Literature DB >> 25699289

Accuracy of Next Generation Sequencing Platforms.

Edward J Fox1, Kate S Reid-Bayliss2, Mary J Emond, Lawrence A Loeb.   

Abstract

Next-generation DNA sequencing has revolutionized genomic studies and is driving the implementation of precision diagnostics. The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates. A Several single molecule barcoding strategies have been propose to reduce the overall error frequency. A Duplex Sequencing additionally exploits the fact that DNA is double-strand, with one strand reciprocally encoding the sequence information of its complement, and can eliminate nearly all sequencing errors by comparing the sequence of individually tagged amplicons derived from one strand of DNA with that of its complementary strand. This method reduces errors to fewer than one per ten million nucleotides sequenced.

Entities:  

Keywords:  Accuracy; Duplex sequencing; Next-generation DNA sequencing; Precision medicine

Year:  2014        PMID: 25699289      PMCID: PMC4331009          DOI: 10.4172/jngsa.1000106

Source DB:  PubMed          Journal:  Next Gener Seq Appl        ISSN: 2469-9853


  61 in total

1.  Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.

Authors:  Katsuyuki Shiroguchi; Tony Z Jia; Peter A Sims; X Sunney Xie
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-09       Impact factor: 11.205

2.  Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID.

Authors:  Cassandra B Jabara; Corbin D Jones; Jeffrey Roach; Jeffrey A Anderson; Ronald Swanstrom
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-30       Impact factor: 11.205

3.  Counting absolute numbers of molecules using unique molecular identifiers.

Authors:  Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

4.  Encoding PCR products with batch-stamps and barcodes.

Authors:  Megan L McCloskey; Reinhard Stöger; R Scott Hansen; Charles D Laird
Journal:  Biochem Genet       Date:  2007-10-23       Impact factor: 1.890

5.  High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.

Authors:  Dianne I Lou; Jeffrey A Hussmann; Ross M McBee; Ashley Acevedo; Raul Andino; William H Press; Sara L Sawyer
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-15       Impact factor: 11.205

6.  A SNP discovery method to assess variant allele probability from next-generation resequencing data.

Authors:  Yufeng Shen; Zhengzheng Wan; Cristian Coarfa; Rafal Drabek; Lei Chen; Elizabeth A Ostrowski; Yue Liu; George M Weinstock; David A Wheeler; Richard A Gibbs; Fuli Yu
Journal:  Genome Res       Date:  2009-12-17       Impact factor: 9.043

7.  Non-degenerate graphical representation of DNA sequences and its applications to phylogenetic analysis.

Authors:  Yan Yang; Yingying Zhang; Meiduo Jia; Chun Li; Liangyu Meng
Journal:  Comb Chem High Throughput Screen       Date:  2013-09       Impact factor: 1.339

Review 8.  Human cancers express mutator phenotypes: origin, consequences and targeting.

Authors:  Lawrence A Loeb
Journal:  Nat Rev Cancer       Date:  2011-05-19       Impact factor: 60.716

9.  Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study.

Authors:  Rossa W K Chiu; Ranjit Akolekar; Yama W L Zheng; Tak Y Leung; Hao Sun; K C Allen Chan; Fiona M F Lun; Attie T J I Go; Elizabeth T Lau; William W K To; Wing C Leung; Rebecca Y K Tang; Sidney K C Au-Yeung; Helena Lam; Yu Y Kung; Xiuqing Zhang; John M G van Vugt; Ryoko Minekawa; Mary H Y Tang; Jun Wang; Cees B M Oudejans; Tze K Lau; Kypros H Nicolaides; Y M Dennis Lo
Journal:  BMJ       Date:  2011-01-11

10.  A method for counting PCR template molecules with application to next-generation sequencing.

Authors:  James A Casbon; Robert J Osborne; Sydney Brenner; Conrad P Lichtenstein
Journal:  Nucleic Acids Res       Date:  2011-04-13       Impact factor: 16.971

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  50 in total

Review 1.  Next-generation sequencing in clinical virology: Discovery of new viruses.

Authors:  Sibnarayan Datta; Raghvendra Budhauliya; Bidisha Das; Soumya Chatterjee; Vijay Veer
Journal:  World J Virol       Date:  2015-08-12

2.  High-Throughput Genotyping Technologies in Plant Taxonomy.

Authors:  Monica F Danilevicz; Cassandria G Tay Fernandez; Jacob I Marsh; Philipp E Bayer; David Edwards
Journal:  Methods Mol Biol       Date:  2021

Review 3.  A Primer on Infectious Disease Bacterial Genomics.

Authors:  Tarah Lynch; Aaron Petkau; Natalie Knox; Morag Graham; Gary Van Domselaar
Journal:  Clin Microbiol Rev       Date:  2016-09-07       Impact factor: 26.132

4.  Sex and Mitonuclear Adaptation in Experimental Caenorhabditis elegans Populations.

Authors:  Riana I Wernick; Stephen F Christy; Dana K Howe; Jennifer A Sullins; Joseph F Ramirez; Maura Sare; McKenna J Penley; Levi T Morran; Dee R Denver; Suzanne Estes
Journal:  Genetics       Date:  2019-01-22       Impact factor: 4.562

Review 5.  Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.

Authors:  Yaqiong Jin; Geng Chen; Wenming Xiao; Huixiao Hong; Joshua Xu; Yongli Guo; Wenzhong Xiao; Tieliu Shi; Leming Shi; Weida Tong; Baitang Ning
Journal:  Sci China Life Sci       Date:  2019-05-20       Impact factor: 6.038

Review 6.  Long-read human genome sequencing and its applications.

Authors:  Glennis A Logsdon; Mitchell R Vollger; Evan E Eichler
Journal:  Nat Rev Genet       Date:  2020-06-05       Impact factor: 53.242

7.  Shouji: a fast and efficient pre-alignment filter for sequence alignment.

Authors:  Mohammed Alser; Hasan Hassan; Akash Kumar; Onur Mutlu; Can Alkan
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

8.  ACKR1 Alleles at 5.6 kb in a Well-Characterized Renewable US Food and Drug Administration (FDA) Reference Panel for Standardization of Blood Group Genotyping.

Authors:  Kshitij Srivastava; Pavel P Khil; Emilia Sippert; Evgeniya Volkova; John P Dekker; Maria Rios; Willy A Flegel
Journal:  J Mol Diagn       Date:  2020-07-17       Impact factor: 5.568

9.  Why Cockayne syndrome patients do not get cancer despite their DNA repair deficiency.

Authors:  Kate S Reid-Bayliss; Sarah T Arron; Lawrence A Loeb; Vladimir Bezrookove; James E Cleaver
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-19       Impact factor: 11.205

10.  geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data.

Authors:  Matthias Döring; Joachim Büch; Georg Friedrich; Alejandro Pironti; Prabhav Kalaghatgi; Elena Knops; Eva Heger; Martin Obermeier; Martin Däumer; Alexander Thielen; Rolf Kaiser; Thomas Lengauer; Nico Pfeifer
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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