How good are pathogenicity predictors in detecting benign variants?

Generalising better: Applying deep learning to integrate deleteriousness prediction scores for whole-exome SNV studies

(2018) Ilia Korvigo et al.   PLoS One

Reports from CAGI: The Critical Assessment of Genome Interpretation

(2017) Roger A Hoskins et al.   HUMAN MUTATION

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation

(2017) Yuya Kobayashi et al.   Genome Medicine

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PON-Sol: prediction of effects of amino acid substitutions on protein solubility

(2016) Yang Yang et al.   BIOINFORMATICS

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

(2016) Haiming Tang et al.   GENETICS

Variation Interpretation Predictors: Principles, Types, Performance, and Choice

(2016) Abhishek Niroula et al.   HUMAN MUTATION

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

(2016) Haiming Tang et al.   GENETICS

Correct machine learning on protein sequences: a peer-reviewing perspective

(2015) Ian Walsh et al.   BRIEFINGS IN BIOINFORMATICS

Guidelines for diagnostic next-generation sequencing

(2015) Gert Matthijs et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

VariSNP, A Benchmark Database for Variations From dbSNP

(2015) Gerard C.P. Schaafsma et al.   HUMAN MUTATION

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

No more hidden solutions in bioinformatics

(2015) Mauno Vihinen   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants

(2015) Abhishek Niroula et al.   PLoS One

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson et al.   JOURNAL OF MOLECULAR BIOLOGY

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

(2012) Mauno Vihinen   BMC GENOMICS

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis

(2012) Mauno Vihinen   HUMAN MUTATION

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Prediction of disease-related mutations affecting protein localization

(2009) Kirsti Laurila et al.   BMC GENOMICS

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION