Predicting the clinical impact of human mutation with deep neural networks

Using high-resolution variant frequencies to empower clinical genome interpretation

(2017) Nicola Whiffin et al.   GENETICS IN MEDICINE

Prevalence and architecture of de novo mutations in developmental disorders

(2017)   NATURE

Evolving health care through personal genomics

(2017) Heidi L. Rehm   NATURE REVIEWS GENETICS

Structure of a eukaryotic voltage-gated sodium channel at near-atomic resolution

(2017) Huaizong Shen et al.   SCIENCE

Impending extinction crisis of the world’s primates: Why primates matter

(2017) Alejandro Estrada et al.   Science Advances

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

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

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

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

(2016) Monkol Lek et al.   NATURE

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

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

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability

(2016) Stefan H Lelieveld et al.   NATURE NEUROSCIENCE

Genetic Background Limits Generalizability of Genotype-Phenotype Relationships

(2016) Laura J. Sittig et al.   NEURON

Chimpanzee genomic diversity reveals ancient admixture with bonobos

(2016) M. de Manuel et al.   SCIENCE

Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans

(2016) Arbel Harpak et al.   PLoS Genetics

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

(2016) Sheng Wang et al.   Scientific Reports

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

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 global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Genetic studies in intellectual disability and related disorders

(2015) Lisenka E. L. M. Vissers et al.   NATURE REVIEWS GENETICS

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

ClinVar: public archive of interpretations of clinically relevant variants

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

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

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

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

De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies

(2014) Silke Appenzeller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation

(2014) Maria Livia Famiglietti et al.   HUMAN MUTATION

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

Large-scale discovery of novel genetic causes of developmental disorders

(2014) T. W. Fitzgerald et al.   NATURE

Guidelines for investigating causality of sequence variants in human disease

(2014) D. G. MacArthur et al.   NATURE

Genome sequencing identifies major causes of severe intellectual disability

(2014) Christian Gilissen et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

One gene, many neuropsychiatric disorders: lessons from Mendelian diseases

(2014) Xiaolin Zhu et al.   NATURE NEUROSCIENCE

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

De novo mutations in epileptic encephalopathies

(2013) et al.   NATURE

Great ape genetic diversity and population history

(2013) Javier Prado-Martinez et al.   NATURE

Clinical spectrum of SCN2A mutations expanding to Ohtahara syndrome

(2013) K. Nakamura et al.   NEUROLOGY

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

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

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

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study

(2012) Anita Rauch et al.   LANCET

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

(2012) Joep de Ligt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

Comparative and demographic analysis of orang-utan genomes

(2011) Devin P. Locke et al.   NATURE

The crystal structure of a voltage-gated sodium channel

(2011) Jian Payandeh et al.   NATURE

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

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

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH