Inferring the molecular and phenotypic impact of amino acid variants with MutPred2
Identifying pathogenic variants and underlying functional alterations is challenging. To this
end, we introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid …
end, we introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid …
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants
Motivation Loss-of-function genetic variants are frequently associated with severe clinical
phenotypes, yet many are present in the genomes of healthy individuals. The available …
phenotypes, yet many are present in the genomes of healthy individuals. The available …
Automated inference of molecular mechanisms of disease from amino acid substitutions
Motivation: Advances in high-throughput genotyping and next generation sequencing have
generated a vast amount of human genetic variation data. Single nucleotide substitutions …
generated a vast amount of human genetic variation data. Single nucleotide substitutions …
Updated benchmarking of variant effect predictors using deep mutational scanning
BJ Livesey, JA Marsh - Molecular systems biology, 2023 - embopress.org
The assessment of variant effect predictor (VEP) performance is fraught with biases
introduced by benchmarking against clinical observations. In this study, building on our …
introduced by benchmarking against clinical observations. In this study, building on our …
Towards precision medicine: advances in computational approaches for the analysis of human variants
TA Peterson, E Doughty, MG Kann - Journal of molecular biology, 2013 - Elsevier
Variations and similarities in our individual genomes are part of our history, our heritage,
and our identity. Some human genomic variants are associated with common traits such as …
and our identity. Some human genomic variants are associated with common traits such as …
The mutation significance cutoff: gene-level thresholds for variant predictions
Next-generation sequencing (NGS) identifies about 20,000 variants per exome, of which
only a few may underlie genetic diseases. Variant-level methods such as PolyPhen-2 …
only a few may underlie genetic diseases. Variant-level methods such as PolyPhen-2 …
The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity
DG Grimm, CA Azencott, F Aicheler, U Gieraths… - Human …, 2015 - Wiley Online Library
Prioritizing missense variants for further experimental investigation is a key challenge in
current sequencing studies for exploring complex and Mendelian diseases. A large number …
current sequencing studies for exploring complex and Mendelian diseases. A large number …
Disease variant prediction with deep generative models of evolutionary data
Quantifying the pathogenicity of protein variants in human disease-related genes would
have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of …
have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of …
Cross-protein transfer learning substantially improves disease variant prediction
Background Genetic variation in the human genome is a major determinant of individual
disease risk, but the vast majority of missense variants have unknown etiological effects …
disease risk, but the vast majority of missense variants have unknown etiological effects …
[HTML][HTML] Improved pathogenicity prediction for rare human missense variants
The success of personalized genomic medicine depends on our ability to assess the
pathogenicity of rare human variants, including the important class of missense variation …
pathogenicity of rare human variants, including the important class of missense variation …