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198 results for “variant analysis”
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>
Comprehensive genomic analysis identifies a diverse landscape of sideroblastic and non-sideroblastic iron related anemias with novel and pathogenic variants in an iron deficient endemic setting
<p>The history for the 5 CMA cases are as follows:-</p> <p> </p> <p>1. <strong>HMA-2 </strong>:- 0.6 month male child presented with poor feeding and noted to have mild-moderate pallor. CBC showed Hemoglobin 9.0gm/dl, MCV- 58fl, MCH 17.3, MCHC 29, Iron 113 ug/dl, Ferritin 297 ug/l, TSAT-45%, TIBC-297 ug/dl, Hepcidin- 20.3ng/ml. No transfusions received and antenatal and neonatal history uneventful. HPLC (both parents), alpha sequencing normal. Targeted NGS shows a heterozygous VUS in GLRX5 gene along with a VUS in BMP6 gene. WES- Does not add anything further significant.</p> <p> </p> <p>2. <strong>HMA-3 </strong>:- 0.8 month male child with transfusion dependent microcytic hypochromic anemia and neurological developmental delay. Expired at 1 year of age due to secondary infection (acinetobacter and toxoplasmosis). Hb- 6.5, MCV-61.5, MCH-18.3, Iron 45 ug/dl, Ferritin 650. Targeted panel and WES - negative.</p> <p> </p> <p>3. <strong>HMA-4:</strong>- 5 year male child with severe microcytic hypochromic anemia and received just one transfusion outside. Has microcephaly and SNHL. Hb 5, MCV- 56, MCH- 18, MCHC- 23, Iron- 75, Ferritin - 330, TIBC- 290, TSAT- 41%. Targeted NGS and WES show a Homozygous VUS in BMP6 gene (? association?) </p> <p> </p> <p>4. <strong>HMA-6:-</strong> 2 year old male child with moderate microcytic hypochromic anemia and focal seizures. Hb -8, MCV- 58, MCH- 16, MCHC-27, Iron- 94, Ferritin -380, Transferrin levels- 10 (very low). Targeted NGS and WES show a single heterozygous VUS mutation in TF gene and another intrinsic rare variant but reported in pop. Database (could it make it compound her for atransferrinemia?) </p> <p> </p> <p>5. <strong>HMA-7:-</strong> 7 year male child with short stature, consanguinity in family, moderate macrocytic anemia with HB-7, MCV-113, Iron-55, Ferritin -209, TSAT-54%. Also Bone marrow shows coarse vacuolations in erythroid cells (12%) and 19% RS. Suspicion PMS- But MLPA for mitochondrial genome normal, no deletions. Targeted panel NGS and WES reveal a heterozygous VUS in LARS2 gene (? nature).</p> <p> </p>
Testing of NBIA Genes: Analysis of Genetic Heterogeneity and Validation of Mitochondrial Markers for Assessing Causality of Sequence Variants.
ClinicalTrials.gov study NCT05615571. IPD Sharing: NO. Countries: 1. Publications: 1.
Select Nutrient and Gene Variant Analysis in a Targeted Diet and Lifestyle Intervention Reduces Preterm Birth
ClinicalTrials.gov study NCT05436119. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence
Open the record for dataset details and reuse information.
Data from: Analysis of VEGFA variants and changes in VEGF levels underscores the contribution of VEGF to polycystic ovary syndrome
Open the record for dataset details and reuse information.
Data from: Whole genome sequencing and rare variant analysis in essential tremor families
Open the record for dataset details and reuse information.
Supplementary material 3 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
United Kingdom variant interactions
Supplementary material 1 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
RBD-ACE2 complexes
Supplementary material 2 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
RBD-ACE2 interface detail
Figure 1 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 1 SARS-CoV-2 viral infection at atomic resolution. Counting eight viruses, each of which has spikes (big protrusions) and E membrane proteins (small protrusions) rainbow colored and a core in sienna color, this picture shows how the viruses approach the cell membrane (green). The ACE2 receptors are colored magenta. The field of view is 1 micrometer.
Figure 3 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 3 Detail of interface between ACE2 and SARS-CoV-2 RBD. Amino acids are labeled as well as distances. For more details please see the movies in supplementary files. Wild type is beige, UK variant is light blue and SA variant is pink (Suppl. material 2, Suppl. material 3).
Figure 2 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 2 Spike glycoprotein bound to ACE2 receptor. PDB 7DF4 (Xu et al. 2020) where ACE2 is cyan and the spike has been colored red, yellow and blue for each subunit of the trimer. This structure has been recently determined at atomic resolution. In spheres, we can see the mutations in the spike glycoprotein from the United Kingdom variant but the only mutation in the receptor binding domain (magenta) is N501Y which is labeled.
Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants
Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, the extent of presence/absence variation and the relative position of inbred-specific regions remain to be elucidated. De novo genome sequencing of the F2 maize inbred line which played a key role in European breeding programs over the past 50 years revealed thousands of novel genomic regions, making up 88Mb of DNA, that are present in the F2 but not in B73. Comparison of B73 and F2 PAV localization revealed contrasted chromosomal distributions between the two inbreds and specific evolutionary dynamics of PAVs as compared to SNPs. Detailed sequence and functional annotation of F2 PAV sequences revealed hundreds of new genes with transcriptional support, but also a large fraction of repetitive sequences. Detailed analysis of sequence breakpoint highlights the role of double strand break repair, but also transposon insertion in PAV generation. Typing of the B73 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Linkage disequilibrium (LD) analysis revealed that LD is strong within PAVs, as expected by the absence of recombination in crosses where PAV is missing in one of the parents.
Figure 4 from: Schmitt M, Uhl G (2017) Oulema septentrionis and O. erichsonii are neither conspecific nor melanic variants of O. melanopus as assessed by micro CT analysis of their lectotypes (Insecta, Coleoptera, Chrysomelidae, Criocerinae). In: Chaboo CS, Schmitt M (Eds) Research on Chrysomelidae 7. ZooKeys 720: 121-130. https://doi.org/10.3897/zookeys.720.19760
Figure 4 - Oulema erichsonii , lectotype; a median lobe with flagellum lateral b apex of median lobe with flagellum dorsal c flagellum (not to scale). 3D reconstructed microCT-scans.
Figure 2 from: Schmitt M, Uhl G (2017) Oulema septentrionis and O. erichsonii are neither conspecific nor melanic variants of O. melanopus as assessed by micro CT analysis of their lectotypes (Insecta, Coleoptera, Chrysomelidae, Criocerinae). In: Chaboo CS, Schmitt M (Eds) Research on Chrysomelidae 7. ZooKeys 720: 121-130. https://doi.org/10.3897/zookeys.720.19760
Figure 2 - Oulema septentrionis , lectotype; a: median lobe with flagellum lateral b apex of median lobe with flagellum dorsal; c: flagellum (not to scale). 3D reconstructed microCT-scans.
Figure 3 from: Schmitt M, Uhl G (2017) Oulema septentrionis and O. erichsonii are neither conspecific nor melanic variants of O. melanopus as assessed by micro CT analysis of their lectotypes (Insecta, Coleoptera, Chrysomelidae, Criocerinae). In: Chaboo CS, Schmitt M (Eds) Research on Chrysomelidae 7. ZooKeys 720: 121-130. https://doi.org/10.3897/zookeys.720.19760
Figure 3 - Oulema erichsonii (Suffrian, 1841), lectotype. a dorsal b lateral from left c labels. Scale bars: 1 mm.
Figure 1 from: Schmitt M, Uhl G (2017) Oulema septentrionis and O. erichsonii are neither conspecific nor melanic variants of O. melanopus as assessed by micro CT analysis of their lectotypes (Insecta, Coleoptera, Chrysomelidae, Criocerinae). In: Chaboo CS, Schmitt M (Eds) Research on Chrysomelidae 7. ZooKeys 720: 121-130. https://doi.org/10.3897/zookeys.720.19760
Figure 1 - Oulema septentrionis (Weise, 1880), lectotype. a dorsal b lateral from left c labels. Scale bars: 1 mm.
Fig. 1 in Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation
Fig. 1. Configuration of landmarks (red dot within yellow circles) as applied to all color pattern variation (CPV) grades of Cichla temensis. (1) the anterior point of the skull; (2) the anterior edge of the base of the first dorsal spine; (3) the center of the base of the 10 th dorsal spine; (4) the base of the first long ray of the second dorsal fin; (5) the base of the 9 th ray of the second dorsal fin; (6) the posterior point of termination of the second dorsal fin; (7) the posterior base of the anal fin; (8) the base of the 7th anal fin ray; (9) the anterior insertion of the anal fin; (10) the cloaca; (11) the ventral termination of the scale row emanating from the insertion of the 10th dorsal spine; (12) the ventral termination of the scale row emanating from the anterior point of the insertion of the pelvic fin.
Fig. 2 in Geometric morphometric analysis of cyclical body shape changes in color pattern variants of Cichla temensis Humboldt, 1821 (Perciformes: Cichlidae) demonstrates reproductive energy allocation
Fig. 2. Thin-plate-spline deformation grids depicting (a) overall body shape differences between extremes of CPV grades (magnified 3x); (b) the increase in area at the bases of the second dorsal and anal fins between extremes of CPV grades (magnified 3x).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.