DNA methylation profiles in FFPE brain tumor samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1148453 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2025-01-15 | GSE274910 | GEO
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.
2020-07-17 | PXD007088 | Pride
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)
2011-03-16 | E-GEOD-18377 | biostudies-arrayexpress
Project description:Technical evaluation of targeted DNA sequencing from FFPE tumor samples
| PRJEB5209 | ENA
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
2011-03-16 | GSE18377 | GEO
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.
2018-09-05 | GSE93337 | GEO
Project description:Transcriptomics of FFPE-derived primary brain tumours
| PRJNA1134745 | ENA
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 RNA sequencing from FFPE-derived biomaterial.
2025-01-15 | GSE272042 | GEO
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.
2018-09-05 | GSE93336 | GEO
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.
2023-09-06 | GSE221029 | GEO