Langdon, WB;
(2014)
Mycoplasma Contamination in The 1000 Genomes Project.
BioData Mining
, 7
, Article 3. 10.1186/1756-0381-7-3.
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Abstract
Background: In silco Biology is increasingly important and is often based on public datasets. While the problem of contamination is well recognised in microbiology labs the corresponding problem of database corruption has received less attention. Results: Mapping 50 billion next generation DNA sequences from The Thousand Genome Project against published genomes reveals many that match one or more Mycoplasma but are not included in the reference human genome GRCh37.p5. Many of these are of low quality but NCBI BLAST searches confirm some high quality, high entropy sequences match Mycoplasma but no human sequences. Conclusions: It appears at least 7percent of 1000G samples are contaminated.
| Type: | Article |
|---|---|
| Title: | Mycoplasma Contamination in The 1000 Genomes Project |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1186/1756-0381-7-3 |
| Publisher version: | http://dx.doi.org/10.1186/1756-0381-7-3 |
| Language: | English |
| Additional information: | © 2014 Langdon; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
| Keywords: | Molecular biology, bicrobiology, genetics, metagenomic, data mining, next-generation DNA sequencing, data cleansing, high throughput, Solexa, 454, SOLiD |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1413303 |
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