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 …

Interpreting protein variant effects with computational predictors and deep mutational scanning

BJ Livesey, JA Marsh - Disease Models & Mechanisms, 2022 - journals.biologists.com
Computational predictors of genetic variant effect have advanced rapidly in recent years.
These programs provide clinical and research laboratories with a rapid and scalable method …

REVEL: an ensemble method for predicting the pathogenicity of rare missense variants

NM Ioannidis, JH Rothstein, V Pejaver… - The American Journal of …, 2016 - cell.com
The vast majority of coding variants are rare, and assessment of the contribution of rare
variants to complex traits is hampered by low statistical power and limited functional data …

Predicting secretory proteins with SignalP

H Nielsen - Protein function prediction: methods and protocols, 2017 - Springer
SignalP is the currently most widely used program for prediction of signal peptides from
amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway …

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 …

Embeddings from protein language models predict conservation and variant effects

C Marquet, M Heinzinger, T Olenyi, C Dallago… - Human genetics, 2022 - Springer
The emergence of SARS-CoV-2 variants stressed the demand for tools allowing to interpret
the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational …

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

V López-Ferrando, A Gazzo, X De La Cruz… - Nucleic acids …, 2017 - academic.oup.com
We present here a full update of the PMut predictor, active since 2005 and with a large
acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine …

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 …

How good are pathogenicity predictors in detecting benign variants?

A Niroula, M Vihinen - PLoS computational biology, 2019 - journals.plos.org
Computational tools are widely used for interpreting variants detected in sequencing
projects. The choice of these tools is critical for reliable variant impact interpretation for …

Variation interpretation predictors: principles, types, performance, and choice

A Niroula, M Vihinen - Human mutation, 2016 - Wiley Online Library
Next‐generation sequencing methods have revolutionized the speed of generating variation
information. Sequence data have a plethora of applications and will increasingly be used for …