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Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
BackgroundA major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five...
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Phenotypic similarity-based approach for variant prioritization for unsolved rare disease: a preliminary methodological report
Rare diseases (RD) have a prevalence of not more than 1/2000 persons in the European population, and are characterised by the difficulty experienced...
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Explicable prioritization of genetic variants by integration of rule-based and machine learning algorithms for diagnosis of rare Mendelian disorders
BackgroundIn the process of finding the causative variant of rare diseases, accurate assessment and prioritization of genetic variants is essential....
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Bayesian network-based Mendelian randomization for variant prioritization and phenotypic causal inference
Mendelian randomization is a powerful method for inferring causal relationships. However, obtaining suitable genetic instrumental variables is often...
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GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation
BackgroundVariant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually...
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Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease
Background5’ untranslated regions (5’UTRs) are essential modulators of protein translation. Predicting the impact of 5’UTR variants is challenging...
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A recurrent synonymous L1CAM variant in a fetus with hydrocephalus
We report the case of a hydrocephalic fetus in which clinical exome sequencing revealed a recurrent synonymous variant of unknown significance,...
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ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization
BackgroundWhole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions....
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Burden re-analysis of neurodevelopmental disorder cohorts for prioritization of candidate genes
This study aimed to uncover novel genes associated with neurodevelopmental disorders (NDD) by leveraging recent large-scale de novo burden analysis...
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APF2: an improved ensemble method for pharmacogenomic variant effect prediction
Lack of efficacy or adverse drug response are common phenomena in pharmacological therapy causing considerable morbidity and mortality. It is...
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Genome sequencing-based discovery of a novel deep intronic APC pathogenic variant causing exonization
Familial adenomatous polyposis (FAP) is a hereditary cancer syndrome that occurs as a result of germline mutations in the APC gene. Despite a clear...
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Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy
BackgroundDilated cardiomyopathy (DCM) is a major cause of sudden cardiac death and heart failure. Up to 50% of all DCM cases have a genetic...
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Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis
We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and...
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Prioritization of disease genes from GWAS using ensemble-based positive-unlabeled learning
A primary challenge in understanding disease biology from genome-wide association studies (GWAS) arises from the inability to directly implicate...
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Copy number variant analysis for syndromic congenital heart disease in the Chinese population
BackgroundSyndromic congenital heart disease (CHD) is among the most severe conditions in the pediatric population. Copy number variant (CNV) is an...
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VARista: a free web platform for streamlined whole-genome variant analysis across T2T, hg38, and hg19
With the increasing importance of genomic data in understanding genetic diseases, there is an essential need for efficient and user-friendly tools...
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Detection of a novel pathogenic variant in KCNH2 associated with long QT syndrome 2 using whole exome sequencing
BackgroundLong QT syndrome (LQTS) is a cardiac channelopathy characterized by impaired myocardial repolarization that predisposes to life-threatening...
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Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Genome-wide association studies (GWASs) have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variants within...
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GM2 Gangliosidosis: Whole-Exome Sequencing Reveals Novel Homozygous Pathogenic Variant within the HEXA Gene in Iranian Family
AbstractGM2 gangliosidosis is a hereditary lysosomal storage disorder resulting from mutations in the Hexosaminidase A (HEXA) gene, which leads to a...
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Somatic and Germline Variant Calling from Next-Generation Sequencing Data
Re-sequencing of the human genome by next-generation sequencing (NGS) has been widely applied to discover pathogenic genetic variants and/or...