Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms of CIMAC-CIDC network
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PROVIDER: PRJNA679859 | ENA |
REPOSITORIES: ENA
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Project description:Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms of CIMAC-CIDC network
| PRJNA679858 | ENA
Project description:Correlative studies in NRG-GY021: Olaparib and tremelimumab in Ovarin cancer (CIMAC-CIDC)
| PRJNA1085796 | ENA
Project description:PurposeThe Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) Network is supported by the NCI to identify biomarkers of response to cancer immunotherapies across clinical trials using state-of-the-art assays. A primary platform for CIMAC-CIDC studies is cytometry by time of flight (CyTOF), performed at all CIMAC laboratories. To ensure the ability to generate comparable CyTOF data across labs, a multistep cross-site harmonization effort was undertaken.Experimental designWe first harmonized standard operating procedures (SOPs) across the CIMAC sites. Because of a new acquisition protocol comparing original narrow- or new wide-bore injector introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed cross-site assay harmonization experiments using five shared cryopreserved and one lyophilized internal control peripheral blood mononuclear cell (PBMC) with a shared lyophilized antibody cocktail consisting of 14 isotype-tagged antibodies previously validated, plus additional liquid antibodies. These reagents and samples were distributed to the CIMAC sites and the data were centrally analyzed by manual gating and automated methods (Astrolabe).ResultsAverage coefficients of variation (CV) across sites for each cell population were reported and compared with a previous multisite CyTOF study. We reached an intersite CV of under 20% for most cell subsets, very similar to a previously published study.ConclusionsThese results establish the ability to reproduce CyTOF data across sites in multicenter clinical trials, and also highlight the importance of quality control procedures, such as the use of spike-in control samples, for tracking variability in this assay.
| S-EPMC8448982 | biostudies-literature
Project description:Correlative studies in Protocol NRG-LU004, which studied radiation and immunotherapy in lung cancer, in collaboration with CIMAC-CIDC
| PRJNA1066948 | ENA
Project description:MiRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. Several measurement platforms, designed to determine their relative RNA abundance levels in biological samples, have been developed. In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which helps to guide informed selection of a quantitative miRNA gene expression platform in function of particular study goals. Sequencing of 20 miRQC samples on Illumina Genome Analyzer IIx System
2013-08-31 | E-GEOD-49816 | biostudies-arrayexpress
Project description:This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision.
2010-03-18 | GSE19248 | GEO
Project description:MiRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. Several measurement platforms, designed to determine their relative RNA abundance levels in biological samples, have been developed. In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which helps to guide informed selection of a quantitative miRNA gene expression platform in function of particular study goals.
2013-08-31 | GSE49816 | GEO
Project description:This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision. Performance of four (4) commercially available miRNA platforms was evaluated using 7 placenta samples spiked with synthetic microRNA spikes (in Latin-square design) absent in placenta. Platforms were primarily evaluated for accuracy and specificity.
2010-06-23 | E-GEOD-19248 | biostudies-arrayexpress
Project description:Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we present ABI's OpenArray and qPCR systems.
2012-10-18 | GSE41388 | GEO
Project description:Evaluation of single-Cell RNA Sequencing Platforms
| PRJNA597861 | ENA