Who are the contaminants in your sequencing project? (crosspost from #microBEnet)

This was originally posted on microBEnet: Who are the contaminants in your sequencing project?

Well, been having many discussions recently about PCR amplification happening from “negative” controls where no sample DNA was added. Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction.  Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs.  But if that does not happen, it is possible to try to detect contamination after it has happened.  Below I post some papers related to post-sequencing detection of contamination:

Any other suggestions or comments would be welcome. UPDATE 10:30 AM 7/25 – Was reminded on Twitter of a new, critically relevant publication on this issue: Reagent contamination can critically impact sequence-based microbiome analyses

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

One thought on “Who are the contaminants in your sequencing project? (crosspost from #microBEnet)”

  1. 2nd try:-(
    A huge but so far little regarded aspect is not contamination of samples or of physical substances but of computer software and databases.
    We have found Mycoplasma genes in a variety of Bioinformatics tools. There are even Mycoplasma genes in the reference human genome at NCBI BioTechniques, Vol. 47, No. 6, December 2009 http://www.biotechniques.com/BiotechniquesJournal/2009/December/Letter-to-the-editor-Unexpected-presence-of-mycoplasma-probes-on-human-microarrays/biotechniques-181035.html pubmed/20047202

    In Silico Infection of the Human Genome
    http://dx.doi.org/doi:10.1007/978-3-642-29066-4_22

    More Mouldy Data: Another mycoplasma gene jumps the silicon barrier into the human genome
    http://arxiv.org/abs/1106.4192

    Sneaky Bacteria Impersonate as Humans
    http://www.labtimes.org/editorial/e_513.lasso

    There is even contamination in the other direction with Human genetic sequences appearing in online publicly accessible plant genomes: Longo 2011

    Bill

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