Rare-variant collapsing analyses for complex traits: guidelines and applications

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance

(2019) Tristan J. Hayeck et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS

(2019) Sahar Gelfman et al.   GENOME RESEARCH

Exome-Based Rare-Variant Analyses in CKD

(2019) Sophia Cameron-Christie et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum

(2018) Andrea Ganna et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mixed-model association for biobank-scale datasets

(2018) Po-Ru Loh et al.   NATURE GENETICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer's disease

(2018) Neha S. Raghavan et al.   Annals of Clinical and Translational Neurology

Burden Testing of Rare Variants Identified through Exome Sequencing via Publicly Available Control Data

(2018) Michael H. Guo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

A map of constrained coding regions in the human genome

(2018) James M. Havrilla et al.   NATURE GENETICS

Diagnostic Utility of Exome Sequencing for Kidney Disease

(2018) Emily E. Groopman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

(2017) Joshua Traynelis et al.   GENOME RESEARCH

Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

(2017) Colleen M. Carlston et al.   HUMAN MUTATION

Ultra-rare genetic variation in common epilepsies: a case-control sequencing study

(2017) Andrew S Allen et al.   LANCET NEUROLOGY

The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability

(2017) Tarjinder Singh et al.   NATURE GENETICS

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

(2017) Ingrid E Christophersen et al.   NATURE GENETICS

Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls

(2017) Céline Bellenguez et al.   NEUROBIOLOGY OF AGING

Annotating pathogenic non-coding variants in genic regions

(2017) Sahar Gelfman et al.   Nature Communications

Determinants of Power in Gene-Based Burden Testing for Monogenic Disorders

(2016) Michael H. Guo et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome-based analysis of cardiac arrhythmia, respiratory control, and epilepsy genes in sudden unexpected death in epilepsy

(2016) Richard D. Bagnall et al.   ANNALS OF NEUROLOGY

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

(2016) Monkol Lek et al.   NATURE

Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

(2016) Giulio Genovese et al.   NATURE NEUROSCIENCE

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

Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study

(2016) Frederick E. Dewey et al.   SCIENCE

Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios

(2015) Xiaolin Zhu et al.   GENETICS IN MEDICINE

XWAS: A Software Toolset for Genetic Data Analysis and Association Studies of the X Chromosome

(2015) Feng Gao et al.   JOURNAL OF HEREDITY

Haploinsufficiency of TBK1 causes familial ALS and fronto-temporal dementia

(2015) Axel Freischmidt et al.   NATURE NEUROSCIENCE

Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways

(2015) E. T. Cirulli et al.   SCIENCE

De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies

(2015) J. Homsy et al.   SCIENCE

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

Rare-Variant Association Analysis: Study Designs and Statistical Tests

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

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

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

RAREMETAL: fast and powerful meta-analysis for rare variants

(2014) S. Feng et al.   BIOINFORMATICS

Meta-Analysis of Sequencing Studies With Heterogeneous Genetic Associations

(2014) Zheng-Zheng Tang et al.   GENETIC EPIDEMIOLOGY

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Large-scale discovery of novel genetic causes of developmental disorders

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

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction

(2014) Ron Do et al.   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

Age-related mutations associated with clonal hematopoietic expansion and malignancies

(2014) Mingchao Xie et al.   NATURE MEDICINE

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

Statistical power and significance testing in large-scale genetic studies

(2014) Pak C. Sham et al.   NATURE REVIEWS GENETICS

Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence

(2014) Giulio Genovese et al.   NEW ENGLAND JOURNAL OF MEDICINE

General Framework for Meta-analysis of Rare Variants in Sequencing Association Studies

(2013) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MASS: meta-analysis of score statistics for sequencing studies

(2013) Z.-Z. Tang et al.   BIOINFORMATICS

Adjusted Sequence Kernel Association Test for Rare Variants Controlling for Cryptic and Family Relatedness

(2013) Karim Oualkacha et al.   GENETIC EPIDEMIOLOGY

Digenic inheritance in medical genetics

(2013) Alejandro A Schäffer   JOURNAL OF MEDICAL GENETICS

Meta-analysis of gene-level tests for rare variant association

(2013) Dajiang J Liu et al.   NATURE GENETICS

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

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

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

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ARIEL and AMELIA: Testing for an Accumulation of Rare Variants Using Next-Generation Sequencing Data

(2012) Jennifer L. Asimit et al.   HUMAN HEREDITY

Clinical application of exome sequencing in undiagnosed genetic conditions

(2012) Anna C Need et al.   JOURNAL OF MEDICAL GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

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

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

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease

(2011) Iuliana Ionita-Laza et al.   PLoS Genetics

Testing for an Unusual Distribution of Rare Variants

(2011) Benjamin M. Neale et al.   PLoS Genetics

Unlocking Mendelian disease using exome sequencing

(2011) Christian Gilissen et al.   GENOME BIOLOGY

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

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

A Data-Adaptive Sum Test for Disease Association with Multiple Common or Rare Variants

(2010) Fang Han et al.   HUMAN HEREDITY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Bias-reduced and separation-proof conditional logistic regression with small or sparse data sets

(2010) Georg Heinze et al.   STATISTICS IN MEDICINE

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

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

An evaluation of statistical approaches to rare variant analysis in genetic association studies

(2009) Andrew P. Morris et al.   GENETIC EPIDEMIOLOGY

Common Genetic Variation and Human Traits

(2009) David B. Goldstein   NEW ENGLAND JOURNAL OF MEDICINE

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