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Beware contaminated research genomes

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While shopping at the gene counter, we learned from The Scientist :

Published genomes are chock-full of contamination. But as awareness of the problem grows, so do methods to help combat it.

When Supratim Mukherjee noticed the same bacteriophage sequence popping up again and again in hundreds of microbial genomes from a database he was analyzing, he got excited. Mukherjee, a bioinformatician at Lawrence Berkeley National Laboratory, was comparing the metabolic pathways of the microbes, and he began to wonder what the nearly ubiquitous sequence was. “I thought we must have discovered something novel,” he recalls. “This entire bacteriophage genome was intact in all these diverse microbes.”

But when Mukherjee looked up the bacteriophage sequence, he learned that it was the sequence of PhiX, a bacteriophage sold by Illumina as part of the company’s sequencing kits to run alongside a genome of interest. Ironically, PhiX is intended as a quality-control measure, to track error rates on any given sequencing run. But in many hundreds of cases, Mukherjee found, researchers had failed to remove the PhiX sequences from their published genomes. More.

One wonders whether some of the wilder findings from genome mapping will fall victim to such embarrassing discoveries.

Only one way to find out, unfortunately. Some good prevention tips in the article.

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One Reply to “Beware contaminated research genomes

  1. 1
    bornagain says:

    OT:

    Quantum physics meets genetic engineering – Oct. 15, 2015
    Excerpt: Nature has had billions of years to perfect photosynthesis (almost 100 percent efficiency), which directly or indirectly supports virtually all life on Earth.,,,
    “We came up with design principles to redesign how the virus is capturing light, and get it to this quantum regime.”,,,
    Once the team engineered the viruses, they were able to use laser spectroscopy and dynamical modeling to watch the light-harvesting process in action, and to demonstrate that the new viruses were indeed making use of quantum coherence to enhance the transport of excitons.
    http://www.sciencedaily.com/re.....115946.htm

    Hmmm, interesting choice of words. Exactly, how does someone ‘redesign’ something that they claim is not designed in the first place?

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