Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

Efficient Variant Set Mixed Model Association Tests for Continuous and Binary Traits in Large-Scale Whole-Genome Sequencing Studies

(2019) Han Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cauchy combination test: a powerful test with analytic p-value calculation under arbitrary dependency structures

(2019) Yaowu Liu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

ACAT: A Fast and Powerful p Value Combination Method for Rare-Variant Analysis in Sequencing Studies

(2019) Yaowu Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dynamic Scan Procedure for Detecting Rare-Variant Association Regions in Whole-Genome Sequencing Studies

(2019) Zilin Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data

(2019) Yiding Ma et al.   PLoS Genetics

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications

(2018) Daniel Backenroth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A large electronic-health-record-based genome-wide study of serum lipids

(2018) Thomas J. Hoffmann et al.   NATURE GENETICS

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies

(2018) Xingjie Hao et al.   PLoS Genetics

Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

(2018) Wei Zhou et al.   NATURE GENETICS

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

(2018) Pradeep Natarajan et al.   Nature Communications

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

(2018) Allison A. Regier et al.   Nature Communications

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

(2018) Derek Klarin et al.   NATURE GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Principles and methods of in-silico prioritization of non-coding regulatory variants

(2017) Phil H. Lee et al.   HUMAN GENETICS

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

(2017) Steven Gazal et al.   NATURE GENETICS

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

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

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia

(2017) Maria Tiana et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

(2017) Reka Nagy et al.   Genome Medicine

Leveraging functional annotations in genetic risk prediction for human complex diseases

(2017) Yiming Hu et al.   PLoS Computational Biology

Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models

(2016) Han Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Model-free Estimation of Recent Genetic Relatedness

(2016) Matthew P. Conomos et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Improved methods for multi-trait fine mapping of pleiotropic risk loci

(2016) Gleb Kichaev et al.   BIOINFORMATICS

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

(2016) Haiming Tang et al.   GENETICS

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

(2016) Haiming Tang et al.   GENETICS

Effect of Naturally Random Allocation to Lower Low-Density Lipoprotein Cholesterol on the Risk of Coronary Heart Disease Mediated by Polymorphisms in NPC1L1, HMGCR, or Both

(2015) Brian A. Ference et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The impact of low-frequency and rare variants on lipid levels

(2015) Ida Surakka et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

Rare-Variant Association Analysis: Study Designs and Statistical Tests

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

Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol

(2014) Leslie A. Lange et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Powerful and Adaptive Association Test for Rare Variants

(2014) Wei Pan et al.   GENETICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

Inactivating Mutations in NPC1L1 and Protection from Coronary Heart Disease

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Loss-of-Function Mutations in APOC3, Triglycerides, and Coronary Disease

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

A Unified Mixed-Effects Model for Rare-Variant Association in Sequencing Studies

(2013) Jianping Sun et al.   GENETIC EPIDEMIOLOGY

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

Optimal tests for rare variant effects in sequencing association studies

(2012) S. Lee et al.   BIOSTATISTICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Exome sequencing and the genetic basis of complex traits

(2012) Adam Kiezun et al.   NATURE GENETICS

Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited

(2011) Joris Deelen et al.   AGING CELL

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

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

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) Tanya M. Teslovich et al.   NATURE

Estimation of effect size distribution from genome-wide association studies and implications for future discoveries

(2010) Ju-Hyun Park et al.   NATURE GENETICS

Genome-wide association study of hematological and biochemical traits in a Japanese population

(2010) Yoichiro Kamatani 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

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Longitudinal Association of PCSK9 Sequence Variations With Low-Density Lipoprotein Cholesterol Levels

(2009) Chiang-Ching Huang et al.   Circulation-Cardiovascular Genetics

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

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

Detection of nonneutral substitution rates on mammalian phylogenies

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

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

APOE/C1/C4/C2 hepatic control region polymorphism influences plasma apoE and LDL cholesterol levels

(2008) Kathy Klos et al.   HUMAN MOLECULAR GENETICS

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population

(2008) Chiara Sabatti et al.   NATURE GENETICS

Common variants at 30 loci contribute to polygenic dyslipidemia

(2008) Sekar Kathiresan et al.   NATURE GENETICS

Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans

(2008) Sekar Kathiresan et al.   NATURE GENETICS

Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts

(2008) Yurii S Aulchenko et al.   NATURE GENETICS