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

Million Veteran Program: A mega-biobank to study genetic influences on health and disease

(2016) John Michael Gaziano et al.   JOURNAL OF CLINICAL EPIDEMIOLOGY

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

(2015) Tudor Groza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Application of clinical text data for phenome-wide association studies (PheWASs)

(2015) Scott J. Hebbring et al.   BIOINFORMATICS

The detection and characterization of pleiotropy: discovery, progress, and promise

(2015) Anna L. Tyler et al.   BRIEFINGS IN BIOINFORMATICS

A Genome-wide Pleiotropy Scan for Prostate Cancer Risk

(2015) Orestis A. Panagiotou et al.   EUROPEAN UROLOGY

Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Mark N. Kvale et al.   GENETICS

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Yambazi Banda et al.   GENETICS

Phenome-Wide Association Studies: Embracing Complexity for Discovery

(2015) Sarah A. Pendergrass et al.   HUMAN HEREDITY

IRF4, MC1R and TYR genes are risk factors for actinic keratosis independent of skin color

(2015) L. C. Jacobs et al.   HUMAN MOLECULAR GENETICS

Incorporating temporal EHR data in predictive models for risk stratification of renal function deterioration

(2015) Anima Singh et al.   JOURNAL OF BIOMEDICAL INFORMATICS

ICD-10-CM Crosswalks in the primary care setting: assessing reliability of the GEMs and reimbursement mappings

(2015) Robert W. Turer et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources

(2015) Sheng Yu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Planning for US Precision Medicine Initiative underway

(2015) Susan Jaffe   LANCET

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

Opportunities for drug repositioning from phenome-wide association studies

(2015) Majid Rastegar-Mojarad et al.   NATURE BIOTECHNOLOGY

Reform of Clinical Research Regulations, Finally

(2015) Ezekiel J. Emanuel   NEW ENGLAND JOURNAL OF MEDICINE

Bringing the Common Rule into the 21st Century

(2015) Kathy L. Hudson et al.   NEW ENGLAND JOURNAL OF MEDICINE

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

MR-PheWAS: hypothesis prioritization among potential causal effects of body mass index on many outcomes, using Mendelian randomization

(2015) Louise A. C. Millard et al.   Scientific Reports

Finding Our Way through Phenotypes

(2015) Andrew R. Deans et al.   PLOS BIOLOGY

Towards a phenome-wide catalog of human clinical traits impacted by genetic ancestry

(2015) Logan Dumitrescu et al.   BioData Mining

Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Mark N. Kvale et al.   GENETICS

Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort

(2015) Yambazi Banda et al.   GENETICS

News from the NIH: potential contributions of the behavioral and social sciences to the precision medicine initiative

(2015) William T. Riley et al.   Translational Behavioral Medicine

Pleiotropic and Sex-Specific Effects of Cancer GWAS SNPs on Melanoma Risk in the Population Architecture Using Genomics and Epidemiology (PAGE) Study

(2015) Jonathan M. Kocarnik et al.   PLoS One

Extracting Primary Open-Angle Glaucoma from Electronic Medical Records for Genetic Association Studies

(2015) Nicole A. Restrepo et al.   PLoS One

A GWAS Study on Liver Function Test Using eMERGE Network Participants

(2015) Bahram Namjou et al.   PLoS One

Return of Genomic Results to Research Participants: The Floor, the Ceiling, and the Choices In Between

(2014) Gail P. Jarvik et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels

(2014) Ronald J. Hause et al.   AMERICAN JOURNAL OF HUMAN GENETICS

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment

(2014) Robert J. Carroll et al.   BIOINFORMATICS

Validation of PhenX measures in the personalized medicine research project for use in gene/environment studies

(2014) Catherine A McCarty et al.   BMC Medical Genomics

Community-level determinants of obesity: harnessing the power of electronic health records for retrospective data analysis

(2014) Caryn Roth et al.   BMC Medical Informatics and Decision Making

Association of Cancer Susceptibility Variants with Risk of Multiple Primary Cancers: The Population Architecture using Genomics and Epidemiology Study

(2014) S. L. Park et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Cross-cancer pleiotropic analysis of endometrial cancer: PAGE and E2C2 consortia

(2014) Veronica Wendy Setiawan et al.   CARCINOGENESIS

Phenome-wide association studies (PheWASs) for functional variants

(2014) Zhan Ye et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

MedXN: an open source medication extraction and normalization tool for clinical text

(2014) Sunghwan Sohn et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Pleiotropic Associations of Risk Variants Identified for Other Cancers With Lung Cancer Risk: The PAGE and TRICL Consortia

(2014) S. Lani Park et al.   JNCI-Journal of the National Cancer Institute

Pleiotropic genes for metabolic syndrome and inflammation

(2014) Aldi T. Kraja et al.   MOLECULAR GENETICS AND METABOLISM

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

(2014) Anubha Mahajan et al.   NATURE GENETICS

Defining the role of common variation in the genomic and biological architecture of adult human height

