High Quality DNA Data from FFPE Samples Using MIP Technology
Author Information
Author(s): Wang Yuker, Carlton Victoria EH, Karlin-Neumann George, Sapolsky Ronald, Zhang Li, Moorhead Martin, Wang Zhigang C, Richardson Andrea L, Warren Robert, Walther Axel, Bondy Melissa, Sahin Aysegul, Krahe Ralf, Tuna Musaffe, Thompson Patricia A, Spellman Paul T, Gray Joe W, Mills Gordon B, Faham Malek
Primary Institution: Affymetrix Inc.
Hypothesis
Can Molecular Inversion Probe (MIP) technology generate high quality copy number and genotype data from degraded FFPE samples?
Conclusion
MIP technology can be used to generate high quality copy number and genotype data in FFPE as well as fresh frozen samples.
Supporting Evidence
- 88% of FFPE samples generated high quality copy number data.
- Genotype concordance averaged 99.9% when matched fresh frozen tissue was available.
- 76% of FFPE samples met the high quality threshold for copy number assessment.
Takeaway
This study shows that a special technology can help scientists get good DNA information from old tissue samples that are usually hard to work with.
Methodology
The study assessed copy number using a MIP panel of 50,000 markers in 93 FFPE tumor samples and compared results with matched fresh frozen samples.
Limitations
The study is limited by the variability in FFPE processing techniques across different institutions.
Participant Demographics
The samples were from diverse tumor types including breast, colorectal, bladder, and liver cancers, collected from multiple institutions.
Digital Object Identifier (DOI)
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