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

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. Overall design: 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.