High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.
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 (approximately 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.


CONCLUSIONS
MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
Wang
Yuker
Y
Affymetrix Inc, Santa Clara, CA, USA. yuker_wang@affymetrix.com
Carlton
Victoria E H
VE
Karlin-Neumann
George
G
Sapolsky
Ronald
R
Zhang
Li
L
Moorhead
Martin
M
Wang
Zhigang C
ZC
Richardson
Andrea L
AL
Warren
Robert
R
Walther
Axel
A
Bondy
Melissa
M
Sahin
Aysegul
A
Krahe
Ralf
R
Tuna
Musaffe
M
Thompson
Patricia A
PA
Spellman
Paul T
PT
Gray
Joe W
JW
Mills
Gordon B
GB
Faham
Malek
M