Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666749 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Performance Comparisons between Clustering Models for Reconstructing NGS Results from Technical Replicates
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Project description:Reproducibility assessment is essential in extracting reliable scientific insights from high-throughput experiments. Inconsistency between technical replicates poses a challenge, particularly evident in NGS technologies based on immunoprecipitations, where the need for reproducibility in peak identification is a well-acknowledged limitation. While the Irreproducibility Discovery Rate (IDR) method has been instrumental in assessing reproducibility, its standard implementation is constrained to handling only two replicates. In the current era of steadly growing sample sizes, facilitated by multiplexing and reduced sequencing costs, highly performing methods that handle any number of replicates are desirable.
2024-01-03 | GSE248884 | GEO
Project description:Circulating tumor DNA (ctDNA) as a biomarker of disease activity in classic Hodgkin lymphoma (cHL) patients are still not well-defined. By profiling primary tumors and ctDNA, we identified common variants between primary tumors and longitudinal plasma samples in most of the cases, confirming high PBatial and temporal heterogeneity. Though ctDNA analyses mirrored HRS cell genetics overall, the prevalence of variants shows that none of them can be used as a single biomarker. Conversely, the estimation of hGE/mL, based in total ctDNA quantification, reflects disease activity and is almost perfectly correlated with standard parameters such as PET/CT that are associated with refractoriness.
2023-12-18 | GSE244989 | GEO
Project description:The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed using peptide MS/MS reference ion assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from shared data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally-generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis we developed a software workflow, SwathXtend, which generates extended peptide assay libraries using a local seed library and delivers statistical analysis of SWATH-based sample comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at different ratios to simulate common protein abundance change comparisons. SWATH-MS data with 2, 5 and 10% of yeast peptides spiked into the human cell lysate were assessed using several local and repository-based assay libraries of different complexities and proteome compositions. We evaluated detection specificity and accuracy to detect differentially abundant proteins and reporting thresholds for statistical analyses. We demonstrate that extended assay libraries integrated with local seed libraries achieve better performance than local limited assay libraries alone from the aspects of the number of peptides and proteins identified and the specificity to detect differentially abundant proteins; the performance of extended assay libraries heavily depend on the similarity of the seed and add-on libraries; statistical analysis with multiple testing correction can improve the statistical rigor needed when using large, extended assay libraries.
2016-05-12 | PXD002836 | Pride
Project description:<p>The Nex-StoCT and ACMG recommend that validation of an NGS-based diagnostic test include performance test characteristics for assay accuracy, analytical sensitivity and specificity, reproducibility and repeatability. To measure these parameters for the GEDi capture and sequencing test, 4 samples (three randomly selected patient samples and the NA12878 HapMap sample) were prepared and sequenced in triplicate on each of three separate days. We also performed WES and SNP array genotyping analyses of these 4 samples using Agilent V4+UTR whole exome enrichment kit and Illumina Omni 2.5 SNP arrays, respectively.</p>
| phs000798 | dbGaP
Project description:Identification of BBX proteins as rate-limiting co-factors of HY5
| PRJNA564640 | ENA
Project description:As part of the Core for Life Proteomics Working group, we have undertaken a four-year harmonization study to enhance the comparability of quality control results, identifying community reference values, intra-laboratory performance drifts, sources of heterogeneity, and improvement opportunities. The outcomes include a new quality control standard for longitudinal assessment of liquid chromatography and mass spectrometry system performance, measures of intra- and inter-laboratory variability, community reference values, and a 4-year longitudinal series of quality control data from multiple instruments and laboratories.
2024-10-11 | PXD049444 | Pride
Project description:The diagnostic and therapeutic use of extracellular vesicles (EV) is under intense investigation and may lead to societal benefits. Reference materials are an invaluable resource for developing, improving and assessing the performance of regulated EV applications and for quantitative and objective data interpretation. We have engineered recombinant extracellular vesicles (rEV) as a biological reference material. rEV have similar biochemical and biophysical characteristics as sample EV and function as an internal quantitative and qualitative control throughout analysis. Spike-in applications of rEV in bodily fluids prior to EV analysis map technical variability of EV applications and promote intra and inter laboratory studies. This protocol describes the production, recovery and quality assurance of rEV, their dilution and addition to bodily fluids, and the detection steps based on fluorescence-, nucleic acid- and protein measurements. Multiple application potentials for rEV are exemplified, including method development, big data normalization and assessment of pre-analytical variables. The protocol can be adopted by researchers with standard laboratory and basic EV separation/characterization experience and requires ~4–5 d.
2023-03-13 | PXD017542 | Pride