DNA methylation profiles in FFPE brain tumor samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1148453 | ENA |
REPOSITORIES: ENA
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Project description:Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 71 samples from multiple brain regions (cerebellum, temporal/occipital/frontal cortex). The goal was to evalute the effect of trisomy 21 on DNA methylation levels and epigenetic age. Explanation of characteristics variables in supplementary file Explanation_of_characteristic_variables2.docx Bisulphite converted DNA from the 71 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Trisomy 21 (Down syndrome status) was related to CpGs.
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Project description:The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
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