Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

Regulatory variants: from detection to predicting impact

E Rojano, P Seoane, JAG Ranea… - Briefings in …, 2019 - academic.oup.com
Variants within non-coding genomic regions can greatly affect disease. In recent years,
increasing focus has been given to these variants, and how they can alter regulatory …

dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

X Liu, C Li, C Mou, Y Dong, Y Tu - Genome medicine, 2020 - Springer
Whole exome sequencing has been increasingly used in human disease studies.
Prioritization based on appropriate functional annotations has been used as an …

Leveraging polygenic functional enrichment to improve GWAS power

G Kichaev, G Bhatia, PR Loh, S Gazal, K Burch… - The American Journal of …, 2019 - cell.com
Functional genomics data has the potential to increase GWAS power by identifying SNPs
that have a higher prior probability of association. Here, we introduce a method that …

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 …

[HTML][HTML] Improved pathogenicity prediction for rare human missense variants

Y Wu, H Liu, R Li, S Sun, J Weile, FP Roth - The American Journal of …, 2021 - cell.com
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 …

Performance evaluation of pathogenicity-computation methods for missense variants

J Li, T Zhao, Y Zhang, K Zhang, L Shi… - Nucleic acids …, 2018 - academic.oup.com
With expanding applications of next-generation sequencing in medical genetics, increasing
computational methods are being developed to predict the pathogenicity of missense …

Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

BJ Livesey, JA Marsh - Molecular systems biology, 2020 - embopress.org
To deal with the huge number of novel protein‐coding variants identified by genome and
exome sequencing studies, many computational variant effect predictors (VEPs) have been …

ClinPred: prediction tool to identify disease-relevant nonsynonymous single-nucleotide variants

N Alirezaie, KD Kernohan, T Hartley, J Majewski… - The American Journal of …, 2018 - cell.com
Advances in high-throughput DNA sequencing have revolutionized the discovery of variants
in the human genome; however, interpreting the phenotypic effects of those variants is still a …

Predicting the clinical impact of human mutation with deep neural networks

L Sundaram, H Gao, SR Padigepati, JF McRae, Y Li… - Nature …, 2018 - nature.com
Millions of human genomes and exomes have been sequenced, but their clinical
applications remain limited due to the difficulty of distinguishing disease-causing mutations …