Settling the score: variant prioritization and Mendelian disease

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity

(2017) Danish Saleheen et al.   NATURE

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

(2017) Yi-Fei Huang et al.   NATURE GENETICS

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories

(2017) Kenneth D. Doig et al.   Genome Medicine

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

Frequency and Complexity of De Novo Structural Mutation in Autism

(2016) William M. Brandler 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

HGVS Recommendations for the Description of Sequence Variants: 2016 Update

(2016) Johan T. den Dunnen et al.   HUMAN MUTATION

The Promise and Peril of Precision Medicine

(2016) Jaeger P. Ackerman et al.   MAYO CLINIC PROCEEDINGS

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

(2016) Monkol Lek et al.   NATURE

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

(2016) Claire Redin et al.   NATURE GENETICS

Publicly Available Data Provide Evidence against NR1H3 R415Q Causing Multiple Sclerosis

(2016) Eric Vallabh Minikel et al.   NEURON

The Human Phenotype Ontology in 2017

(2016) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

A federated ecosystem for sharing genomic, clinical data

(2016)   SCIENCE

Alternate-locus aware variant calling in whole genome sequencing

(2016) Marten Jäger et al.   Genome Medicine

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

(2016) Regis A. James et al.   Genome Medicine

The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities

(2015) Jessica X. Chong et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi 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

Homozygous loss-of-function variants in European cosmopolitan and isolate populations

(2015) Vera B. Kaiser et al.   HUMAN MOLECULAR GENETICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

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

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

(2015) Hui Yang et al.   NATURE METHODS

Next-generation diagnostics and disease-gene discovery with the Exomiser

(2015) Damian Smedley et al.   Nature Protocols

TBX6 Null Variants and a Common Hypomorphic Allele in Congenital Scoliosis

(2015) Nan Wu et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Phenotype-driven strategies for exome prioritization of human Mendelian disease genes

(2015) Damian Smedley et al.   Genome Medicine

Rare variant association studies: considerations, challenges and opportunities

(2015) Paul L Auer et al.   Genome Medicine

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Improving the Sequence Ontology terminology for genomic variant annotation

(2015) Fiona Cunningham et al.   Journal of Biomedical Semantics

Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings

(2015) Laurel K Willig et al.   Lancet Respiratory Medicine

Variant Association Tools for Quality Control and Analysis of Large-Scale Sequence and Genotyping Array Data

(2014) Gao T. Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Compound Heterozygosity of Low-Frequency Promoter Deletions and Rare Loss-of-Function Mutations in TXNL4A Causes Burn-McKeown Syndrome

(2014) Dagmar Wieczorek et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rare-Variant Association Analysis: Study Designs and Statistical Tests

(2014) Seunggeung Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families

(2014) Marc V. Singleton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FLAGS, frequently mutated genes in public exomes

(2014) Casper Shyr et al.   BMC Medical Genomics

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

(2014) Iakes Ezkurdia et al.   HUMAN MOLECULAR GENETICS

Guidelines for investigating causality of sequence variants in human disease

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

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data

(2014) Hao Hu et al.   NATURE BIOTECHNOLOGY

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

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

(2014) Martin Kircher et al.   NATURE GENETICS

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

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

bam.iobio: a web-based, real-time, sequence alignment file inspector

(2014) Chase A Miller et al.   NATURE METHODS

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

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray 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

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

VariantDB: a flexible annotation and filtering portal for next generation sequencing data

(2014) Geert Vandeweyer et al.   Genome Medicine

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

(2014) Catherine A Brownstein et al.   GENOME BIOLOGY

Clinical analysis of genome next-generation sequencing data using the Omicia platform

(2013) Emily M Coonrod et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

VAAST 2.0: Improved Variant Classification and Disease-Gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix

(2013) Hao Hu et al.   GENETIC EPIDEMIOLOGY

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

PhenoTips: Patient Phenotyping Software for Clinical and Research Use

(2013) Marta Girdea et al.   HUMAN MUTATION

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

A synonymous change, p.Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett Syndrome patient

(2013) Taimoor I Sheikh et al.   Orphanet Journal of Rare Diseases

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

(2013) Slavé Petrovski et al.   PLoS Genetics

Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation

(2012) Jeffrey M. Kidd et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies

(2012) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

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

Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users

(2012) Ana Rath et al.   HUMAN MUTATION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012)   NATURE

Truncations of Titin Causing Dilated Cardiomyopathy

(2012) Daniel S. Herman et al.   NEW ENGLAND JOURNAL OF MEDICINE

dbVar and DGVa: public archives for genomic structural variation

(2012) Ilkka Lappalainen et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

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

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Population genetics of malaria resistance in humans

(2011) P W Hedrick   HEREDITY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The case for locus-specific databases

(2011) Mark E. Samuels et al.   NATURE REVIEWS GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

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

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

(2010) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

(2010) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Keratin gene mutations in disorders of human skin and its appendages

(2010) Jean Christopher Chamcheu et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Do commonin silicotools predict the clinical consequences of amino-acid substitutions in the CFTR gene?

(2010) R Dorfman et al.   CLINICAL GENETICS

Huntington's disease: from molecular pathogenesis to clinical treatment

(2010) Christopher A Ross et al.   LANCET NEUROLOGY

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

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang 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

A Novel Adaptive Method for the Analysis of Next-Generation Sequencing Data to Detect Complex Trait Associations with Rare Variants Due to Gene Main Effects and Interactions

(2010) Dajiang J. Liu et al.   PLoS Genetics

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

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

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

(2009) Bo Eskerod Madsen et al.   PLoS Genetics

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

(2008) Bingshan Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS