Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes

Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power

(2021) Elizabeth G. Atkinson et al.   NATURE GENETICS

The open targets post-GWAS analysis pipeline

(2020) Gareth Peat et al.   BIOINFORMATICS

Big data in digital healthcare: lessons learnt and recommendations for general practice

(2020) Raag Agrawal et al.   HEREDITY

A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn’s disease

(2020) David González-Serna et al.   Scientific Reports

A practical view of fine-mapping and gene prioritization in the post-genome-wide association era

(2020) R. V. Broekema et al.   Open Biology

Polygenic risk scores: from research tools to clinical instruments

(2020) Cathryn M. Lewis et al.   Genome Medicine

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

(2020) Paul M. Thompson et al.   Translational Psychiatry

Monogenic and polygenic inheritance become instruments for clonal selection

(2020) Po-Ru Loh et al.   NATURE

Novel methods for epistasis detection in genome-wide association studies

(2020) Lotfi Slim et al.   PLoS One

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo

(2019) Tingxian Deng et al.   Frontiers in Genetics

Integrating Germline and Somatic Mutation Information for the Discovery of Biomarkers in Triple-Negative Breast Cancer

(2019) Jiande Wu et al.   International Journal of Environmental Research and Public Health

Joint Analysis of Multiple Phenotypes in Association Studies based on Cross-Validation Prediction Error

(2019) Xinlan Yang et al.   Scientific Reports

DeepPVP: phenotype-based prioritization of causative variants using deep learning

(2019) Imane Boudellioua et al.   BMC BIOINFORMATICS

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

Reverse GWAS: Using genetics to identify and model phenotypic subtypes

(2019) Andy Dahl et al.   PLoS Genetics

Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor

(2019) Jiantao Zhao et al.   Nature Communications

Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

(2019) Eleonora Porcu et al.   Nature Communications

Effect of non-normality and low count variants on cross-phenotype association tests in GWAS

(2019) Debashree Ray et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer’s Disease-Related Genes

(2019) Tianyi Zhao et al.   Frontiers in Genetics

Tissue specific regulation of transcription in endometrium and association with disease

(2019) Sally Mortlock et al.   HUMAN REPRODUCTION

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger

(2018) Anurag Verma et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes

(2018) Miaoyan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of shared heritability in common disorders of the brain

(2018) et al.   SCIENCE

Functional Variants Identified Efficiently through an Integrated Transcriptome and Epigenome Analysis

(2018) Fanlin Meng et al.   Scientific Reports

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations

(2018) Arunabha Majumdar et al.   PLoS Genetics

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

(2018) Po-Ru Loh et al.   NATURE

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

(2018) Imane Boudellioua et al.   Scientific Reports

Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses

(2018) Mahdi Rivandi et al.   Frontiers in Genetics

Deciphering the Emerging Complexities of Molecular Mechanisms at GWAS Loci

(2018) Maren E. Cannon et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human-Disease Phenotype Map Derived from PheWAS across 38,682 Individuals

(2018) Anurag Verma et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis

(2018) Zahra Mortezaei et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

A practical approach to adjusting for population stratification in genome-wide association studies: principal components and propensity scores (PCAPS)

(2018) Huaqing Zhao et al.   Statistical Applications in Genetics and Molecular Biology

Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study

(2017) Zahra Mortezaei et al.   GENOMICS

Genetic variation associated with cardiovascular risk in autoimmune diseases

(2017) Pedro P. Perrotti et al.   PLoS One

Differences between germline and somatic mutation rates in humans and mice

(2017) Brandon Milholland et al.   Nature Communications

Semantic prioritization of novel causative genomic variants

(2017) Imane Boudellioua et al.   PLoS Computational Biology

Pathway-based discovery of genetic interactions in breast cancer

(2017) Wen Wang et al.   PLoS Genetics

A pathway analysis of genome-wide association study highlights novel type 2 diabetes risk pathways

(2017) Yang Liu et al.   Scientific Reports

A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants

(2016) K. Alaine Broadaway et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GWASeq: targeted re-sequencing follow up to GWAS

(2016) Matthew P. Salomon et al.   BMC GENOMICS

Cross-phenotype association tests uncover genes mediating nutrient response in Drosophila

(2016) Christopher S. Nelson et al.   BMC GENOMICS

Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia

(2016) Jhih-Rong Lin et al.   GENETICS

Epistasis and Pleiotropy Affect the Modularity of the Genotype–Phenotype Map of Cross-Resistance in HIV-1

(2016) Robert Polster et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Unravelling the human genome–phenome relationship using phenome-wide association studies

(2016) William S. Bush et al.   NATURE REVIEWS GENETICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Text mining resources for the life sciences

(2016) Piotr Przybyła et al.   Database-The Journal of Biological Databases and Curation

Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia

(2016) Jhih-Rong Lin et al.   GENETICS

Associations between cancer and Alzheimer's disease in a U.S. Medicare population

(2016) Daryl Michal Freedman et al.   Cancer Medicine

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

Differences in Breast Cancer Stage at Diagnosis and Cancer-Specific Survival by Race and Ethnicity in the United States

(2015) Javaid Iqbal et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The co-occurrence of multiple sclerosis and type 1 diabetes: Shared aetiologic features and clinical implication for MS aetiology

(2015) Prudence Tettey et al.   JOURNAL OF THE NEUROLOGICAL SCIENCES

Roadmap for regulation

(2015) Casey E. Romanoski et al.   NATURE

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

(2015) Xin Zhou et al.   NATURE BIOTECHNOLOGY

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

(2015) Suna Onengut-Gumuscu et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

(2015) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

A Multivariate Genome-Wide Association Analysis of 10 LDL Subfractions, and Their Response to Statin Treatment, in 1868 Caucasians

(2015) Heejung Shim et al.   PLoS One

Neurodegeneration and Cancer: Where the Disorder Prevails

(2015) Petr Klus et al.   Scientific Reports

Using Somatic Mutations to Guide Treatment Decisions

(2015) Hugo M. Horlings et al.   JAMA Oncology

Inverse association between cancer and neurodegenerative disease: review of the epidemiologic and biological evidence

(2014) Jane A. Driver   BIOGERONTOLOGY

Genetics of gene expression in immunity to infection

(2014) Benjamin P Fairfax et al.   CURRENT OPINION IN IMMUNOLOGY

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

(2014) Gary D Wu et al.   GUT

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

A Fasting Insulin–Raising Allele at IGF1 Locus Is Associated with Circulating Levels of IGF-1 and Insulin Sensitivity

(2014) Gaia Chiara Mannino et al.   PLoS One

Genome-wide Association Analysis for Multiple Continuous Secondary Phenotypes

(2013) Elizabeth D. Schifano et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Reflections on univariate and multivariate analysis of metabolomics data

(2013) Edoardo Saccenti et al.   Metabolomics

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Expression quantitative trait loci: present and future

(2013) A. C. Nica et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS

(2012) Paul F. O’Reilly et al.   PLoS One

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

MamPhEA: a web tool for mammalian phenotype enrichment analysis

(2010) Meng-Pin Weng et al.   BIOINFORMATICS

Genome-wide association study identifies five new breast cancer susceptibility loci

(2010) Clare Turnbull et al.   NATURE GENETICS

Cancer and Neurodegeneration: Between the Devil and the Deep Blue Sea

(2010) Hélène Plun-Favreau et al.   PLoS Genetics

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT