Exome sequencing and complex disease: practical aspects of rare variant association studies

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

(2012) Lukas Habegger et al.   BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

Genetics of Human Cardiovascular Disease

(2012) Sekar Kathiresan et al.   CELL

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

(2012) Pablo Cingolani et al.   FLY

A mutation in APP protects against Alzheimer’s disease and age-related cognitive decline

(2012) Thorlakur Jonsson et al.   NATURE

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

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Exome sequencing and the genetic basis of complex traits

(2012) Adam Kiezun et al.   NATURE GENETICS

Differential confounding of rare and common variants in spatially structured populations

(2012) Iain Mathieson et al.   NATURE GENETICS

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

(2012)   NATURE GENETICS

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

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

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

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

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

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation

(2012) Jason Flannick et al.   PLoS Computational Biology

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

(2012) Benjamin F. Voight et al.   PLoS Genetics

A General Framework for Detecting Disease Associations with Rare Variants in Sequencing Studies

(2011) Dan-Yu Lin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

Excess of Rare Variants in Non–Genome-Wide Association Study Candidate Genes in Patients With Hypertriglyceridemia

(2011) Christopher T. Johansen et al.   Circulation-Cardiovascular Genetics

Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies

(2011) Dalin Li et al.   GENETIC EPIDEMIOLOGY

Low-coverage sequencing: Implications for design of complex trait association studies

(2011) Y. Li et al.   GENOME RESEARCH

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A rare penetrant mutation in CFH confers high risk of age-related macular degeneration

(2011) Soumya Raychaudhuri et al.   NATURE GENETICS

A rare variant in MYH6 is associated with high risk of sick sinus syndrome

(2011) Hilma Holm et al.   NATURE GENETICS

Genome-wide association study identifies five new schizophrenia loci

(2011)   NATURE GENETICS

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

(2011) Heribert Schunkert et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

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

Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci

(2011) Alexandra Zhernakova et al.   PLoS Genetics

Testing for an Unusual Distribution of Rare Variants

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

Extending Rare-Variant Testing Strategies: Analysis of Noncoding Sequence and Imputed Genotypes

(2010) Matthew Zawistowski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

METAL: fast and efficient meta-analysis of genomewide association scans

(2010) C. J. Willer et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

(2010) S. Q. Le et al.   GENOME RESEARCH

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency

(2010) Sarah E Calvo et al.   NATURE GENETICS

Exome Sequencing,ANGPTL3Mutations, and Familial Combined Hypolipidemia

(2010) Kiran Musunuru et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Validating, augmenting and refining genome-wide association signals

(2009) John P. A. Ioannidis et al.   NATURE REVIEWS GENETICS

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

(2009) T. LaFramboise   NUCLEIC ACIDS RESEARCH

Power of deep, all-exon resequencing for discovery of human trait genes

(2009) G. V. Kryukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes

(2009) S. Nejentsev et al.   SCIENCE

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms

(2008) Ivan P. Gorlov et al.   AMERICAN JOURNAL OF HUMAN 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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Rare independent mutations in renal salt handling genes contribute to blood pressure variation

(2008) Weizhen Ji et al.   NATURE GENETICS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

A Null Mutation in Human APOC3 Confers a Favorable Plasma Lipid Profile and Apparent Cardioprotection

(2008) T. I. Pollin et al.   SCIENCE

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE