TY - JOUR
T1 - High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays
AU - Wang, Yuker
AU - Carlton, Victoria Eh
AU - Karlin-Neumann, George
AU - Sapolsky, Ronald
AU - Zhang, Li
AU - Moorhead, Martin
AU - Wang, Zhigang C.
AU - Richardson, Andrea L.
AU - Warren, Robert
AU - Walther, Axel
AU - Bondy, Melissa
AU - Sahin, Aysegul
AU - Krahe, Ralf
AU - Tuna, Musaffe
AU - Thompson, Patricia A.
AU - Spellman, Paul T.
AU - Gray, Joe W.
AU - Mills, Gordon B.
AU - Faham, Malek
N1 - Funding Information:
RK and MT were supported in part by grants from the NIH-NCI (P01 CA34936). MB, and GBM were supported by P50 CA116199, R01 CA89608. This work was supported in part by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, by the USAMRMC BC 061995, and by the National Institutes of Health, National Cancer Institute grants P50 CA 58207, the P50 CA 83639, the P30 CA 82103, the U54 CA 112970, the U24 CA 126477 and the P01 CA 64602, the NHGRI U24 CA 126551 and by the SmithKline Beecham Corporation grant to JWG.
PY - 2009
Y1 - 2009
N2 - 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 (∼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.
AB - 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 (∼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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U2 - 10.1186/1755-8794-2-8
DO - 10.1186/1755-8794-2-8
M3 - Article
C2 - 19228381
AN - SCOPUS:63449110271
SN - 1755-8794
VL - 2
JO - BMC Medical Genomics
JF - BMC Medical Genomics
M1 - 8
ER -