Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples
2008
Analyzing Genomes to Detect Non-Human DNA
Sample size: 433
publication
Evidence: moderate
Author Information
Author(s): Liu Zhandong, Venkatesh Santosh S, Maley Carlo C
Primary Institution: University of Pennsylvania
Hypothesis
The human genome is more compact in sequence space than a random genome.
Conclusion
The study provides methods for detecting non-human DNA in human samples using unique oligomers.
Supporting Evidence
- The human genome has less coverage of n-mer space than a pseudo-human genome.
- The study identified 2.6 million 15-mers that could be used as probes to detect microbes in human samples.
- The human genome is significantly more compact in sequence space than a random genome.
Takeaway
Scientists looked at the DNA of different organisms to find patterns that can help spot germs in human samples.
Methodology
The study analyzed the frequency of oligomers in various genomes and used stochastic sampling to estimate sequence space coverage.
Limitations
The analysis may not account for gaps in the sequenced genomes, which could affect the estimates of entropy.
Statistical Information
P-Value
p<0.01
Confidence Interval
99.9% predicted interval: 0.412–0.713
Statistical Significance
p<0.01
Digital Object Identifier (DOI)
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