Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes

Negative evidence for a role of APH1B T27I variant in Alzheimer’s disease

(2020) Xulun Zhang et al.   HUMAN MOLECULAR GENETICS

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

(2020) Solveig K. Sieberts et al.   Scientific Data

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

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

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

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks

(2019) Shradha Mukherjee et al.   Frontiers in Neuroscience

Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

(2019) Brian W. Kunkle et al.   NATURE GENETICS

Blood–brain barrier transcytosis genes, risk of dementia and stroke: a prospective cohort study of 74,754 individuals

(2019) Ida Juul Rasmussen et al.   EUROPEAN JOURNAL OF EPIDEMIOLOGY

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

A functional variant in the miR‐142 promoter modulating its expression and conferring risk of Alzheimer disease

(2019) Mohsen Ghanbari et al.   HUMAN MUTATION

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

(2019) Hai Fang et al.   NATURE GENETICS

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks: The GR@ACE project

(2019) Sonia Moreno-Grau et al.   Alzheimers & Dementia

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

3-O -Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake

(2019) Jing Zhao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s disease

(2018) Arne De Roeck et al.   ACTA NEUROPATHOLOGICA

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

(2018) Kaur Alasoo et al.   NATURE GENETICS

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

(2018) Andrew E. Jaffe et al.   NATURE NEUROSCIENCE

GWAS on family history of Alzheimer’s disease

(2018) Riccardo E. Marioni et al.   Translational Psychiatry

Regulation of Leukocytes by TspanC8 Tetraspanins and the “Molecular Scissor” ADAM10

(2018) Alexandra L. Matthews et al.   Frontiers in Immunology

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci

(2018) David Stacey et al.   NUCLEIC ACIDS RESEARCH

Somatic variants in autosomal dominant genes are a rare cause of sporadic Alzheimer's disease

(2018) Gaël Nicolas et al.   Alzheimers & Dementia

Human stem cell–derived monocytes and microglia-like cells reveal impaired amyloid plaque clearance upon heterozygous or homozygous loss of TREM2

(2018) Christel Claes et al.   Alzheimers & Dementia

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

Alzheimer's Disease Risk Factor Pyk2 Mediates Amyloid-β Induced Synaptic Dysfunction and Loss

(2018) Santiago V. Salazar et al.   JOURNAL OF NEUROSCIENCE

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

An atlas of genetic associations in UK Biobank

(2018) Oriol Canela-Xandri et al.   NATURE GENETICS

Meta-analysis of Alzheimer’s disease on 9,751 samples from Norway and IGAP study identifies four risk loci

(2018) Aree Witoelar et al.   Scientific Reports

Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease

(2018) Nisha Rathore et al.   PLoS Genetics

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Case–control association mapping by proxy using family history of disease

(2017) Jimmy Z Liu et al.   NATURE GENETICS

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

(2017) Rebecca Sims et al.   NATURE 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

Molecular and functional variation in iPSC-derived sensory neurons

(2017) Jeremy Schwartzentruber et al.   NATURE GENETICS

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer’s disease

(2017) Qiongshi Lu et al.   PLoS Genetics

APP, PSEN1, and PSEN2 mutations in early-onset Alzheimer disease: A genetic screening study of familial and sporadic cases

(2017) Hélène-Marie Lanoiselée et al.   PLOS MEDICINE

Risk factor SORL1: from genetic association to functional validation in Alzheimer’s disease

(2016) Olav M. Andersen et al.   ACTA NEUROPATHOLOGICA

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

(2016) Christian Benner et al.   BIOINFORMATICS

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

(2016) Yohann Nédélec et al.   CELL

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach et al.   CELL

Schizophrenia risk from complex variation of complement component 4

(2016) Aswin Sekar et al.   NATURE

The BioGRID interaction database: 2017 update

(2016) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Influence of Coding Variability in APP-Aβ Metabolism Genes in Sporadic Alzheimer’s Disease

(2016) Celeste Sassi et al.   PLoS One

Deletion of the γ-secretase subunits Aph1B/C impairs memory and worsens the deficits of knock-in mice modeling the Alzheimer-like familial Danish dementia

(2016) Fabrizio Biundo et al.   Oncotarget

Loss of Bin1 Promotes the Propagation of Tau Pathology

(2016) Sara Calafate et al.   Cell Reports

Loss-of-function mutation in ABCA1 and risk of Alzheimer's disease and cerebrovascular disease

(2015) Liv Tybjærg Nordestgaard et al.   Alzheimers & Dementia

An angiotensin-converting enzyme (ACE) polymorphism may mitigate the effects of angiotensin-pathway medications on posttraumatic stress symptoms

(2015) K. M. Nylocks et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

(2015) Jimmy Z Liu et al.   NATURE GENETICS

Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease

(2015) Stacy Steinberg et al.   NATURE GENETICS

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka 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

Efficient Bayesian mixed-model analysis increases association power in large cohorts

(2015) Po-Ru Loh et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

CD33 modulates TREM2: convergence of Alzheimer loci

(2015) Gail Chan et al.   NATURE NEUROSCIENCE

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

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

Genomic modulators of gene expression in human neutrophils

(2015) Vivek Naranbhai et al.   Nature Communications

Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors

(2015) Martijn van de Bunt et al.   PLoS Genetics

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

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

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

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

(2014) T. Raj et al.   HUMAN MOLECULAR GENETICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

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

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Efficient computation with a linear mixed model on large-scale data sets with applications to genetic studies

(2013) Matti Pirinen et al.   Annals of Applied Statistics

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

CD33 Alzheimer's Risk-Altering Polymorphism, CD33 Expression, and Exon 2 Splicing

(2013) M. Malik et al.   JOURNAL OF NEUROSCIENCE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

(2013) Jean-Charles Lambert et al.   NATURE GENETICS

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Fine-Mapping Angiotensin-Converting Enzyme Gene: Separate QTLs Identified for Hypertension and for ACE Activity

(2013) Chia-Min Chung et al.   PLoS One

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

Bayesian refinement of association signals for 14 loci in 3 common diseases

(2012) Julian B Maller et al.   NATURE GENETICS

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

Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

(2012) Jian Yang et al.   NATURE GENETICS

Variant of TREM2 Associated with the Risk of Alzheimer's Disease

(2012) Thorlakur Jonsson et al.   NEW ENGLAND JOURNAL OF MEDICINE

TREM2 Variants in Alzheimer's Disease

(2012) Rita Guerreiro et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome-wide association study of Alzheimer's disease

(2012) M I Kamboh et al.   Translational Psychiatry

A robust clustering algorithm for identifying problematic samples in genome-wide association studies

(2011) Céline Bellenguez et al.   BIOINFORMATICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

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

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

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

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY