The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

A variant by any name: quantifying annotation discordance across tools and clinical databases

(2017) Jennifer L. Yen et al.   Genome Medicine

Improving the in silico assessment of pathogenicity for compensated variants

(2016) Luisa Azevedo et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples

(2016) Roddy Walsh et al.   GENETICS IN MEDICINE

Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population

(2016) Sujatha Jagannathan et al.   GENOME RESEARCH

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants

(2016) Thomas A. Peterson et al.   HUMAN MUTATION

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

(2016) Meng Li et al.   HUMAN MUTATION

Actionable Genes, Core Databases, and Locus-Specific Databases

(2016) Amélie Pinard 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

IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome

(2016) Akihide Shibata et al.   JOURNAL OF HUMAN GENETICS

Molecular findings from 537 individuals with inherited retinal disease

(2016) Jamie M Ellingford et al.   JOURNAL OF MEDICAL GENETICS

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

(2016) Monkol Lek et al.   NATURE

Genome-wide significance testing of variation from single case exomes

(2016) Amy B Wilfert 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

Deep sequencing of 10,000 human genomes

(2016) Amalio Telenti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease

(2016) Jose Lugo-Martinez et al.   PLoS Computational Biology

Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations

(2015) Jennifer J. Johnston et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

(2015) Lukas Folkman et al.   BIOINFORMATICS

Complex and multi-allelic copy number variation in human disease

(2015) Christina L. Usher et al.   Briefings in Functional Genomics

Assessment of incidental findings in 232 whole-exome sequences from the Baylor–Hopkins Center for Mendelian Genomics

(2015) Julie Jurgens et al.   GENETICS IN MEDICINE

Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing

(2015) Lisa R. Susswein et al.   GENETICS IN MEDICINE

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns

(2015) Tychele N. Turner et al.   HUMAN MOLECULAR GENETICS

A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease

(2015) Mihir Anant Kamat et al.   HUMAN MUTATION

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

(2015) Christopher Douville et al.   HUMAN MUTATION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes

(2015) Albino Bacolla et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of interpretations of clinically relevant variants

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

The human gene damage index as a gene-level approach to prioritizing exome variants

(2015) Yuval Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

(2015) Y. Xue et al.   SCIENCE

Effect of predicted protein-truncating genetic variants on the human transcriptome

(2015) M. A. Rivas et al.   SCIENCE

Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data

(2015) Mengmeng Wu et al.   Scientific Reports

Secondary findings and carrier test frequencies in a large multiethnic sample

(2015) Tomasz Gambin et al.   Genome Medicine

Pathogenic Variants for Mendelian and Complex Traits in Exomes of 6,517 European and African Americans: Implications for the Return of Incidental Results

(2014) Holly K. Tabor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Copy number variations and human genetic disease

(2014) Fady M. Mikhail   CURRENT OPINION IN PEDIATRICS

Novel genotype–phenotype associations demonstrated by high-throughput sequencing in patients with hypertrophic cardiomyopathy

(2014) Luis R Lopes et al.   HEART

Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation

(2014) X. Zhang et al.   HUMAN MOLECULAR GENETICS

Elucidating Common Structural Features of Human Pathogenic Variations Using Large-Scale Atomic-Resolution Protein Networks

(2014) Jishnu Das et al.   HUMAN MUTATION

Diagnostic Exome Sequencing to Elucidate the Genetic Basis of Likely Recessive Disorders in Consanguineous Families

(2014) Periklis Makrythanasis et al.   HUMAN MUTATION

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Phen-Gen: combining phenotype and genotype to analyze rare disorders

(2014) Asif Javed et al.   NATURE METHODS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes 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

MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing

(2014) Matthew Mort et al.   GENOME BIOLOGY

Actionable, Pathogenic Incidental Findings in 1,000 Participants’ Exomes

(2013) Michael O. Dorschner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using Exome Data to Identify Malignant Hyperthermia Susceptibility Mutations

(2013) Stephen G. Gonsalves et al.   ANESTHESIOLOGY

CRAVAT: cancer-related analysis of variants toolkit

(2013) Christopher Douville et al.   BIOINFORMATICS

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

Interpreting Secondary Cardiac Disease Variants in an Exome Cohort

(2013) David Ng et al.   Circulation-Cardiovascular Genetics

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease

(2013) David N. Cooper et al.   HUMAN GENETICS

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

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

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

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

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

(2013) Albino Bacolla et al.   PLoS Genetics

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

(2012) Yali Xue et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Secondary Variants in Individuals Undergoing Exome Sequencing: Screening of 572 Individuals Identifies High-Penetrance Mutations in Cancer-Susceptibility Genes

(2012) Jennifer J. Johnston et al.   AMERICAN JOURNAL OF HUMAN GENETICS

regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions

(2012) Mingxiang Teng et al.   BIOINFORMATICS

Exploring concordance and discordance for return of incidental findings from clinical sequencing

(2012) Robert C. Green et al.   GENETICS IN MEDICINE

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain

(2012) George P. Patrinos 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

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

(2012) S. E. Calvo et al.   Science Translational Medicine

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

(2011) David N. Cooper et al.   HUMAN MUTATION

LOVD v.2.0: the next generation in gene variant databases

(2011) Ivo F. A. C. Fokkema et al.   HUMAN MUTATION

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

(2011) Guangmei Yan et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The functional spectrum of low-frequency coding variation

(2011) Gabor T Marth et al.   GENOME BIOLOGY

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

(2010) David N. Cooper et al.   HUMAN MUTATION

Sequencing and analysis of an Irish human genome

(2010) Pin Tong et al.   GENOME BIOLOGY

Automated inference of molecular mechanisms of disease from amino acid substitutions

(2009) B. Li et al.   BIOINFORMATICS

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE