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

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

(2021) Daniel Taliun et al.   NATURE

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk

(2021) Joshua Chiou et al.   NATURE GENETICS

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes

(2020) Joan Camunas-Soler et al.   Cell Metabolism

Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

(2020) Yingsong Lin et al.   Nature Communications

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

(2019) Iris E. Jansen et al.   NATURE GENETICS

Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data

(2019) Ioanna Tachmazidou et al.   NATURE GENETICS

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference

(2019) Xuran Wang et al.   Nature Communications

Identification of common genetic risk variants for autism spectrum disorder

(2019) Jakob Grove et al.   NATURE GENETICS

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways

(2019) Philip R. Jansen et al.   NATURE GENETICS

Genome-wide association study identifies 30 loci associated with bipolar disorder

(2019) Eli A. Stahl et al.   NATURE GENETICS

Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa

(2019) Hunna J. Watson et al.   NATURE GENETICS

A catalog of genetic loci associated with kidney function from analyses of a million individuals

(2019) Matthias Wuttke et al.   NATURE GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

(2019) Elena López-Isac et al.   Nature Communications

Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response

(2018) Yurong Xin et al.   DIABETES

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

(2018) Naomi R. Wray et al.   NATURE GENETICS

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence

(2018) Jeanne E. Savage et al.   NATURE GENETICS

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

The role of the carboxyl ester lipase ( CEL ) gene in pancreatic disease

(2018) Bente B. Johansson et al.   PANCREATOLOGY

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels

(2018) Xia Jiang et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

(2018) Loic Yengo et al.   HUMAN MOLECULAR GENETICS

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

(2018) Jonas B. Nielsen et al.   NATURE GENETICS

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

(2018) Wei Zhou et al.   NATURE GENETICS

A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas

(2018) H. Efsun Arda et al.   Cell Systems

Pancreas Volume Declines During the First Year After Diagnosis of Type 1 Diabetes and Exhibits Altered Diffusion at Disease Onset

(2018) John Virostko et al.   DIABETES CARE

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

(2018) Anthony Aylward et al.   HUMAN MOLECULAR GENETICS

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation

(2018) Alexander Teumer et al.   Nature Communications

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

(2017) Katrina M de Lange et al.   NATURE GENETICS

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

(2017) Felix R Day et al.   NATURE GENETICS

Association analyses based on false discovery rate implicate new loci for coronary artery disease

(2017) Christopher P Nelson et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

(2017) Eleanor Wheeler et al.   PLOS MEDICINE

Type 1 diabetes mellitus

(2017) Anastasia Katsarou et al.   Nature Reviews Disease Primers

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

FINEMAP: efficient variable selection using summary data from genome-wide association studies

(2016) Christian Benner et al.   BIOINFORMATICS

Dissection of transcriptional andcis‐regulatory control of differentiation in human pancreatic cancer

(2016) Giuseppe R Diaferia et al.   EMBO JOURNAL

Genome-wide associations for birth weight and correlations with adult disease

(2016) Momoko Horikoshi et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease

(2016) Sun-Gou Ji et al.   NATURE GENETICS

Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants

(2016) Ying Jin et al.   NATURE GENETICS

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Abnormalities of the Exocrine Pancreas in Type 1 Diabetes

(2015) Martha Campbell-Thompson et al.   Current Diabetes Reports

Loss of cftr function leads to pancreatic destruction in larval zebrafish

(2015) Adam Navis et al.   DEVELOPMENTAL BIOLOGY

Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index

(2015) Janine F. Felix et al.   HUMAN MOLECULAR GENETICS

Pancreatic pathophysiology in cystic fibrosis

(2015) Katherine N Gibson-Corley et al.   JOURNAL OF PATHOLOGY

New genetic loci link adipose and insulin biology to body fat distribution

(2015) Dmitry Shungin et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

(2015) James Bentham et al.   NATURE GENETICS

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis

(2015) Lavinia Paternoster et al.   NATURE GENETICS

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

(2015) Hilary K Finucane et al.   NATURE GENETICS

Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

(2015) Felix R Day et al.   NATURE GENETICS

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan 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

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

(2015) Heather J. Cordell et al.   Nature Communications

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

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

A novel common variant in DCST2 is associated with length in early life and height in adulthood

(2014) Ralf J.P. van der Valk et al.   HUMAN MOLECULAR GENETICS

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer

(2014) Brian M Wolpin et al.   NATURE GENETICS

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Reduction of Circulating Neutrophils Precedes and Accompanies Type 1 Diabetes

(2013) A. Valle et al.   DIABETES

Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity

(2013) Diana L. Cousminer et al.   HUMAN MOLECULAR GENETICS

Genetics of rheumatoid arthritis contributes to biology and drug discovery

(2013) Yukinori Okada et al.   NATURE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Discovery and refinement of loci associated with lipid levels

(2013) Cristen J Willer et al.   NATURE GENETICS

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

Common variants at 12q15 and 12q24 are associated with infant head circumference

(2012) H Rob Taal et al.   NATURE GENETICS

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance

(2012) Alisa K Manning et al.   NATURE GENETICS

Genome-Wide Association Identifies Nine Common Variants Associated With Fasting Proinsulin Levels and Provides New Insights Into the Pathophysiology of Type 2 Diabetes

(2011) R. J. Strawbridge et al.   DIABETES

A Comprehensive Analysis of Shared Loci between Systemic Lupus Erythematosus (SLE) and Sixteen Autoimmune Diseases Reveals Limited Genetic Overlap

(2011) Paula S. Ramos 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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Obesity adversely affects survival in pancreatic cancer patients

(2010) Robert R. McWilliams et al.   CANCER

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Genome-wide meta-analyses identify multiple loci associated with smoking behavior

(2010)   NATURE GENETICS

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge

(2010) Richa Saxena et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li 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

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

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY