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15 results for “variant interpretation”
Tissue-aware interpretation of genetic variants advances the etiology of rare diseases
<p>Pathogenic variants underlying Mendelian diseases often disrupt the normal physiology of a<br>few tissues and organs. However, variant effect prediction tools that aim to identify<br>pathogenic variants are typically oblivious to tissue contexts. Here we report a machine-<br>learning framework, denoted ‘Tissue Risk Assessment of Causality by Expression for<br>variants’ (TRACEvar, https://netbio.bgu.ac.il/TRACEvar/), that offers two advancements.<br>First, TRACEvar predicts pathogenic variants that disrupt the normal physiology of specific<br>tissues. This was achieved by creating 14 tissue-specific models that were trained on over<br>14,000 variants and combined 84 attributes of genetic variants with 495 attributes derived<br>from tissue omics. TRACEvar outperformed 10 well-established and tissue-oblivious variant<br>effect prediction tools. Second, the resulting models are interpretable, thereby illuminating<br>variants' mode-of-action. Application of TRACEvar to variants of 52 rare-disease patients<br>highlighted pathogenicity mechanisms and relevant disease processes. Lastly, interpretation<br>of large-scale models revealed that top-ranking determinants of pathogenicity included<br>attributes of disease-affected tissues, particularly cellular process activities. Hence, tissue<br>contexts and interpretable machine-learning models can greatly enhance the etiology of rare<br>diseases.</p> <p>Article link: https://www.embopress.org/doi/full/10.1038/s44320-024-00061-6</p> <p> </p>
Additional datasets and code accompanying the article "Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines"
<p> </p> <p> </p> <p>Datasets and code accompanying the manuscript titled “Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines” by Rajarshi Ghosh, Ninak Oak and Sharon E. Plon.</p>
Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics
<p>Bridging the Chromosome-Centric and Biology and Disease Human Proteome Projects: Accessible and automated tools for interpreting biological and pathological impact of protein sequence variants detected via proteogenomics</p>
Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome
<p><span>Modern sequencing technologies have revolutionised our detection of gene variants. However, in most genes, including <em>KCNH2</em>, the majority of missense variants are currently classified as variants of uncertain significance (VUS). The aim of this study </span><span class="normaltextrun"><span>was to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the <em>KCNH2 </em>gene. </span></span><span>The assay was designed according to recommendations proposed by the ClinGen Sequence Variant Interpretation Working Group. Thirty-one variants (17 pathogenic/likely pathogenic, 14 benign/likely benign) were classified internally as variant controls. They were heterozygously expressed in Flp-In HEK293 cells for assessing the effects of variant on current density and channel gating in order to determine the sensitive and specificity of the assay. All 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for VUS reclassification. Inclusion of <em>KCNH2</em> functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic. The high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical <em>KCNH2</em> variants and </span><span>demonstrates the value of developing automated patch clamp assays for functional characterisation of ion channel gene variants.</span></p>
Patch-clamp dataset (SyncroPatch384PE) for control variants used in a calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome
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A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ATAC-seq]
GEO Series GSE263338. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [ChIP-seq]
GEO Series GSE263337. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [wt RNA-seq]
GEO Series GSE267549. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [STARR-RNA-seq]
GEO Series GSE263335. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
DAVI: A Dataset for Automatic Variant Interpretation
<p><span>The analysis of an individual’s genetic material may uncover genetic variants, which can be classified as disease-causing (pathogenic) or benign. Identifying pathogenic variants among millions of variants relies on the research of evidence in support of or against variant pathogenicity, a process regulated by the American College of Molecular Genetics (ACMG) guidelines, which leverages data from the scientific literature. Despite recent improvements towards automation, searching shreds of evidence for pathogenicity in the literature still requires manual curation, a time-consuming process, due to the ever-growing number of published papers. </span></p> <p><span>In this work, we built DAVI (Dataset for Automatic Variant Interpretation), a reliable, manually curated dataset comprising 1239 sentences extracted from 311 (variant, article) associations </span><span>for a pool of 41 variants. 597 sentences </span>contain (positive) evidence activating two opposing ACGM criteria, namely PS3 and BS3, while the remaining 642 do not contain (negative) evidence activating either of the two considered ACGM criteria. (variant, article) associations containing<span> at least one positive sentence are classified as positive, while (variant, article) associations containing any positive sentence are negative. Therefore DAVI also contains 154 positive and 157 negative (variant, article) associations. </span></p> <p> </p>
A functional genomics atlas enhanced by convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements [plasmid DNA-seq]
GEO Series GSE263336. Homo sapiens. 4 samples. Type: Other.
CRISPR gene editing, cardiac disease modelling and transcriptomics interpretation of a novel GATA4 patient genetic variant
GEO Series GSE229879. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing; Other.
Deep mutational scanning of CHD2 for variant interpretation in neurodevelopmental disorders
GEO Series GSE316550. Homo sapiens. 16 samples. Type: Methylation profiling by genome tiling array.
Deep mutational scanning of CHD2 for variant interpretation in neurodevelopmental disorders [RNA-seq]
GEO Series GSE316724. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Clinical Interpretation of Variants in Cancer
CIViC provides an educational resource to support better understanding of the current state of precision medicine. It may also provide useful summaries and links to relevant published evidence for the clinical relevance of specific variants. With appropriate validation (e.g., in a CLIA certified, CAP accredited environment) it may also be used to develop panels or software for variant interpretation in a clinical diagnostic setting. However, direct use of the CIViC application and website is intended for purely research purposes. It should not be used for emergencies or for medical or professional advice.
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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.