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A trivial explanation for the observation of mixed populations in this sample would be contamination during sample collection, processing, or analysis.
The reason why we decided to randomise general practices instead of patients or individual GPs is that we assumed there would be contamination, for three reasons.
A third, in our opinion more probable, explanation would be contamination or colonization of the surgical wound with resistant bacteria from the skin during repeat surgery especially since each additional debridement is another disturbance of the already compromised soft tissues.
Another possibility for decreased hit frequency of singleton sequences would be contamination of the cDNA preparation with genomic DNA, resulting in reads derived from genomic DNA that remained unassembled.
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In this study we aimed (1) to quantify the dispersion of a surrogate pathogen from a simulated patient's mouth to the anesthesia workstation during routine anesthetic induction, (2) to test the hypothesis that there would be fewer contamination sites by providers who used a double-gloving technique, and (3) to examine the effectiveness of between-case anesthesia apparatus disinfection.
However, one serious potential drawback in integrating large scale indexing would be data contamination due to index switching, or the transfer of an index from one individual to the sequencing read of another individual.
Despite precautions to remove nematodes from root tissues prior to library construction, it was anticipated that there would be some contamination of the pineapple gall libraries with nematode derived sequences.
Homospecific contamination would be undetectable because contaminant DNA would be identical to sample DNA; however, this would not change our current conclusions about paternal leakage because we cannot detect paternal mtDNA in homospecific crosses for the same reason.
An exception would be where this contamination would cause destruction of microbial ecosystems.
"It's unlikely that there would be a significant contamination problem," says Rummel.
Current buffers between fields, she says, could not ensure that there would be absolutely no contamination.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com