(2014) Andrew R Wood et al.   NATURE GENETICS

A Genome-Wide “Pleiotropy Scan” Does Not Identify New Susceptibility Loci for Estrogen Receptor Negative Breast Cancer

(2014) Daniele Campa et al.   PLoS One

A Comparison of Multivariate Genome-Wide Association Methods

(2014) Tessel E. Galesloot et al.   PLoS One

GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

(2014) Eric P. Xing et al.   PLoS One

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Generalized estimating equations for genome-wide association studies using longitudinal phenotype data

(2014) Colleen M. Sitlani et al.   STATISTICS IN MEDICINE

Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study

(2014) Molly A. Hall et al.   PLoS Genetics

A Rigorous Algorithm To Detect And Clean Inaccurate Adult Height Records Within EHR Systems

(2014) A. Muthalagu et al.   Applied Clinical Informatics

Investigating the relationship between mitochondrial genetic variation and cardiovascular-related traits to develop a framework for mitochondrial phenome-wide association studies

(2014) Sabrina L Mitchell et al.   BioData Mining

eMERGEing progress in genomics—the first seven years

(2014) Dana C. Crawford et al.   Frontiers in Genetics

Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis

(2014) Bahram Namjou et al.   Frontiers in Genetics

Phenome-wide association studies demonstrating pleiotropy of genetic variants within FTO with and without adjustment for body mass index

(2014) Robert M. Cronin et al.   Frontiers in Genetics

Phenome-wide Association Study Relating Pretreatment Laboratory Parameters With Human Genetic Variants in AIDS Clinical Trials Group Protocols

(2014) C. B. Moore et al.   Open Forum Infectious Diseases

Genome- and Phenome-Wide Analyses of Cardiac Conduction Identifies Markers of Arrhythmia Risk

(2013) Marylyn D. Ritchie et al.   CIRCULATION

A PheWAS approach in studying HLA-DRB1*1501

(2013) S J Hebbring et al.   GENES AND IMMUNITY

Ethical, legal and social implications of incorporating genomic information into electronic health records

(2013) Ribhi Hazin et al.   GENETICS IN MEDICINE

Pleiotropic effects of genetic risk variants for other cancers on colorectal cancer risk: PAGE, GECCO and CCFR consortia

(2013) Iona Cheng et al.   GUT

A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects

(2013) Khader Shameer et al.   HUMAN GENETICS

Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus

(2013) Chirag J. Patel et al.   HUMAN GENETICS

Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans

(2013) Mingfeng Zhang et al.   HUMAN MOLECULAR GENETICS

The challenges, advantages and future of phenome-wide association studies

(2013) Scott J. Hebbring   IMMUNOLOGY

Prevalence of Actinic Keratosis and Its Risk Factors in the General Population: The Rotterdam Study

(2013) Sophie C. Flohil et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Automated extraction of clinical traits of multiple sclerosis in electronic medical records

(2013) Mary F Davis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A comparison of phenotype definitions for diabetes mellitus

(2013) Rachel L Richesson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

ICD-9 tobacco use codes are effective identifiers of smoking status

(2013) Laura K Wiley et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

Meta-analysis methods for genome-wide association studies and beyond

(2013) Evangelos Evangelou et al.   NATURE REVIEWS GENETICS

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

Enhancing the Power of Genetic Association Studies through the Use of Silver Standard Cases Derived from Electronic Medical Records

(2013) Andrew McDavid et al.   PLoS One

Computational Phenotype Discovery Using Unsupervised Feature Learning over Noisy, Sparse, and Irregular Clinical Data

(2013) Thomas A. Lasko et al.   PLoS One

A Unified Framework for Association Analysis with Multiple Related Phenotypes

(2013) Matthew Stephens   PLoS One

Identifying Personal Genomes by Surname Inference

(2013) M. Gymrek et al.   SCIENCE

Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics

(2013) Antoine Neuraz et al.   PLoS Computational Biology

TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies

(2013) Sophie van der Sluis et al.   PLoS Genetics

Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

(2013) Sarah A. Pendergrass et al.   PLoS Genetics

Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls

(2012) Katherine P. Liao et al.   ARTHRITIS AND RHEUMATISM

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network

(2012) Stephanie M. Fullerton et al.   GENETICS IN MEDICINE

Using PhenX measures to identify opportunities for cross-study analysis

(2012) Huaqin Pan et al.   HUMAN MUTATION

What makes UK Biobank special?

