Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria

Opportunities and challenges for the computational interpretation of rare variation in clinically important genes

(2021) Gregory McInnes et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Variant curation expert panel recommendations for RYR1 pathogenicity classifications in malignant hyperthermia susceptibility

(2021) Jennifer J. Johnston et al.   GENETICS IN MEDICINE

Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes

(2021) C. Cubuk et al.   GENETICS IN MEDICINE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Problems in variation interpretation guidelines and in their implementation in computational tools

(2020) Mauno Vihinen   Molecular Genetics & Genomic Medicine

Fitting a naturally scaled point system to the ACMG/AMP variant classification guidelines

(2020) Sean V. Tavtigian et al.   HUMAN MUTATION

Assessing performance of pathogenicity predictors using clinically relevant variant datasets

(2020) Adam C Gunning et al.   JOURNAL OF MEDICAL GENETICS

Calibrating variant-scoring methods for clinical decision making

(2020) Silvia Benevenuta et al.   BIOINFORMATICS

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

(2020) Vikas Pejaver et al.   Nature Communications

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

(2020) Xiaoming Liu et al.   Genome Medicine

VIPdb, a genetic Variant Impact Predictor Database

(2019) Zhiqiang Hu et al.   HUMAN MUTATION

REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification

(2019) Yuan Tian et al.   Scientific Reports

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

(2019) Sarah E. Brnich et al.   Genome Medicine

Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework

(2018) Sean V Tavtigian et al.   GENETICS IN MEDICINE

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar

(2017) Steven M. Harrison et al.   GENETICS IN MEDICINE

PERCH: A Unified Framework for Disease Gene Prioritization

(2017) Bing-Jian Feng   HUMAN MUTATION

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Nilah M. Ioannidis et al.   AMERICAN 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

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

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

(2014) Panagiotis Katsonis et al.   GENOME RESEARCH

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

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

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

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

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

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

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH