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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