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69 results for “biallelic”
Data files and videos for manuscript "Biallelic pathogenic variants in ROBO1 associate with syndromic CAKUT"
<p>#2021-11-20<br> #Summary<br> This ZIP-file contains the supplementary files of our ROBO1 study. <br> Suppl. File S1 details the next-generation sequencing-based gene panel comprising 426 CKD-associated genes performed in ID 1.<br> Suppl. File S2 contains a variant information and raw in silico data.<br> Suppl. Videos SV1A and SV1B show cardiac valve anomalies comprising mitral valve prolapse in ID 1.<br> Suppl. Video SV2 shows renal anomalies and hydroureter as documented in-vivo by microCT-scan of the mutant mice.</p> <p>#Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S1 and Suppl.File S2)<br> ./Videos/ (contains the Suppl. Videos)</p> <p><br> #Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 2BCB0774F8303FC5DBA2313DFD19FBEE Files\FileS1_Panel-Content.xlsx<br> MD5 015F01832AE1C6610D9C1FB8902FDF17 Files\FileS2_Variants-and-Domains_2021-05-18.xlsx<br> MD5 8BBE3DE1C21F161BCE07A2AFB4A6F7CD Videos\Supplementary Video SV1\Supplementary Video SV1.docx<br> MD5 5EA354253D7E489B48EDFBDE59CFB798 Videos\Supplementary Video SV1\Supplementary Video SV1A.mov<br> MD5 61796C4A5F7EAD79D642ED9D11514A95 Videos\Supplementary Video SV1\Supplementary Video SV1B.mov<br> MD5 4098A23D5CE1C67C1D507D4DD5F4F866 Videos\Supplementary Video SV2\Lo_Robo mutant.mov<br> MD5 D0B219332F227DBECF1A2A1A6AD0925A Videos\Supplementary Video SV2\Supplementary Video SV2.mov</p>
Data from: The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally
The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IAs) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IAs values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America.
ENDOG_NGS data related to article "Biallelic variants in ENDOG associated with mitochondrial myopathy and multiple mtDNA deletions" submitted to Cells
<p>vcf file of the targeted NGS; csv of the top 50 rare variants from WES prioritized by eVAI software; csv of WES rare variants prioritized by eVAI software using patient's phenotype information.</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
<p class="MsoNormal"><span>We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from an F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies</span><span>. To </span><span>demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of three true albino bison and 45 wild-type pelage color bison. Through the examination of genomic </span>variants fixed in the albino cohort and absent in the controls<span>, we identified a nonsynonymous</span> single nucleotide polymorphism (SNP) <span>mutation on chromosome 29 </span>in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provide a highly robust and informative resource for <span>genomics </span>investigations for this iconic North American species.</p>
Gene annotation for TAMU_BisBis3 in GTF format and biallelic population SNV in VCF format
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Data from: The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally
Open the record for dataset details and reuse information.
Data from: Biallelic SQSTM1 mutations in early-onset, variably progressive neurodegeneration
Objective: To characterize clinically and molecularly an early-onset, variably progressive neurodegenerative disorder characterized by a cerebellar syndrome with severe ataxia, gaze palsy, dyskinesia, dystonia, and cognitive decline affecting 11 individuals from 3 consanguineous families. Methods: We used whole-exome sequencing (WES) (families 1 and 2) and a combined approach based on homozygosity mapping and WES (family 3). We performed in vitro studies to explore the effect of the nontruncating SQSTM1 mutation on protein function and the effect of impaired SQSTM1 function on autophagy. We analyzed the consequences of sqstm1 down-modulation on the structural integrity of the cerebellum in vivo using zebrafish as a model. Results: We identified 3 homozygous inactivating variants, including a splice site substitution (c.301+2T>A) causing aberrant transcript processing and accelerated degradation of a resulting protein lacking exon 2, as well as 2 truncating changes (c.875_876insT and c.934_936delinsTGA). We show that loss of SQSTM1 causes impaired production of ubiquitin-positive protein aggregates in response to misfolded protein stress and decelerated autophagic flux. The consequences of sqstm1 down-modulation on the structural integrity of the cerebellum in zebrafish documented a variable but reproducible phenotype characterized by cerebellum anomalies ranging from depletion of axonal connections to complete atrophy. We provide a detailed clinical characterization of the disorder; the natural history is reported for 2 siblings who have been followed up for >20 years. Conclusions: This study offers an accurate clinical characterization of this recently recognized neurodegenerative disorder caused by biallelic inactivating mutations in SQSTM1 and links this phenotype to defective selective autophagy.
Study of Efficacy and Safety of Voretigene Neparvovec in Japanese Patients With Biallelic RPE65 Mutation-associated Retinal Dystrophy
ClinicalTrials.gov study NCT04516369. IPD Sharing: YES. Countries: 1. Publications: 0.
Study of Subretinally Injected ATSN-101 Administered in Patients With Leber Congenital Amaurosis Caused by Biallelic Mutations in GUCY2D
ClinicalTrials.gov study NCT03920007. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: Biallelic SQSTM1 mutations in early-onset, variably progressive neurodegeneration
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Biallelic loss-of-function mutations in MAD1 result in systemic inflammation, clonal selection of aneuploid cells and high tumor susceptibility
GEO Series GSE197267. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Human biallelic deletion involving MAB21L2 regulatory sequences reveals key to structural eye anomalies across species
GEO Series GSE241711. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression (3)
GEO Series GSE35553. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Biallelic PAX5 mutations cause hypogammaglobulinemia,sensorimotor deficits and autism spectrum disorder
GEO Series GSE182463. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Human germline biallelic complete NFAT1 deficiency causes the triad of joint contractures, osteochondromas, and susceptibility to B cell malignancy [Bulk]
GEO Series GSE193414. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Human germline biallelic complete NFAT1 deficiency causes the triad of joint contractures, osteochondromas, and susceptibility to B cell malignancy [Single]
GEO Series GSE193410. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of overgrown interscapular adipose tissue with biallelic MFN2 mutations
GEO Series GSE97156. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Biallelic and complicated inactivation of Pten in radiation-induced mouse thymic lymphomas
GEO Series GSE17751. Mus musculus. 3 samples. Type: Genome variation profiling by array.
Mono and biallelic inactivation of Huntingtin gene in patient-specific iPS cells reveal HTT roles in striatal development and in neuronal functions impaired in Huntington’s disease
GEO Series GSE228254. Homo sapiens. 31 samples. Type: Expression profiling by high throughput sequencing.
A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus [RNA-Seq]
GEO Series GSE231747. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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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.