Using Amplified DNA from FFPE Samples for Genetic Analysis
Author Information
Author(s): Angela Stokes, Ignat Drozdov, Eliete Guerra, Christos A. Ouzounis, Saman Warnakulasuriya, Michael J. Gleeson, Mark McGurk, Mahvash Tavassoli, Edward W. Odell
Primary Institution: King's College London Dental Institute
Hypothesis
Can whole-genome amplification of DNA from formalin-fixed, paraffin-embedded tissues provide reliable data for genetic analysis?
Conclusion
The study supports the use of whole-genome amplification for DNA from FFPE tissues for SNP array analysis, although it introduces some inaccuracies.
Supporting Evidence
- An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples.
- Concordance between the two sample types was 82.4%.
- Copy number changes were reduced in amplified DNA, but 99.5% concordance was observed when detected.
- Approximately 50% of gene changes detected in unamplified DNA were also detected in amplified DNA.
Takeaway
Scientists found a way to study tiny samples of DNA from preserved tissues, but sometimes the results can be a bit off.
Methodology
The study used a ligation adaptor amplification method to analyze DNA from laser capture micro-dissected tissues and compared results from amplified and non-amplified samples using SNP arrays.
Potential Biases
There may be allelic amplification bias affecting the results, particularly for homozygous calls.
Limitations
The study was limited by the small sample size and the potential for inaccuracies in the amplified DNA results.
Participant Demographics
The study involved six individuals with dysplastic oral epithelium and normal muscle tissues.
Statistical Information
P-Value
0.038
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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