Accurate proteome-wide missense variant effect prediction with AlphaMissense

J Cheng, G Novati, J Pan, C Bycroft, A Žemgulytė… - Science, 2023 - science.org
The vast majority of missense variants observed in the human genome are of unknown
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …

Rhapsody: predicting the pathogenicity of human missense variants

L Ponzoni, DA Peñaherrera, ZN Oltvai, I Bahar - Bioinformatics, 2020 - academic.oup.com
Motivation The biological effects of human missense variants have been studied
experimentally for decades but predicting their effects in clinical molecular diagnostics …

Genome-wide prediction of disease variant effects with a deep protein language model

N Brandes, G Goldman, CH Wang, CJ Ye, V Ntranos - Nature Genetics, 2023 - nature.com
Predicting the effects of coding variants is a major challenge. While recent deep-learning
models have improved variant effect prediction accuracy, they cannot analyze all coding …

[PDF][PDF] Quantitative missense variant effect prediction using large-scale mutagenesis data

VE Gray, RJ Hause, J Luebeck, J Shendure… - Cell systems, 2018 - cell.com
Large datasets describing the quantitative effects of mutations on protein function are
becoming increasingly available. Here, we leverage these datasets to develop Envision …

[PDF][PDF] 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 …

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models

HA Shihab, J Gough, DN Cooper, PD Stenson… - Human …, 2013 - Wiley Online Library
The rate at which nonsynonymous single nucleotide polymorphisms (ns SNP s) are being
identified in the human genome is increasing dramatically owing to advances in whole …

Regional missense constraint improves variant deleteriousness prediction

KE Samocha, JA Kosmicki, KJ Karczewski… - BioRxiv, 2017 - biorxiv.org
Given increasing numbers of patients who are undergoing exome or genome sequencing, it
is critical to establish tools and methods to interpret the impact of genetic variation. While the …

Cross-protein transfer learning substantially improves disease variant prediction

M Jagota, C Ye, C Albors, R Rastogi, A Koehl… - Genome Biology, 2023 - Springer
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 …

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 …

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

S Castellana, T Mazza - Briefings in bioinformatics, 2013 - academic.oup.com
A remarkable degree of genetic variation has been found in the protein-encoding regions of
DNA through deep sequencing of samples obtained from thousands of subjects from several …