Related Experiment Video
Updated: Apr 28, 2026
06:01
Optimized PCR-based Detection of Mycoplasma
Published on: June 20, 2011
56.1K
Mycoplasma contamination in the 1000 Genomes Project
1Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.
Biodata Mining
|May 30, 2014
Summary
Database corruption is a significant issue in bioinformatics, potentially impacting public data integrity. Our study found at least 7% of The Thousand Genomes Project samples show evidence of Mycoplasma contamination.
Area of Science:
- Bioinformatics and Genomics
- Microbial Contamination Analysis
Background:
- In silico biology relies heavily on public data, making data integrity crucial.
- While laboratory contamination is recognized, database corruption is less understood.
- Publicly available genomic datasets may harbor undetected contaminants.
Purpose of the Study:
- To investigate the prevalence of database corruption in large-scale genomic projects.
- To assess the impact of potential contaminants on human genome reference data.
Main Methods:
- Analysis of 50 billion next-generation DNA sequences from The Thousand Genomes Project.
- Comparison of sequences against published reference genomes, including human (GRCh37.p5).
- Utilized NCBI BLAST for sequence identification and quality assessment.
Main Results:
- Numerous sequences from The Thousand Genomes Project matched Mycoplasma genomes.
- These Mycoplasma sequences were absent from the human reference genome.
- High-quality, high-entropy sequences confirmed Mycoplasma presence, distinct from human DNA.
Conclusions:
- A significant portion of The Thousand Genomes Project samples are contaminated with Mycoplasma.
- At least 7% of analyzed samples exhibit detectable contamination.
- Highlights the need for rigorous quality control in public genomic databases.
Related Concept Videos
02:55Synthetic Biology
4.4K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.4K
01:22Introduction to the Human Microbiota
199
Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity,...
199
00:46Genomic DNA in Prokaryotes
42.4K
The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
Genomic Diversity in Bacteria
Although bacterial genomes are much...
42.4K
01:11Genome-wide Association Studies-GWAS
12.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.6K
01:29Modern Molecular Taxonomy
834
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
834
02:46Genome Copying Errors
4.3K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
4.3K