期刊
BMC MEDICAL GENOMICS
卷 2, 期 -, 页码 -出版社
BIOMED CENTRAL LTD
DOI: 10.1186/1755-8794-2-8
关键词
-
资金
- NIH-NCI [P01 CA34936]
- U. S. Department of Energy [DE-AC02-05CH11231]
- USAMRMC [BC 061995]
- National Institutes of Health
- National Cancer Institute [P50 CA 58207, P50 CA 83639, P30 CA 82103, U54 CA 112970, U24 CA 126477, P01 CA 64602, NHGRI U24 CA 126551]
- SmithKline Beecham Corporation
- [P50 CA116199]
- [R01 CA89608]
Background: A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (similar to 40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Results: Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. Conclusion: MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
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