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6 results for “variant calling file”
Fastq files for benchmarking somatic variant calling pipelines
<p>The <a href="https://download.imgag.de/public/validation_dataset_somatic/readme.html" target="_blank" rel="noopener">original .bam files</a> were provided by <a href="https://www.medizin.uni-tuebingen.de/de/das-klinikum/mitarbeiter/profil/3377" target="_blank" rel="noopener">Marc Sturm</a> from the <a href="https://www.medizin.uni-tuebingen.de/de/das-klinikum/einrichtungen/institute/medizinische-genetik-und-angewandte-genomik" target="_blank" rel="noopener">Institut für Medizinische Genetik und Angewandte Genomik at the University Clinic Tübingen.</a></p> <p>The files were transformed into .fq.gz files using the <a href="https://github.com/nf-core/bamtofastq" target="_blank" rel="noopener">nf-core/bamtofastq pipeline.</a> All information on the pipeline run can be found in the <a href="../api/records/10805134/draft/files/execution_report_2024-03-11_11-44-17.html/content" target="_blank" rel="noopener noreferrer">execution_report_2024-03-11_11-44-17.html</a>. The FASTQ files for the normal sample were directly uploaded to <a href="https://osf.io/cduyq/files/onedrive">the corresponding osf project</a>.</p> <p> </p> <p> </p>
spindle cell variant diffuse large B-cell lymphoma (NGS annotation file; high confidence calls) hematolrep-2136295
<p>Diffuse large B-cell lymphoma with spindle cell morphology is a rare variant. We present the case of a 74-year-old male who initially presented with a right supraclavicular (lymph) node enlargement. Histological analysis showed a proliferation of spindle-shaped cells with narrow cytoplasms. An immunohistochemical panel was used to exclude other tumors, such as melanoma, carcinoma, and sarcoma. The lymphoma was characterized by a cell-of-origin subtype of germinal center B-cell-like (GCB) based on Hans’ classifier (CD10-negative, BCL6-positive, and MUM1-negative); EBER negativity, and the absence of BCL2, BCL6, and MYC rearrangements. Mutational profiling using a custom panel of 168 genes associated with aggressive B-cell lymphomas confirmed mutations in ACTB, ARID1B, DUSP2, DTX1, HLA-B, PTEN, and TNFRSF14. Based on the LymphGen 1.0 classification tool, this case had an ST2 subtype prediction. The immune microenvironment was characterized by moderate infiltration of M2-like tumor-associated macrophages (TMAs) with positivity of CD163, CSF1R, CD85A (LILRB3), and PD-L1; moderate PD-1 positive T cells, and low FOXP3 regulatory T lymphocytes (Tregs). Immunohistochemical expression of PTX3 and TNFRSF14 was absent. Interestingly, the lymphoma cells were positive for HLA-DP-DR, IL-10, and RGS1, which are markers associated with poor prognosis in DLBCL. The patient was treated with R-CHOP therapy, and achieved a metabolically complete response.</p> <p>Carreras J, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Ikoma H, Kondo Y, Ito A, Nagase S, Miura H, Roncador G, Colomo L, Hamoudi R, Campo E, Nakamura N. Mutational Profile and Pathological Features of a Case of Interleukin-10 and RGS1-Positive Spindle Cell Variant Diffuse Large B-Cell Lymphoma. <em>Hematology Reports</em>. 2023; 15(1):188-200. https://doi.org/10.3390/hematolrep15010020</p>
Variant call file for mountain yellow-legged frog (MYLF) selection analysis
Open the record for dataset details and reuse information.
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
<p>A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as <em>Cannabis</em> <em>sativa </em>(<em>C. sativa</em>), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of <em>C. sativa</em>. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high <span>𝐹̅</span>ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene <em>SMALLER TRICHOMES</em> <em>WITH VARIABLE BRANCHES 2 </em>to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in <em>C. sativa</em>.</p>
Variant Calling Files supporting leptospira analysis
<p>This data set contains the results of a variant calling analysis performed on 20 samples named X_SX for sample 1 to 16 and named B3288_2 B3288_8 B3288_10 and B3288_16 for samples named 17 to 20.</p> <p> </p> <p>All variant calling analysis were performed with Sequana variant calling pipeline (https://github.com/sequana/variant_calling) but only the final VCF files are provided in this dataset. One VCF file per sample and per reference genome used. There were 273 core genomes used; Therefore we have here 273 time 20 VCF files. In the summary directory one can also find the CSV files for SNPs and INDELs that were extracted from the VCF files using several filtering (depth of 10, strand balance >0.2, min frequency >=0.5).</p> <p>More information and notebooks generating and using those files can be found here: https://github.com/biomics-pasteur-fr/manuscript_capture_leptospira/ A tagged version of this github repository is provided as version 1 : manuscript_capture_leptospira-1.tar.gz</p>
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
Open the record for dataset details and reuse information.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.