Literature DB >> 26150097

Here, there, and everywhere: From PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places.

Karl Gruber1.   

Abstract

Mesh：

Year:  2015        PMID： 26150097      PMCID： PMC4552482          DOI： 10.15252/embr.201540822

Source DB:  PubMed          Journal:  EMBO Rep        ISSN： 1469-221X            Impact factor:   8.807


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  10 in total

1.  The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns.

Authors:  Samia N Naccache; Alexander L Greninger; Deanna Lee; Lark L Coffey; Tung Phan; Annie Rein-Weston; Andrew Aronsohn; John Hackett; Eric L Delwart; Charles Y Chiu
Journal:  J Virol       Date:  2013-09-11       Impact factor: 5.103

2.  An assessment of air as a source of DNA contamination encountered when performing PCR.

Authors:  Nina Witt; Gillian Rodger; Jo Vandesompele; Vladimir Benes; Alimuddin Zumla; Graham A Rook; Jim F Huggett
Journal:  J Biomol Tech       Date:  2009-12

3.  Anthropology. Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

Authors:  Kay Prüfer; Matthias Meyer
Journal:  Science       Date:  2015-02-20       Impact factor: 47.728

Review 4.  MSMB variation and prostate cancer risk: clues towards a possible fungal etiology.

Authors:  Siobhan Sutcliffe; Angelo M De Marzo; Karen S Sfanos; Martin Laurence
Journal:  Prostate       Date:  2014-01-24       Impact factor: 4.104

5.  Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans.

Authors:  James C Chatters; Douglas J Kennett; Yemane Asmerom; Brian M Kemp; Victor Polyak; Alberto Nava Blank; Patricia A Beddows; Eduard Reinhardt; Joaquin Arroyo-Cabrales; Deborah A Bolnick; Ripan S Malhi; Brendan J Culleton; Pilar Luna Erreguerena; Dominique Rissolo; Shanti Morell-Hart; Thomas W Stafford
Journal:  Science       Date:  2014-05-16       Impact factor: 47.728

6.  Abundant human DNA contamination identified in non-primate genome databases.

Authors:  Mark S Longo; Michael J O'Neill; Rachel J O'Neill
Journal:  PLoS One       Date:  2011-02-16       Impact factor: 3.240

7.  Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data.

Authors:  Richard W Lusk
Journal:  PLoS One       Date:  2014-10-29       Impact factor: 3.240

8.  Unexpected cross-species contamination in genome sequencing projects.

Authors:  Samier Merchant; Derrick E Wood; Steven L Salzberg
Journal:  PeerJ       Date:  2014-11-20       Impact factor: 2.984

9.  Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.

Authors:  Martin Laurence; Christos Hatzis; Douglas E Brash
Journal:  PLoS One       Date:  2014-05-16       Impact factor: 3.240

10.  Mycoplasma contamination in the 1000 Genomes Project.

Authors:  William B Langdon
Journal:  BioData Min       Date:  2014-04-29       Impact factor: 2.522
  10 in total
  8 in total

1.  Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity.

Authors:  Michael P Heaton; Timothy P L Smith; Bradley A Freking; Aspen M Workman; Gary L Bennett; Jacky K Carnahan; Theodore S Kalbfleisch
Journal:  F1000Res       Date:  2017-08-02

2.  Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases.

Authors:  David F Nieuwenhuijse; Marion P G Koopmans
Journal:  Front Microbiol       Date:  2017-02-15       Impact factor: 5.640

3.  Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis.

Authors:  Kirsten van de Groep; Martine P Bos; Paul H M Savelkoul; Anna Rubenjan; Christel Gazenbeek; Willem J G Melchers; Tom van der Poll; Nicole P Juffermans; David S Y Ong; Marc J M Bonten; Olaf L Cremer
Journal:  Eur J Clin Microbiol Infect Dis       Date:  2018-04-26       Impact factor: 3.267

4.  Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.

Authors:  Casper S Poulsen; Claus T Ekstrøm; Frank M Aarestrup; Sünje J Pamp
Journal:  Microbiol Spectr       Date:  2022-03-15

5.  Parallel DNA Extraction From Whole Blood for Rapid Sample Generation in Genetic Epidemiological Studies.

Authors:  Kiara Lee; Anubhav Tripathi
Journal:  Front Genet       Date:  2020-04-29       Impact factor: 4.599

6.  Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding.

Authors:  Kristina Noreikiene; Mikhail Ozerov; Freed Ahmad; Toomas Kõiv; Siim Kahar; Riho Gross; Margot Sepp; Antonia Pellizzone; Eero J Vesterinen; Veljo Kisand; Anti Vasemägi
Journal:  Parasit Vectors       Date:  2020-08-28       Impact factor: 3.876

7.  Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.

Authors:  María P Martín; Pablo P Daniëls; David Erickson; John L Spouge
Journal:  PLoS One       Date:  2020-08-19       Impact factor: 3.240

Review 8.  Unlocking the efficiency of genomics laboratories with robotic liquid-handling.

Authors:  Houriiyah Tegally; James Emmanuel San; Jennifer Giandhari; Tulio de Oliveira
Journal:  BMC Genomics       Date:  2020-10-20       Impact factor: 3.969
  8 in total

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