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:
- Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes.
- Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
- Fast identification and removal of sequence contamination from genomic and metagenomic datasets
- Mycoplasma contamination in the 1000 Genomes Project
- ContEst: estimating cross-contamination of human samples ...
- DeconSeq @ SourceForge.net
- AlienTrimmer: A tool to quickly and accurately trim off ...
- Blobology: exploring raw genome data for contaminants, symbionts, and parasites using taxon-annotated GC-coverage plots
@pathogenomenick @gregcaporaso crap - can't believe I left that off — Jonathan Eisen (@phylogenomics) July 25, 2014
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
More Mouldy Data: Another mycoplasma gene jumps the silicon barrier into the human genome
Sneaky Bacteria Impersonate as Humans
There is even contamination in the other direction with Human genetic sequences appearing in online publicly accessible plant genomes: Longo 2011