Project description:Primary brain cancers are highly heterogeneous and include the most prevalent and aggressive glioblastomas. To understand the key factors underlying brain tumourigenesis, we have built our own database based on hybridization of DNA methylation beadchips from FFPE-derived biomaterial.
Project description:Accessing the proteome of formalin fixed, paraffin-embedded (FFPE) tissue could lead to discovery of new biomarkers and development of clinically useful assays. A critical step to realizing this potential is developing a simple and reproducible method to obtain proteomic profiles from FFPE tissue. An objective of this work is to develop and optimize a method to obtain proteomic profiles from FFPE breast tissue using a protocol commonly applied in pathology laboratories. The outcome is a method that incorporates steps used for immunohistochemical analyses of FFPE tissue that results in highly reproducible proteomic profiles. Implementing this assay with normal breast tissue and breast tumor tissue produced proteome profiles that reproducibly demonstrate substantial differences between normal vs. tumor tissue.
Project description:DNA methylation profiling of human FFPE meningioma samples These samples were processed as part of a study developing and validating a targeted gene expression biomarker of meningioma outcomes and benefit from radiotherapy.
Project description:Genome wide DNA methylation profiling of formalin-fixed paraffin-embedded (FFPE) meningioma samples. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 methylation sites across the genome at single-nucleotide resolution.
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
Project description:We profiled human DLBCL tumor samples (FF and FFPE matched pairs) to identify the transcripts which are less prone to degradation in FFPE Keywords: DLBCL FF FFPE RNA profiles of human FF and FFPE samples (DLBCL)
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.