Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912995 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
2012-12-31 | GSE40299 | GEO
Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach. Phylogenetic study of the Treponema taxa found in digital dermatitis lesions of Holstein cows.
2013-06-25 | E-GEOD-42426 | biostudies-arrayexpress
Project description:We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the exomes of tumor normal pairs for all 21 cases, the whole genome copy number for a subset of 6 samples, and telomere length in diploid and aneuploid nuclei from 9 cases. Additionally, we screened the 20 FFPE cases for EGFR expression with an established IHC assay.
2024-02-21 | GSE240339 | GEO
Project description:MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling can be successfully conducted on FFPE cancer tissues using SOLiD ligation based sequencing. Tissue storage times (3-9 years) appeared to not affect the number of detected microRNAs in FFPE samples compared to matched frozen samples (paired t-test p>0.7). Correlations of microRNA expression values were very high across microRNAs in a given sample (Pearson’s r=0.71-0.95). Higher variance of expression values among samples was associated with higher correlation coefficients between FFPE and frozen tissues. One of the FFPE samples in this study was degraded for unknown reasons with a peak read length of 17 nucleotides compared to 21 in all other samples. The number of detected microRNAs in this sample was within the range of microRNAs detected in all other samples. Ligation-based microRNA deep sequencing on FFPE cancer tissues is feasible and RNA degradation to the degree observed in our study appears to not affect the number of microRNAs that can be quantified.
2013-04-15 | GSE45740 | GEO
Project description:MicroRNAs are useful biomarkers for various disease states, and their preservation in formalin-fixed, paraffin-embedded (FFPE) tissue makes them particularly useful for clinicogenetic studies. Although global microRNA expression in FFPE samples is routinely measured with microarrays, the utility of RNA sequencing for such profiling has yet to be established. In this study, to appraise the suitability of RNA sequencing, microRNAs in RNA from pathologic stage I lung adenocarcinoma FFPE samples were quantified with 8x60K Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray and Illumina® HiSeq™ 2000 sequencing platforms.
2014-12-31 | GSE57835 | GEO
Project description:Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples. A total of 23 test samples were each hybridized with a pooled 46,XX commercial reference (Promega catalog# G1521, Madison, WI). Twenty-two of the test samples included flow-sorted fresh frozen and formalin-fixed paraffin-embedded tumor samples. The tissues included pancreatic adenocarcinomas, breast carcinomas, small cell carcinoma of the ovary, glioblastoma, and bladder carcinoma. The last test sample was a pancreatic adenocarcinoma cell line (A10-74).
2012-12-31 | E-GEOD-40299 | biostudies-arrayexpress
Project description:DNA copy number changes with or without accompanying copy neutral changes such as unparental disomy (UPD) is a feature of the cancer genome that is linked to cancer development. However, technical problems with archived formalin-fixed, paraffin-embedded (FFPE) tissue samples have limited their general use in genomic profiling studies done using high-density single nucleotide polymorphism (SNP) microarray. To overcome the current problems with the use of this material in the detection of DNA copy number and copy neutral changes, we have devised two new protocols for extracting DNA from FFPE tissue. Genotyping efficiency and accuracy were improved using our novel protocols. After censoring the larger fragments, we obtained call rates for FFPE DNA equivalent to those for FF tissue DNA, with concordance rates between FFPE and FF tumor exceeding 99%. Identical DNA copy number changes were obtained for FFPE and FF; and between two new extraction protocols in tumor samples by using Affymetrix® high-density oligo-based SNP microarray platform. We observed UPD and recurrent gains and losses in tumor samples. Interestingly, we also identified UPD in the 5q and 13q regions in matching normal blood, FF adjacent breast tissue and tumor tissue in two samples. In conclusion, our new two DNA extraction protocols should substantially improve the ability to use archived material to help elucidate the complexity of early-stage breast cancer genomes. Keywords: SNP based array
2008-09-18 | GSE9154 | GEO
Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach.
2013-06-25 | GSE42426 | GEO