:  Genome Res       Date:  2010-03-19       Impact factor: 9.043

3.  Facilitated sequence counting and assembly by template mutagenesis.

Authors:  Dan Levy; Michael Wigler
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-13       Impact factor: 11.205

4.  Trial and error: how the unclonable human mitochondrial genome was cloned in yeast.

Authors:  Brian W Bigger; Ai-Yin Liao; Ana Sergijenko; Charles Coutelle
Journal:  Pharm Res       Date:  2011-07-09       Impact factor: 4.200

5.  Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment.

Authors:  Kevin J McKernan; Jessica Spangler; Lei Zhang; Vasisht Tadigotla; Stephen McLaughlin; Jason Warner; Amir Zare; Richard G Boles
Journal:  PLoS One       Date:  2014-05-02       Impact factor: 3.240

6.  Sequencing intractable DNA to close microbial genomes.

Authors:  Richard A Hurt; Steven D Brown; Mircea Podar; Anthony V Palumbo; Dwayne A Elias
Journal:  PLoS One       Date:  2012-07-31       Impact factor: 3.240

7.  An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.

Authors:  Botond Sipos; Tim Massingham; Adrian M Stütz; Nick Goldman
Journal:  PLoS One       Date:  2012-08-17       Impact factor: 3.240

8.  Characterizing and measuring bias in sequence data.

Authors:  Michael G Ross; Carsten Russ; Maura Costello; Andrew Hollinger; Niall J Lennon; Ryan Hegarty; Chad Nusbaum; David B Jaffe
Journal:  Genome Biol       Date:  2013-05-29       Impact factor: 13.583

9.  Development of a high sensitivity TaqMan-based PCR assay for the specific detection of Mycobacterium tuberculosis complex in both pulmonary and extrapulmonary specimens.

Authors:  Hsin-Yao Wang; Jang-Jih Lu; Ching-Yu Chang; Wen-Pin Chou; Jason Chia-Hsun Hsieh; Chien-Ru Lin; Min-Hsien Wu
Journal:  Sci Rep       Date:  2019-01-14       Impact factor: 4.379

  9 in total

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