Microarray gene-expression data to identify a robust biomarker signature in PDAC and validate it in formalin-fixed paraffin-embedded tissue material.

To identify a robust diagnostic biomarker for PDAC, we used FF samples in a meta-analysis with five other publicly available data sets. The identified biomarker genes were subsequently validated in the remaining samples to test the detection performance of FFPE samples. Total RNA was obtained from 31 fresh-frozen tissue samples; 18 with pancreatic tumor and 13 non-tumor panreatic tissue samples. Furthermore, total RNA was extracted from 12 formalin-fixed paraffin-embedded tissue samples; 6 with pancreatic tumor and 6 non-tumor pancreatic tissues. Gene expression was analyzed using the Illumina HumanHT-12v4 expression beadchip. Data was quantile normalized and manufactor IDs were matched to unique Entrez IDs using the probe with the largest interquartile range. Subsequently, data was split into fresh-frozen samples that were used to identify a robust biomarker gene signature for PDAC, and FFPE samples that were used to validate the biomarker signature in FFPE material.