Gaining insight into metabolic diseases from human genetic discoveries

Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity

(2021) Xiangchen Gu et al.   Science Translational Medicine

Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium

(2021) Bridget M Lin et al.   EBioMedicine

A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density

(2021) Nasa Sinnott-Armstrong et al.   Cell Metabolism

Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a regulator of insulin secretion

(2021) Ming Hu et al.   Cell Reports

Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5

(2021) Débora R. Sobreira et al.   SCIENCE

Rare Genetic Variants of Large Effect Influence Risk of Type 1 Diabetes.

(2020) Vincenzo Forgetta et al.   DIABETES

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

(2020) John P. Ray et al.   Nature Communications

Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals

(2020) Agata Wesolowska-Andersen et al.   eLife

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan

(2020) Saori Sakaue et al.   NATURE MEDICINE

Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis

(2020) Marijana Vujkovic et al.   NATURE GENETICS

Human organoids: model systems for human biology and medicine

(2020) Jihoon Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cross-species regulatory sequence activity prediction

(2020) David R. Kelley   PLoS Computational Biology

A Multi-omic Integrative Scheme Characterizes Tissues of Action at Loci Associated with Type 2 Diabetes

(2020) Jason M. Torres et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SHARE-seq reveals chromatin potential

(2020) Dorothy Clyde   NATURE REVIEWS GENETICS

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

(2019) Xuran Wang et al.   Nature Communications

Fine-mapping cis-regulatory variants in diverse human populations

(2019) Ashley Tehranchi et al.   eLife

Discovering metabolic disease gene interactions by correlated effects on cellular morphology

(2019) Yang Jiao et al.   Molecular Metabolism

Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

(2019) Juan Fernández-Tajes et al.   Genome Medicine

Selene: a PyTorch-based deep learning library for sequence data

(2019) Kathleen M. Chen et al.   NATURE METHODS

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

Clinical use of current polygenic risk scores may exacerbate health disparities

(2019) Alicia R. Martin et al.   NATURE GENETICS

Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood

(2019) Amit V. Khera et al.   CELL

Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls

(2019) Jason Flannick et al.   NATURE

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

(2019) Žiga Avsec et al.   NATURE BIOTECHNOLOGY

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

Multi-tissue transcriptome analyses identify genetic mechanisms underlying neuropsychiatric traits

(2019) Eric R. Gamazon et al.   NATURE GENETICS

Heritability of Type 2 Diabetes in the Washington State Twin Registry

(2019) Ally R. Avery et al.   Twin Research and Human Genetics

Understanding the kidney one cell at a time

(2019) Jihwan Park et al.   KIDNEY INTERNATIONAL

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

(2019) Irene Miguel-Escalada 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

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

(2019) Rajiv Movva et al.   PLoS One

Genetic Risk Scores for Diabetes Diagnosis and Precision Medicine

(2019) Miriam S Udler et al.   ENDOCRINE REVIEWS

The expression of genes in top obesity-associated loci is enriched in insula and substantia nigra brain regions involved in addiction and reward

(2019) Fatou K. Ndiaye et al.   INTERNATIONAL JOURNAL OF OBESITY

Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen

(2019) Rany M. Salem et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

Contribution of genetics to visceral adiposity and its relation to cardiovascular and metabolic disease

(2019) Torgny Karlsson et al.   NATURE MEDICINE

Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits

(2019) Chelsea K. Raulerson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The genetics of the mood disorder spectrum: genome-wide association analyses of over 185,000 cases and 439,000 controls

(2019) Jonathan R.I. Coleman et al.   BIOLOGICAL PSYCHIATRY

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Colocalization of GWAS and eQTL signals at loci with multiple signals identifies additional candidate genes for body fat distribution

(2019) Ying Wu et al.   HUMAN MOLECULAR GENETICS

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Glomerular filtration rate by differing measures, albuminuria and prediction of cardiovascular disease, mortality and end-stage kidney disease

(2019) Jennifer S. Lees et al.   NATURE MEDICINE

Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program

(2019) Jacklyn N. Hellwege et al.   Nature Communications

Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria

(2019) Alexander Teumer et al.   Nature Communications

Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data – a case study of schizophrenia

(2019) Daniel S. Buxton et al.   Scientific Reports

Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytes

(2019) Prashant Rajbhandari et al.   eLife

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

A Bayesian framework for multiple trait colocalization from summary association statistics

(2018) Claudia Giambartolomei et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes

(2018) Anubha Mahajan et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells

(2018) Soren K. Thomsen et al.   NATURE GENETICS

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease

(2018) Jihwan Park et al.   SCIENCE

Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS

(2018) David Z. Pan et al.   Nature Communications

Causal associations between risk factors and common diseases inferred from GWAS summary data

(2018) Zhihong Zhu et al.   Nature Communications

Novel subgroups of adult-onset diabetes and their association with outcomes: a data-driven cluster analysis of six variables

(2018) Emma Ahlqvist et al.   Lancet Diabetes & Endocrinology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

Renal compartment–specific genetic variation analyses identify new pathways in chronic kidney disease

(2018) Chengxiang Qiu et al.   NATURE MEDICINE

Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease

(2018) Chen Yao et al.   Nature Communications

Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis

(2018) Miriam S. Udler et al.   PLOS MEDICINE

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE 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

Trans-ethnic association study of blood pressure determinants in over 750,000 individuals

(2018) Ayush Giri et al.   NATURE GENETICS

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data

(2018) Jonathan Y. Hsu et al.   NATURE METHODS

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

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

(2018) Xinchen Wang et al.   Nature Communications

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

(2018) Ling Chen et al.   PLoS Computational Biology

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

(2017) Sarah Kim-Hellmuth et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

(2017) Flannick Jason et al.   Scientific Data

Colocalization of GWAS and eQTL Signals Detects Target Genes

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

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Systematic Functional Characterization of Candidate Causal Genes for Type 2 Diabetes Risk Variants

(2016) Soren K. Thomsen et al.   DIABETES

The genetic architecture of type 2 diabetes

(2016) Christian Fuchsberger et al.   NATURE

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

The human-induced pluripotent stem cell initiative—data resources for cellular genetics

(2016) Ian Streeter et al.   NUCLEIC ACIDS RESEARCH

The landscape of genomic imprinting across diverse adult human tissues

(2015) Yael Baran et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

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

(2015) Hilary K Finucane 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

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

Genetics of Type 2 Diabetes—Pitfalls and Possibilities

(2015) Rashmi Prasad et al.   Genes

Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms

(2014) Melina Claussnitzer et al.   CELL

Association of a Low-Frequency Variant inHNF1AWith Type 2 Diabetes in a Latino Population

(2014) Karol Estrada et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Loss-of-function mutations in SLC30A8 protect against type 2 diabetes

(2014) Jason Flannick et al.   NATURE GENETICS

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

(2014) Anubha Mahajan et al.   NATURE GENETICS

Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes

(2014) A. R. Majithia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The pancreatic β cell: recent insights from human genetics

(2014) Soren K. Thomsen et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Association of Estimated Glomerular Filtration Rate and Urinary Uromodulin Concentrations with Rare Variants Identified by UMOD Gene Region Sequencing

(2012) Anna Köttgen et al.   PLoS One

Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function

(2012) Cristian Pattaro et al.   PLoS 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

Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque

(2011) Joshua C Bis et al.   NATURE GENETICS

Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function

(2011) Ching-Ti Liu et al.   PLoS Genetics

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

(2010) Benjamin F Voight et al.   NATURE GENETICS