Statistical power and significance testing in large-scale genetic studies

Searching for missing heritability: Designing rare variant association studies

(2014) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics

(2013) Yi-Juan Hu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Analysis of copy number variations at 15 schizophrenia-associated loci

(2013) Elliott Rees et al.   BRITISH JOURNAL OF PSYCHIATRY

Empirical power of very rare variants for common traits and disease: results from sanger sequencing 1998 individuals

(2013) Martin Ladouceur et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Family-based association tests for sequence data, and comparisons with population-based association tests

(2013) Iuliana Ionita-Laza et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Rare Complete Knockouts in Humans: Population Distribution and Significant Role in Autism Spectrum Disorders

(2013) Elaine T. Lim et al.   NEURON

Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls

(2013) Li Liu et al.   PLoS Genetics

Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes

(2013) Xin He et al.   PLoS Genetics

Five Years of GWAS Discovery

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

SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits

(2012) B. Li et al.   BIOINFORMATICS

Optimal tests for rare variant effects in sequencing association studies

(2012) S. Lee et al.   BIOSTATISTICS

Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants

(2012) Brian D. Juran et al.   HUMAN MOLECULAR GENETICS

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

Including known covariates can reduce power to detect genetic effects in case-control studies

(2012) Matti Pirinen 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

De Novo Gene Disruptions in Children on the Autistic Spectrum

(2012) Ivan Iossifov et al.   NEURON

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

(2012) Miao-Xin Li et al.   NUCLEIC ACIDS RESEARCH

Statistical Guidance for Experimental Design and Data Analysis of Mutation Detection in Rare Monogenic Mendelian Diseases by Exome Sequencing

(2012) Degui Zhi et al.   PLoS One

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

(2012) M. R. Nelson et al.   SCIENCE

The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals

(2012) Martin Ladouceur et al.   PLoS Genetics

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

Robust Association Tests Under Different Genetic Models, Allowing for Binary or Quantitative Traits and Covariates

(2011) Hon-Cheong So et al.   BEHAVIOR GENETICS

Detecting multiple causal rare variants in exome sequence data

(2011) Kenny Q. Ye et al.   GENETIC EPIDEMIOLOGY

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

(2011) Dalin Li et al.   GENETIC EPIDEMIOLOGY

Comparison of statistical tests for disease association with rare variants

(2011) Saonli Basu et al.   GENETIC EPIDEMIOLOGY

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Linkage Analysis in the Next-Generation Sequencing Era

(2011) Joan E. Bailey-Wilson et al.   HUMAN HEREDITY

What should the genome-wide significance threshold be? Empirical replication of borderline genetic associations

(2011) Orestis A Panagiotou et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Exome sequencing as a tool for Mendelian disease gene discovery

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

Design Considerations for Massively Parallel Sequencing Studies of Complex Human Disease

(2011) Bing-Jian Feng et al.   PLoS One

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

Pooled Association Tests for Rare Variants in Exon-Resequencing Studies

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

Replication Strategies for Rare Variant Complex Trait Association Studies via Next-Generation Sequencing

(2010) Dajiang J. Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Functional impact of global rare copy number variation in autism spectrum disorders

(2010) Dalila Pinto et al.   NATURE

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Three Ways of Combining Genotyping and Resequencing in Case-Control Association Studies

(2010) Jeffrey A. Longmate et al.   PLoS One

Novel Sib Pair Selection Strategy Increases Power in Quantitative Association Analysis

(2009) Johnny S. H. Kwan et al.   BEHAVIOR GENETICS

Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies

(2009) Priya Duggal et al.   BMC GENOMICS

A new measure of the effective number of tests, a practical tool for comparing families of non-independent significance tests

(2009) Nicholas W. Galwey   GENETIC EPIDEMIOLOGY

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

How Many Genetic Variants Remain to Be Discovered?

(2009) Yudi Pawitan et al.   PLoS One

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

(2009) S. Nejentsev et al.   SCIENCE

Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies

(2009) Bingshan Li et al.   PLoS Genetics

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

(2009) Bo Eskerod Madsen et al.   PLoS Genetics

Estimating Odds Ratios in Genome Scans: An Approximate Conditional Likelihood Approach

(2008) Arpita Ghosh 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

Efficient Approximation of P-value of the Maximum of Correlated Tests, with Applications to Genome-Wide Association Studies

(2008) Qizhai Li et al.   ANNALS OF HUMAN GENETICS

Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies

(2008) H. Zhong et al.   BIOSTATISTICS

Why Most Discovered True Associations Are Inflated

(2008) John P. A. Ioannidis   EPIDEMIOLOGY

Maximizing association statistics over genetic models

(2008) Juan R. González et al.   GENETIC EPIDEMIOLOGY

Estimation of significance thresholds for genomewide association scans

(2008) Frank Dudbridge et al.   GENETIC EPIDEMIOLOGY

Genome-wide significance for dense SNP and resequencing data

(2008) Clive J. Hoggart et al.   GENETIC EPIDEMIOLOGY

On multiple-testing correction in genome-wide association studies

(2008) Valentina Moskvina et al.   GENETIC EPIDEMIOLOGY

Estimation of the multiple testing burden for genomewide association studies of nearly all common variants

(2008) Itsik Pe'er et al.   GENETIC EPIDEMIOLOGY

Bayes factors for genome-wide association studies: comparison withP-values

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

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

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