Literature DB >> 27076659

Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis.

Robyn S Lee1,2,3, Marcel A Behr4,3,5.   

Abstract

When using genome sequencing for molecular epidemiology, short sequence reads are aligned to an arbitrary reference strain to detect single nucleotide polymorphisms. We investigated whether reference genome selection influences epidemiological inferences of Mycobacterium tuberculosis transmission by aligning sequence reads from 162 closely related lineage 4 (Euro-American) isolates to 7 different genomes. Phylogenetic trees were consistent with use of all but the most divergent genomes, suggesting that reference choice can be based on considerations other than M. tuberculosis lineage.
Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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Year:  2016        PMID： 27076659      PMCID： PMC4922084          DOI： 10.1128/JCM.00364-16

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  26 in total

1.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

2.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

3.  Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases.

Authors:  K Tamura
Journal:  Mol Biol Evol       Date:  1992-07       Impact factor: 16.240

4.  Complete genome sequences of Mycobacterium tuberculosis strains CCDC5079 and CCDC5080, which belong to the Beijing family.

Authors:  Yuanyuan Zhang; Chen Chen; Jie Liu; Haijun Deng; Aizhen Pan; Lishui Zhang; Xiuqin Zhao; Mingxiang Huang; Bing Lu; Haiyan Dong; Pengcheng Du; Weijun Chen; KangLin Wan
Journal:  J Bacteriol       Date:  2011-10       Impact factor: 3.490

Review 5.  The bacterial pan-genome:a new paradigm in microbiology.

Authors:  Alex Mira; Ana B Martín-Cuadrado; Giuseppe D'Auria; Francisco Rodríguez-Valera
Journal:  Int Microbiol       Date:  2010-06       Impact factor: 2.479

6.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.

Authors:  Jennifer L Gardy; James C Johnston; Shannan J Ho Sui; Victoria J Cook; Lena Shah; Elizabeth Brodkin; Shirley Rempel; Richard Moore; Yongjun Zhao; Robert Holt; Richard Varhol; Inanc Birol; Marcus Lem; Meenu K Sharma; Kevin Elwood; Steven J M Jones; Fiona S L Brinkman; Robert C Brunham; Patrick Tang
Journal:  N Engl J Med       Date:  2011-02-24       Impact factor: 91.245

7.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

8.  The complete genome sequence of Mycobacterium bovis.

Authors:  Thierry Garnier; Karin Eiglmeier; Jean-Christophe Camus; Nadine Medina; Huma Mansoor; Melinda Pryor; Stephanie Duthoy; Sophie Grondin; Celine Lacroix; Christel Monsempe; Sylvie Simon; Barbara Harris; Rebecca Atkin; Jon Doggett; Rebecca Mayes; Lisa Keating; Paul R Wheeler; Julian Parkhill; Bart G Barrell; Stewart T Cole; Stephen V Gordon; R Glyn Hewinson
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-03       Impact factor: 11.205

9.  Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.

Authors:  R D Fleischmann; D Alland; J A Eisen; L Carpenter; O White; J Peterson; R DeBoy; R Dodson; M Gwinn; D Haft; E Hickey; J F Kolonay; W C Nelson; L A Umayam; M Ermolaeva; S L Salzberg; A Delcher; T Utterback; J Weidman; H Khouri; J Gill; A Mikula; W Bishai; W R Jacobs; J C Venter; C M Fraser
Journal:  J Bacteriol       Date:  2002-10       Impact factor: 3.490

10.  Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints.

Authors:  Stefan Niemann; Claudio U Köser; Sebastien Gagneux; Claudia Plinke; Susanne Homolka; Helen Bignell; Richard J Carter; R Keira Cheetham; Anthony Cox; Niall A Gormley; Paula Kokko-Gonzales; Lisa J Murray; Roberto Rigatti; Vincent P Smith; Felix P M Arends; Helen S Cox; Geoff Smith; John A C Archer
Journal:  PLoS One       Date:  2009-10-12       Impact factor: 3.240
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  10 in total

1.  Genomic sequencing is required for identification of tuberculosis transmission in Hawaii.

Authors:  Kent J Koster; Angela Largen; Jeffrey T Foster; Kevin P Drees; Lishi Qian; Ed Desmond; Xuehua Wan; Shaobin Hou; James T Douglas
Journal:  BMC Infect Dis       Date:  2018-12-03       Impact factor: 3.090

2.  Mycobacterium avium in Community and Household Water, Suburban Philadelphia, Pennsylvania, USA, 2010-2012.

Authors:  Leah Lande; David C Alexander; Richard J Wallace; Rebecca Kwait; Elena Iakhiaeva; Myra Williams; Andrew D S Cameron; Stephen Olshefsky; Ronit Devon; Ravikiran Vasireddy; Donald D Peterson; Joseph O Falkinham
Journal:  Emerg Infect Dis       Date:  2019-03       Impact factor: 6.883

3.  Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.

Authors:  Christine Jandrasits; Stefan Kröger; Walter Haas; Bernhard Y Renard
Journal:  PLoS Comput Biol       Date:  2019-12-09       Impact factor: 4.475

4.  Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.

Authors:  Stephen J Bush; Dona Foster; David W Eyre; Emily L Clark; Nicola De Maio; Liam P Shaw; Nicole Stoesser; Tim E A Peto; Derrick W Crook; A Sarah Walker
Journal:  Gigascience       Date:  2020-02-01       Impact factor: 6.524

5.  One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.

Authors:  Carlos Valiente-Mullor; Beatriz Beamud; Iván Ansari; Carlos Francés-Cuesta; Neris García-González; Lorena Mejía; Paula Ruiz-Hueso; Fernando González-Candelas
Journal:  PLoS Comput Biol       Date:  2021-01-27       Impact factor: 4.475

Review 6.  Mycobacterium bovis: From Genotyping to Genome Sequencing.

Authors:  Ana M S Guimaraes; Cristina K Zimpel
Journal:  Microorganisms       Date:  2020-05-03

7.  Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts.

Authors:  Maxime Godfroid; Tal Dagan; Anne Kupczok
Journal:  Genome Biol Evol       Date:  2018-08-01       Impact factor: 3.416

8.  Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission.

Authors:  Michael A Martin; Robyn S Lee; Lauren A Cowley; Jennifer L Gardy; William P Hanage
Journal:  Microb Genom       Date:  2018-10-11

9.  Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences.

Authors:  Katharine S Walter; Caroline Colijn; Ted Cohen; Barun Mathema; Qingyun Liu; Jolene Bowers; David M Engelthaler; Apurva Narechania; Darrin Lemmer; Julio Croda; Jason R Andrews
Journal:  Microb Genom       Date:  2020-07-31

10.  Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv.

Authors:  C N'Dira Sanoussi; Mireia Coscolla; Boatema Ofori-Anyinam; Isaac Darko Otchere; Martin Antonio; Stefan Niemann; Julian Parkhill; Simon Harris; Dorothy Yeboah-Manu; Sebastien Gagneux; Leen Rigouts; Dissou Affolabi; Bouke C de Jong; Conor J Meehan
Journal:  Microb Genom       Date:  2021-07
  10 in total

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