Whole Exome Sequencing and RNAseq of SEER Ovarian FFPE Tissues
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PROVIDER: PRJNA289035 | ENA |
REPOSITORIES: ENA
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Project description:<p>Next Generation Sequencing (NGS) technologies are being used for detection of somatic mutations in tumors and studies of germline variation. However, most NGS studies used DNA isolated either from whole blood or fresh frozen tissue specimens. Meanwhile, the tissue specimens available from most National Cancer Institute (NCI) funded cohorts and the Surveillance, Epidemiology and End Results (SEER) registries (<a href="http://seer.cancer.gov/biospecimen">http://seer.cancer.gov/biospecimen</a>) are primarily formalin fixed paraffin embedded (FFPE). There are limited data, on a small number of FFPE tissue samples, which suggest NGS is feasible. Much less is known about the feasibility of these technologies for large scale studies or using older FFPE specimens (e.g. 5-30 years old).</p> <p>The SEER cancer registries cover approximately 28% of the United States population, providing high quality demographic, clinical, pathologic, and survival data. The SEER Residual Tissue Repository (RTR) program was established in 2003. The RTR maintains biospecimens obtained from three of SEER' population-based cancer registries: Iowa, Hawaii, and Los Angeles. Investigators at government, academic, and nonprofit institutions may apply to the program to obtain annotated FFPE tumor tissue specimens to study biomarkers, etiology, and other aspects with a population-based sample of cancer cases. </p> <p>The main objective of this project was to conduct a pilot study to determine whether the DNA obtained from archival FFPE tissue from 3 SEER Registries is of sufficient quality and quantity to conduct NGS. For Exome sequencing, sixty high-grade serous ovarian adenocarcinomas from FFPE tissues which were between 7 and 31 years old were obtained from three SEER registries. DNA was extracted, quantified, quality assessed, and subjected to whole exome sequencing. DNA extraction (yields and quality) and whole exome sequencing (depths of coverage and exome coverage obtained) results from this study will be presented. For RNA-sequencing, sixty-seven high-grade serous ovarian adenocarcinomas from FFPE tissues which were between 7 and 31 years old were obtained from three SEER registries. Total RNA was extracted, quantified, quality assessed, and subjected to whole transcriptome sequencing. Ultimately data derived from this analysis could serve as the basis for determining the utility of archival FFPE biospecimens for characterization and discovery projects utilizing NGS technologies instead of relying on frozen biospecimens. </p>
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Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from ovarian cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions.
2014-07-01 | GSE55056 | GEO
Project description:We have performed in-depth examination of single tissue sections from a collection of FFPE and Frozen treated tumors, as well as cell line material all originating from different subtypes of epithelial ovarian cancer (high-grade serous, clear cell, endometrioid). Data were prepared using a tandem mass tag 10plex protocol with MS3 analysis on an Orbitrap Fusion.
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Project description:The recent introduction of poly ADP-ribose polymerase (PARP) inhibitors has significantly improved the survival outcomes of ovarian cancer. This study aimed to identify protein biomarkers and signatures predicting therapeutic responses to PARP inhibitors in high-grade serous ovarian cancer (HGSOC). To identify prognostic biomarkers, we conducted an in-depth proteomic analysis on formalin-fixed paraffin-embedded (FFPE) cancer tissues obtained from 24 HGSOC patients who received PARP inhibitor maintenance therapy for platinum-sensitive recurrence. In total, 7825 proteins were quantified with the tandem mass tag (TMT) labelling method. There were 56 and 131 proteins significantly upregulated in the good and poor response groups, respectively.
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Project description:RNA profiling from ovarian and prostate FFPE specimens
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Project description:To study feasibility of gene expression profiling from FFPE tissues using NanoString nCounter platform, we designed a pilot study utilizing samples from ovarian cancer cohort. We selected samples from large-scale epidemiologic studies and clinical trials representative of a wide variety of fixation times, block ages and block storage conditions. five serous carcinoma and six clear cell carcinoma samples with technical replicates
2014-07-01 | E-GEOD-55056 | biostudies-arrayexpress
Project description:Analysis of 60 FFPE (formalin-fixed, paraffin-embedded) ovarian cancer tissue samples to evaluate preservation quality and viability of global and phosphoproteomic analysis
2018-10-19 | PXD008832 | Pride
Project description:We present FFPE-ATAC, a new ATAC-seq tool for chromatin accessibility profiling that decodes the chromatin accessibility from mouse FFPE tissue and clinical archived FFPE tissues. The FFPE-ATAC generates the high-quality chromatin accessibility profiles from clinical FFPE tissue sections with 5-20 µm thickness, and reveals the disease-associated regulatory elements in different types of FFPE archived tissue. FFPE-ATAC enables to decode the chromatin states regulating the gene regulation in the cancer and understand the epigenetic regulation in the translational studies.
2021-06-30 | GSE163306 | GEO
Project description:Whole Exome Sequencing and RNAseq of SEER Ovarian FFPE Tissues
| PRJNA289036 | ENA
Project description:Performance assayed with formalin-fixed, paraffin-embedded (FFPE) ovarian tumor tissues.
2010-01-13 | GSE18769 | GEO