(2012) Rory Collins   LANCET

Informed consent: A broken contract

(2012) Erika Check Hayden   NATURE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Mining electronic health records: towards better research applications and clinical care

(2012) Peter B. Jensen et al.   NATURE REVIEWS GENETICS

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

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

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

(2012) Athma A. Pai et al.   PLoS Genetics

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Patterns of Cis Regulatory Variation in Diverse Human Populations

(2012) Barbara E. Stranger et al.   PLoS Genetics

Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View

(2012) Sarah A Pendergrass et al.   BioData Mining

The PhenX Toolkit: Get the Most From Your Measures

(2011) C. M. Hamilton et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

The Next PAGE in Understanding Complex Traits: Design for the Analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study

(2011) Tara C. Matise et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Variants Near FOXE1 Are Associated with Hypothyroidism and Other Thyroid Conditions: Using Electronic Medical Records for Genome- and Phenome-wide Studies

(2011) Joshua C. Denny et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Abundant Pleiotropy in Human Complex Diseases and Traits

(2011) Shanya Sivakumaran et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Study newsletters, community and ethics advisory boards, and focus group discussions provide ongoing feedback for a large biobank

(2011) Catherine A. McCarty et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Body Mass Index and the Built and Social Environments in Children and Adolescents Using Electronic Health Records

(2011) Brian S. Schwartz et al.   AMERICAN JOURNAL OF PREVENTIVE MEDICINE

The eMERGE Network: A consortium of biorepositories linked to electronic medical records data for conducting genomic studies

(2011) Catherine A McCarty et al.   BMC Medical Genomics

Genome-Wide "Pleiotropy Scan" Identifies HNF1A Region as a Novel Pancreatic Cancer Susceptibility Locus

(2011) B. L. Pierce et al.   CANCER RESEARCH

Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience

(2011) Siiri N. Bennett et al.   GENETIC EPIDEMIOLOGY

The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery

(2011) S.A. Pendergrass et al.   GENETIC EPIDEMIOLOGY

Identifiability in biobanks: models, measures, and mitigation strategies

(2011) Bradley Malin et al.   HUMAN GENETICS

Normalized names for clinical drugs: RxNorm at 6 years

(2011) Stuart J Nelson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study

(2011) Abel N Kho et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Using electronic health records to drive discovery in disease genomics

(2011) Isaac S. Kohane   NATURE REVIEWS 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

Dietary intake in the Personalized Medicine Research Project: a resource for studies of gene-diet interaction

(2011) Lacie Strobush et al.   Nutrition Journal

Knowledge-Driven Multi-Locus Analysis Reveals Gene-Gene Interactions Influencing HDL Cholesterol Level in Two Independent EMR-Linked Biobanks

(2011) Stephen D. Turner et al.   PLoS One

Gene–environment interactions in human disease: nuisance or opportunity?

(2011) Carole Ober et al.   TRENDS IN GENETICS

A Phenomics-Based Strategy Identifies Loci on APOC1, BRAP, and PLCG1 Associated with Metabolic Syndrome Phenotype Domains

(2011) Christy L. Avery et al.   PLoS Genetics

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

(2011) Logan Dumitrescu et al.   PLoS Genetics

Robust Replication of Genotype-Phenotype Associations across Multiple Diseases in an Electronic Medical Record

(2010) Marylyn D. Ritchie et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-Wide Association Studies and Beyond

(2010) John S. Witte   Annual Review of Public Health

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations

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

Identification of Genomic Predictors of Atrioventricular Conduction

(2010) Joshua C. Denny et al.   CIRCULATION

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

MedEx: a medication information extraction system for clinical narratives

(2010) H. Xu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease

(2010) Iftikhar J Kullo et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Genome-wide association studies in diverse populations

(2010) Noah A. Rosenberg et al.   NATURE REVIEWS GENETICS

An Environment-Wide Association Study (EWAS) on Type 2 Diabetes Mellitus

(2010) Chirag J. Patel et al.   PLoS One

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

(2010) Nicholas Eriksson et al.   PLoS Genetics

A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke

(2009) Daniel F Gudbjartsson et al.   NATURE GENETICS

Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci

(2009) Philip L De Jager et al.   NATURE GENETICS

Erratum: Common disorders are quantitative traits

(2009) Robert Plomin et al.   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Meta-analysis in genome-wide association studies

(2009) Eleftheria Zeggini et al.   PHARMACOGENOMICS

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

A multivariate test of association

(2008) Manuel A. R. Ferreira et al.   BIOINFORMATICS

Bivariate association analyses for the mixture of continuous and binary traits with the use of extended generalized estimating equations

(2008) Jianfeng Liu et al.   GENETIC EPIDEMIOLOGY

Common variants at CD40 and other loci confer risk of rheumatoid arthritis

(2008) Soumya Raychaudhuri et al.   NATURE GENETICS

Common variants at 30 loci contribute to polygenic dyslipidemia

(2008) Sekar Kathiresan et al.   NATURE GENETICS

Detecting shared pathogenesis from the shared genetics of immune-related diseases

(2008) Alexandra Zhernakova et al.   NATURE REVIEWS GENETICS

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation

(2008) Jiali Han et al.   PLoS Genetics

Pleiotropy and principal components of heritability combine to increase power for association analysis

(2007) Lambertus Klei et al.   GENETIC EPIDEMIOLOGY

Identifying Patient Smoking Status from Medical Discharge Records

(2007) O. Uzuner et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION