Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases.
Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases. RNA was extracted from FFPE Familial breast tumours and analysed using the WG-DASL assay for Illumina.
Project description:RAS genotyping is mandatory for the prescription of anti-EGFR (epidermal growth factor receptor) therapies in patients with metastatic colorectal cancer. The standard genotyping is assessed on formalin-fixed paraffin embedded tumour tissue. This study compares RAS and BRAF genotyping results achieved in analyzing circulating plasma DNA using OncoBEAM technique with those achieved using the standard genotyping techniques and formalin-fixed paraffin embedded samples.
Project description:Formalin-fixed, paraffin-embedded (FFPE) samples of varying grade (II-IV) malignant gliomas were measured by Illumina cDNA-mediated Annealing, Selection, extension and ligration (DASL) platform. DASL platform was selected for its specialized design for partially degraded RNA.
Project description:Type of experiment: This study used microarray experiments to evaluate the reproducibility and fidelity of Whole Transcriptome Amplification (WTA). Experimental factors: This study contains multiple categories of microarray experiments. Self-self hybridizations from WTA amplified total RNA were performed to evaluate the reproducibility of WTA. To evaluate the fidelity of WTA, the same total RNA, isolated from tissue samples or cell lines, was either directly used for microarray analysis or subjected to WTA amplification before hybridization. The amount of input total RNA for WTA amplification was varied for different hybridizations. To demonstrate the usefulness of WTA, benign epithelia, cancerous epithelia and stroma isolated by laser capture microdissection from frozen prostate tissue specimens were subjected to WTA and hybridized. To demonstrate the fidelity of WTA with degraded samples, total RNA from cell lines was artificially degraded before WTA and hybridization. Total RNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues containing benign and cancerous prostate tissue were also subjected to WTA and hybridized. Keywords: other
Project description:Type of experiment: This study used microarray experiments to evaluate the reproducibility and fidelity of Whole Transcriptome Amplification (WTA). Experimental factors: This study contains multiple categories of microarray experiments. Self-self hybridizations from WTA amplified total RNA were performed to evaluate the reproducibility of WTA. To evaluate the fidelity of WTA, the same total RNA, isolated from tissue samples or cell lines, was either directly used for microarray analysis or subjected to WTA amplification before hybridization. The amount of input total RNA for WTA amplification was varied for different hybridizations. To demonstrate the usefulness of WTA, benign epithelia, cancerous epithelia and stroma isolated by laser capture microdissection from frozen prostate tissue specimens were subjected to WTA and hybridized. To demonstrate the fidelity of WTA with degraded samples, total RNA from cell lines was artificially degraded before WTA and hybridization. Total RNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues containing benign and cancerous prostate tissue were also subjected to WTA and hybridized.
Project description:We examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors.
Project description:Data includes all available Affymetrix SNP data from a cohort of Pediatric malignant glioma samples, isolated from Formalin-fixed Paraffin embedded tissue. No clinical data is available.
