Exome sequencing and the genetic basis of complex traits

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

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

On the follow-up of genome-wide association studies: an overall test for the most promising SNPs

(2011) Peter J. Lipman et al.   GENETIC EPIDEMIOLOGY

Comparison of statistical tests for disease association with rare variants

(2011) Saonli Basu et al.   GENETIC EPIDEMIOLOGY

An Optimal Weighted Aggregated Association Test for Identification of Rare Variants Involved in Common Diseases

(2011) Jae Hoon Sul et al.   GENETICS

Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed

(2011) Stephanie Hicks et al.   HUMAN MUTATION

Performance of mutation pathogenicity prediction methods on missense variants

(2011) Janita Thusberg et al.   HUMAN MUTATION

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei 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

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 Reveals Comprehensive Genomic Alterations across Eight Cancer Cell Lines

(2011) Han Chang et al.   PLoS One

Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

(2011) Dale J. Hedges et al.   PLoS One

Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

(2011) N. Agrawal et al.   SCIENCE

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

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

Mutations in the DBP-Deficiency Protein HSD17B4 Cause Ovarian Dysgenesis, Hearing Loss, and Ataxia of Perrault Syndrome

(2010) Sarah B. Pierce et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

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

Rare Variant Association Analysis Methods for Complex Traits

(2010) Jennifer Asimit et al.   Annual Review of Genetics

TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing

(2010) Jun Ling Wang et al.   BRAIN

Human allelic variation: perspective from protein function, structure, and evolution

(2010) Daniel M Jordan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

Loss-of-function variants in the genomes of healthy humans

(2010) D. G. MacArthur et al.   HUMAN MOLECULAR GENETICS

Massively parallel sequencing and rare disease

(2010) S. B. Ng et al.   HUMAN MOLECULAR GENETICS

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome

(2010) Peter M Krawitz et al.   NATURE GENETICS

De novo mutations of SETBP1 cause Schinzel-Giedion syndrome

(2010) Alexander Hoischen et al.   NATURE GENETICS

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

(2010) Yingrui Li et al.   NATURE GENETICS

Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia

(2010) Christopher T Johansen et al.   NATURE GENETICS

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

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

(2010) Hyun Min Kang et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

(2010) Gregory M Cooper et al.   NATURE METHODS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Exome Sequencing,ANGPTL3Mutations, and Familial Combined Hypolipidemia

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

Comprehensive Approach to Analyzing Rare Genetic Variants

(2010) Thomas J. Hoffmann et al.   PLoS One

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

Deep resequencing reveals excess rare recent variants consistent with explosive population growth

(2010) Alex Coventry et al.   Nature Communications

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

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

(2010) Qi Zhao et al.   GENOME BIOLOGY

Rare, Evolutionarily Unlikely Missense Substitutions in ATM Confer Increased Risk of Breast Cancer

(2009) Sean V. Tavtigian 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

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

(2009) Yali Xue et al.   CURRENT BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

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

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

(2009) S. Nejentsev et al.   SCIENCE

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

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

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

(2008) Weizhen Ji et al.   NATURE GENETICS

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics