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2,880 results for “variant”
Gaps and complex structurally variant loci in phased genome assemblies
<p>Supplementary data including code for an science article 'Gaps and complex structurally variant loci in phased genome assemblies'.</p>
Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants
<p>Scripts and Data to reproduce plots in</p> <p>Sören von Bülow, Mateusz Sikora, Florian E.C. Blanc, Roberto Covino, Gerhard Hummer, "Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants", PLoS Computational Biology 202X</p>
dataset related to article "Pathogenic variants in ATP5F1B are associated with dominantly inherited dystonia" submitted to BRAIN
<p>Raw Data supporting results of the article mentioned at title: Images of JC-1 and mitotracker staining on fibroblasts from members of families A and B</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>
FIGURE 2 in A new species of bamboo-feeding leafhopper genus Mukariella Viraktamath and Webb (Hemiptera: Cicadellidae) along with its morphological variant from India
FIGURE 2 (A–J). Mukariella viraktamathi sp. nov., (variant of new species) A. Dorsal habitus; B. Lateral habitus; C. Pronotum; D. Face; E.Geniatal capsule, lateral view; F. Pygofer, ventral view; G. style; H. Subgenital plate with valve & style; I. Aedeagus dorsal view; J. Aedeagus lateral view.
FIGURE 1 in A new species of bamboo-feeding leafhopper genus Mukariella Viraktamath and Webb (Hemiptera: Cicadellidae) along with its morphological variant from India
FIGURE 1 (A–J). Mukariella viraktamathi sp. nov., A. Dorsal habitus; B. Lateral habitus; C. Pronotum; D. Face; E.Geniatal capsule, lateral view; F.Pygofer, ventral view; G. style; H. Subgenital plate with valve & style; I. Aedeagus dorsal view; J. Aedeagus lateral view.
FIGURE 3 in A new species of bamboo-feeding leafhopper genus Mukariella Viraktamath and Webb (Hemiptera: Cicadellidae) along with its morphological variant from India
FIGURE 3 (A–I). Mukariella viraktamathi sp. nov., (Female) A. Dorsal habitus; A. Lateral habitus; C. Pronotum; D. Face; E. sternite VII; (F–G). Valvulae I; (H–I). Valvulae II.
Data for: Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs
<p><span>Hundreds of genetic variants implicated in Mendelian disease have been characterized in dogs and commercial screening is being offered for most of them worldwide. There is typically limited information available regarding the broader population frequency of variants and uncertainty regarding their functional and clinical impact in ancestry backgrounds beyond the discovery breed. Genetic panel screening of disease variants, commercially offered directly to the consumer or via a veterinary clinician, provides an opportunity to establish large-scale cohorts with phenotype data available to address open questions related to variant prevalence and relevance. We screened the largest canine cohort examined in a single study to date (1,054,293 representative dogs from our existing cohort of 3.5 million; a total of 811,628 mixed breed dogs and 242,665 purebreds from more than 150 countries) to examine the prevalence and distribution of a total of 250 genetic disease-associated variants in the general population. Electronic medical records from veterinary clinics were available for 43.5% of the genotyped dogs, enabling the clinical impact of variants to be investigated. We provide detailed frequencies for all tested variants across breeds and find that 57% of dogs carry at least one copy of a studied Mendelian disease-associated variant. Focusing on a subset of variants, we provide evidence of full penetrance for 10 variants, and at minimum plausible evidence for clinical significance of 22 variants, on diverse breed backgrounds. Specifically, we report that inherited hypocatalasia is a notable oral health condition, confirm that factor VII deficiency presents as subclinical bleeding propensity and verify two genetic causes of reduced leg length. We further assess genome-wide heterozygosity levels in over 100 breeds and show that a reduction in genome-wide heterozygosity is associated with an increased Mendelian disease load. The accumulated knowledge represents a resource to guide discussions on genetic test relevance by breed.</span></p>
Dataset related to article "BEHAVIORAL AND COGNITIVE PHENOTYPES OF PATIENTS WITH AMYOTROPHIC LATERAL SCLEROSIS CARRYING SOD1 VARIANTS"
<p><strong>ngs_analysis performedn as part of the study mentioned at title</strong></p>
Phylogenomic data of Litsea complex based on genome-wide single-nucleotide variants (SNVs) and plastomes
<p>In this study, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of evergreen broadleaved forests (EBLFs) in East Asia to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) and plastomes. Finally, the dataset of phylogenomic matrices was generated, including five genome-wide SNVs dataset and plastomes matrix used for phylogenetic analysis.</p>
FIGURE2. Platynaspis flavoguttata (Gorham) (non-type material): a. adult, dorsal view; b. adult, lateral view; c. adult, frontal view; d. adult, variant; e. abdominal postcoxal line; f–h. male genitalia: f. tegmen, lateral view; g. tegmen, ventral view; h. penis. in A review of Platynaspini (Coleoptera: Coccinellidae) of the Indian subcontinent, including description of a new genus from north-eastern India and Bangladesh
FIGURE2. Platynaspis flavoguttata (Gorham) (non-type material): a. adult, dorsal view; b. adult, lateral view; c. adult, frontal view; d. adult, variant; e. abdominal postcoxal line; f–h. male genitalia: f. tegmen, lateral view; g. tegmen, ventral view; h. penis.
FIGURE11. Life stages of Platynaspis variegata Crotch: a, b, d–i. larva; c. adult, nominate form; j–m. darker variant (Image credits: Dr Rojeet Thangjam, CAU, Imphal). in A review of Platynaspini (Coleoptera: Coccinellidae) of the Indian subcontinent, including description of a new genus from north-eastern India and Bangladesh
FIGURE11. Life stages of Platynaspis variegata Crotch: a, b, d–i. larva; c. adult, nominate form; j–m. darker variant (Image credits: Dr Rojeet Thangjam, CAU, Imphal).
FIGURE 10. Platynaspis variegata Crotch: a–c. variants; d. abdomen, male; e. abdominal postcoxal line; f. coxites; g. spermatheca; h–j. male genitalia: h. tegmen, lateral view; i. tegmen, lateral view; j. penis. in A review of Platynaspini (Coleoptera: Coccinellidae) of the Indian subcontinent, including description of a new genus from north-eastern India and Bangladesh
FIGURE 10. Platynaspis variegata Crotch: a–c. variants; d. abdomen, male; e. abdominal postcoxal line; f. coxites; g. spermatheca; h–j. male genitalia: h. tegmen, lateral view; i. tegmen, lateral view; j. penis.
A complete list of filtered variants and gene lists of frequently and recurrently mutated genes in 25 MCL patients at diagnosis compared to relapse, as well as a CNV genelist
<p>Supplemental Table 1 shows a complete list of variants which passed filtering described in supplemental methods, that were found in both diagnostic samples and relapsed samples (i.e., shared variants, sheet 1A), variants that were newly detected – N/D (sheet 1B) or newly undetected – N/U (sheet 1C). Gene lists for filtration of variants and CNV changes in genes of special interest are included in the table (sheet 1D). Chr - Chromosome, REF - Reference allele, ALT - Alternative allele, AA change - Amino acid change, DG_AF – Variant Allele frequency in the diagnostic sample, DG_Depth - Read depth in the diagnostic sample, REL_AF - Variant Allele frequency in the relapsed sample, REL_Depth - Read depth in the relapsed sample, SNV - Single Nucleotide Variant, and CNV - Copy Number Variation. </p>
Data for: Biochemical properties of naturally occurring human bloom helicase variants
<p>Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human <em>BLM</em> cause Bloom syndrome (BS), an autosomal recessive disorder that leads to myriad negative health impacts including a predisposition to cancer. BS-causing mutations in <em>BLM</em> often negatively impact BLM ATPase and helicase activity. While <em>BLM</em> mutations that cause BS have been well characterized both in vitro and in vivo, there are other less studied <em>BLM</em> mutations that exist in the human population that do not lead to BS. Two of these non-BS mutations, encoding BLM P868L and BLM G1120R, when homozygous, increase sister chromatid exchanges in human cells. To characterize these naturally occurring BLM mutant proteins <em>in vitro</em>, we purified the BLM catalytic core with either the P868L or G1120R substitution. We also purified a BLM K869A K870A mutant protein, which alters a lysine-rich loop proximal to the P868 residue. We found that BLM P868L and BLM G1120R were both able to hydrolyze ATP, bind diverse DNA substrates, and unwind G-quadruplex and duplex DNA structures. Molecular dynamics simulations suggest that the P868L substitution weakens the DNA interaction with the winged-helix domain of BLM and alters the orientation of lobe 1 of the ATPase domain. Because BLM P868L and BLM G1120R retain helicase function in vitro, it is likely that the increased genome instability is caused by specific impacts of the mutant proteins in vivo. Interestingly, we found that BLM K869A K870A has diminished ATPase activity compared to wild-type BLM, weakened binding to duplex DNA structures, and less robust helicase activity. Thus, the lysine-rich loop may have an important role in ATPase activity and specific binding and DNA unwinding functions in BLM.</p>
Supplementary data for "Engineering PD-1-targeted small protein variants for in vitro diagnostics and in vivo PET imaging"
<p>Supplementary data for "Engineering PD-1-targeted small protein variants for in vitro diagnostics and in vivo PET imaging". The docking.zip file contains ClusPro protein/protein docking results for all binding protein variants using either murine PD-1 structure (3bikB) or human PD-1 AF2 model as receptors. The pymol session contains data and scenes used to generate the Figures in the paper.</p>
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
<p>Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (<a href="https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts">https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts</a>).</p>
Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data
<p>Source data for the paper "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data"</p>
Benchmarking splice variant prediction algorithms using massively parallel splicing assays
<p>Dataset, jupyter notebooks, and support python modules for "Benchmarking splice variant prediction algorithms using massively parallel splicing assays" (Smith and Kitzman, 2023)</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>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.