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Variants that alter gene splicing are estimated to comprise up to a third of all disease-causing variants, yet they are hard to predict from DNA sequencing data alone. To overcome this, many groups are incorporating RNA-based analyses, which are resource intensive, particularly for diagnostic laboratories. There are thousands of functionally validated variants that induce mis-splicing; however, this information is not consolidated, and they are under-represented in ClinVar, which presents a barrier to variant interpretation and can result in duplication of validation efforts. To address this issue, we developed SpliceVarDB, an online database consolidating over 50,000 variants assayed for their effects on splicing in over 8,000 human genes. We evaluated over 500 published data sources and established a spliceogenicity scale to standardize, harmonize, and consolidate variant validation data generated by a range of experimental protocols. According to the strength of their supporting evidence, variants were classified as "splice-altering" (∼25%), "not splice-altering" (∼25%), and "low-frequency splice-altering" (∼50%), which correspond to weak or indeterminate evidence of spliceogenicity. Importantly, 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). These variants can support the variant curation diagnostic pathway and can be used to provide the high-quality data necessary to develop more accurate in silico splicing predictors. The variants are accessible through an online platform, SpliceVarDB, with additional features for visualization, variant information, in silico predictions, and validation metrics. SpliceVarDB is a very large collection of splice-altering variants and is available at https://splicevardb.org.
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http://dx.doi.org/10.1016/j.ajhg.2024.08.002 | DOI Listing |
Epilepsia Open
December 2024
Integrated Diagnostics for Epilepsy, Department of Diagnostic and Technology, European Reference Network EPIcare, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
Neuronal ceroid lipofuscinoses (NCLs) are genetically heterogeneous neurodegenerative disorders, characterized by progressive cognitive and motor decline, epilepsy, visual impairment, and shortened life-expectancy. CLN6-related NCLs include both late-infantile and adult myoclonic form. We report a 21-year-old patient, with mild developmental delay, who developed occipital seizures at 14 years, and subsequently cognitive decline, cortical myoclonus, and photosensitivity at low and higher frequencies.
View Article and Find Full Text PDFBioinformatics
December 2024
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States.
Motivation: The Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150,000 genome VCF would occupy 900 TiB, making it costly and complicated to produce, analyze, and store. The issue stems from VCF's requirement to densely represent both reference-genotypes and allele-indexed arrays.
View Article and Find Full Text PDFSurg Radiol Anat
December 2024
Department of Anatomy, School of Medicine, Faculty of Health Sciences, National and Kapodistrian University of Athens, 75 Mikras Asias street, Goudi, 11527, Athens, Greece.
Background: Bipartite medial cuneiform bone (BMC) is located at the Lisfranc joint of the midfoot, and it represents a rare variant involving two separate ossification centers in the medial cuneiform bone. Although BMC is typically asymptomatic, it can become clinically relevant under conditions of trauma or chronic stress, affecting foot stability.
Case Report: The current imaging report describes a 48-year-old female presenting with chronic dorsal midfoot pain, worsened by extended standing and ambulation.
Ann Hum Genet
December 2024
Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
Introduction: The common genetic underpinnings of psoriasis and pulmonary comorbidities have yet to be explored.
Material And Methods: In this cross-sectional study, we investigated the single-nucleotide polymorphisms (SNPs) associated with psoriasis and their relationship with pulmonary function using data from the UK Biobank (UKBB) and the Vanderbilt University Medical Center Biobank (BioVU).
Results: Out of the 63 psoriasis-associated SNPs identified in previous genome-wide association studies within the European population, we successfully identified 53 SNPs, including proxy SNPs in UKBB database.
Eur J Cancer Prev
December 2024
Department of Digestive Endoscopy, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, China.
This study examines the global burden of pancreatic cancer from 1990 to 2021 and projects future trends, aiming to provide insights for health policy and resource allocation to mitigate the disease's impact. We assessed the pancreatic cancer burden globally and by subgroups, employing linear regression models to analyze trends from 1990 to 2021. Cluster analysis was used to evaluate burden patterns across Global Burden of Disease regions.
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