Assessing Bias in Whole Genome Amplification Techniques
Author Information
Author(s): Pinard Robert, de Winter Alex, Sarkis Gary J, Gerstein Mark B, Tartaro Karrie R, Plant Ramona N, Egholm Michael, Rothberg Jonathan M, Leamon John H
Primary Institution: 454 Life Sciences, Branford CT, USA
Hypothesis
How do different whole genome amplification methods affect the accuracy and yield of DNA sequencing?
Conclusion
Multiple displacement amplification methods produced the least bias and highest yields compared to PCR-based methods.
Supporting Evidence
- GenomiPhi generated 16.1 μg of DNA, a 640-fold amplification.
- Repli-G amplified input DNA 2100 fold to 53.6 μg.
- PEP generated 3.0 μg, a 120-fold increase.
- DOP amplified the input DNA 92-fold to 2.3 μg.
- All amplification methodologies induced statistically significant bias relative to the unamplified control.
Takeaway
This study looked at different ways to make more DNA from tiny samples and found that some methods work better than others without messing up the DNA too much.
Methodology
Whole genome sequencing was used to compare the bias introduced by different amplification methods on two bacterial genomes.
Potential Biases
PCR-based methods showed higher bias compared to multiple displacement amplification methods.
Limitations
The study focused only on two bacterial genomes and may not generalize to other organisms.
Statistical Information
P-Value
< 0.001
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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