Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

Interpreting type 1 diabetes risk with genetics and single-cell epigenomics

(2021) Joshua Chiou et al.   NATURE

Trends in Incidence of Type 1 and Type 2 Diabetes Among Youths — Selected Counties and Indian Reservations, United States, 2002–2015

(2020) Jasmin Divers et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations

(2020) Abhay Hukku et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Development and Standardization of an Improved Type 1 Diabetes Genetic Risk Score for Use in Newborn Screening and Incident Diagnosis

(2019) Seth A. Sharp et al.   DIABETES CARE

Type 1 Diabetes Risk in African-Ancestry Participants and Utility of an Ancestry-Specific Genetic Risk Score

(2019) Suna Onengut-Gumuscu et al.   DIABETES CARE

Predicting Islet Cell Autoimmunity and Type 1 Diabetes: An 8-Year TEDDY Study Progress Report

(2019) Jeffrey P. Krischer et al.   DIABETES CARE

Abundant associations with gene expression complicate GWAS follow-up

(2019) Boxiang Liu et al.   NATURE GENETICS

Identification of Novel T1D Risk Loci and Their Association With Age and Islet Function at Diagnosis in Autoantibody-Positive T1D Individuals: Based on a Two-Stage Genome-Wide Association Study

(2019) Meng Zhu et al.   DIABETES CARE

Genetic analyses of diverse populations improves discovery for complex traits

(2019) Genevieve L. Wojcik et al.   NATURE

A genetics-led approach defines the drug target landscape of 30 immune-related traits

(2019) Hai Fang et al.   NATURE GENETICS

An Anti-CD3 Antibody, Teplizumab, in Relatives at Risk for Type 1 Diabetes

(2019) Kevan C. Herold et al.   NEW ENGLAND JOURNAL OF MEDICINE

Stochastic search and joint fine-mapping increases accuracy and identifies previously unreported associations in immune-mediated diseases

(2019) Jennifer L. Asimit et al.   Nature Communications

Anti-CD3 Antibody for the Prevention of Type 1 Diabetes: A Story of Perseverance

(2019) Jason Gaglia et al.   BIOCHEMISTRY

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes

(2019) Mireia Ramos-Rodríguez et al.   NATURE GENETICS

Are drug targets with genetic support twice as likely to be approved? Revised estimates of the impact of genetic support for drug mechanisms on the probability of drug approval

(2019) Emily A. King et al.   PLoS Genetics

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

(2018) Harm-Jan Westra et al.   NATURE GENETICS

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

Shared genetic risk contributes to type 1 and type 2 diabetes etiology

(2018) Anthony Aylward et al.   HUMAN MOLECULAR GENETICS

Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types

(2017) Sung Chun et al.   NATURE GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Tofacitinib as Induction and Maintenance Therapy for Ulcerative Colitis

(2017) William J. Sandborn et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

(2017) Arushi Varshney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells

(2017) Silva Kasela et al.   PLoS Genetics

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

(2016) Biola M. Javierre et al.   CELL

Environmental risk factors for type 1 diabetes

(2016) Marian Rewers et al.   LANCET

Genetic predisposition for beta cell fragility underlies type 1 and type 2 diabetes

(2016) James Dooley et al.   NATURE GENETICS

BACH2 regulates CD8+ T cell differentiation by controlling access of AP-1 factors to enhancers

(2016) Rahul Roychoudhuri et al.   NATURE IMMUNOLOGY

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

(2015) Gosia Trynka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies

(2015) Gleb Kichaev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

Statistical colocalization of genetic risk variants for related autoimmune diseases in the context of common controls

(2015) Mary D Fortune et al.   NATURE GENETICS

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of the genetic regulation of gene expression in human neutrophils

(2015) Anand Kumar Andiappan et al.   Nature Communications

Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping

(2015) Chris Wallace et al.   PLoS Genetics

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

A Method for Gene-Based Pathway Analysis Using Genomewide Association Study Summary Statistics Reveals Nine New Type 1 Diabetes Associations

(2014) Marina Evangelou et al.   GENETIC EPIDEMIOLOGY

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Bach2 maintains T cells in a naive state by suppressing effector memory-related genes

(2013) S.-i. Tsukumo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional IL6R 358Ala Allele Impairs Classical IL-6 Receptor Signaling and Influences Risk of Diverse Inflammatory Diseases

(2013) Ricardo C. Ferreira et al.   PLoS Genetics

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data

(2012) Jie Huang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Incorporating Genotype Uncertainties Into the Genotypic TDT for Main Effects and Gene-Environment Interactions

(2012) Margaret A. Taub et al.   GENETIC EPIDEMIOLOGY

Annotation of functional variation in personal genomes using RegulomeDB

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promise and pitfalls of the Immunochip

(2011) Adrian Cortes et al.   ARTHRITIS RESEARCH & THERAPY

Pervasive Sharing of Genetic Effects in Autoimmune Disease

(2011) Chris Cotsapas et al.   PLoS Genetics

A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci

(2011) Jonathan P. Bradfield et al.   PLoS Genetics

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

METAL: fast and efficient meta-analysis of genomewide association scans

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

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Long-Range LD Can Confound Genome Scans in Admixed Populations

(2008) Alkes L. Price et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Novel Susceptibility Locus for Type 1 Diabetes on Chr12q13 Identified by a Genome-Wide Association Study

(2008) H. Hakonarson et al.   DIABETES

Follow-Up Analysis of Genome-Wide Association Data Identifies Novel Loci for Type 1 Diabetes

(2008) S. F.A. Grant et al.   DIABETES

Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci

(2008) Jason D Cooper et al.   NATURE GENETICS