Coexistence of Multiple Functional Variants and Genes Underlies Genetic Risk Locus 11p11.2 of Alzheimer’s Disease

[1]  J. Weissman,et al.  MTCH2 is a mitochondrial outer membrane protein insertase , 2022, bioRxiv.

[2]  Qingbo S. Wang,et al.  Methods for statistical fine-mapping and their applications to auto-immune diseases , 2022, Seminars in Immunopathology.

[3]  T. Raj,et al.  Genetic analysis of the human microglia transcriptome across brain regions, aging and disease pathologies , 2022, Nature Genetics.

[4]  E. Gamazon,et al.  Genetically regulated expression in late-onset Alzheimer’s disease implicates risk genes within known and novel loci , 2021, Translational Psychiatry.

[5]  Laurent F. Thomas,et al.  A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease , 2021, Nature Genetics.

[6]  Alicia R. Martin,et al.  Genome-wide association studies , 2021, Nature Reviews Methods Primers.

[7]  D. Geschwind,et al.  Functional regulatory variants implicate distinct transcriptional networks in dementia , 2021, bioRxiv.

[8]  R. Dolmetsch,et al.  Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons , 2021, Communications biology.

[9]  Nathan S. Abell,et al.  Multiple Causal Variants Underlie Genetic Associations in Humans , 2021, bioRxiv.

[10]  K. Lunetta,et al.  Cell-type-specific expression quantitative trait loci associated with Alzheimer disease in blood and brain tissue , 2021, Translational Psychiatry.

[11]  Anastasia G. Efthymiou,et al.  Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes , 2021, Nature Communications.

[12]  Daniel J. Gaffney,et al.  Genome-wide meta-analysis, fine-mapping, and integrative prioritization implicate new Alzheimer’s disease risk genes , 2021, Nature Genetics.

[13]  A. Goate,et al.  Alzheimer's-associated PU.1 expression levels regulate microglial inflammatory response , 2020, Neurobiology of Disease.

[14]  Howard Y. Chang,et al.  Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases , 2020, Nature Genetics.

[15]  Tim Bartels,et al.  Microglia modulate neurodegeneration in Alzheimer’s and Parkinson’s diseases , 2020, Science.

[16]  B. Garcia,et al.  An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease , 2020, Nature Genetics.

[17]  R. Frikke-Schmidt,et al.  APOE and dementia – resequencing and genotyping in 105,597 individuals , 2020, Alzheimer's & dementia : the journal of the Alzheimer's Association.

[18]  M. Kampmann.  CRISPR-based functional genomics for neurological disease , 2020, Nature Reviews Neurology.

[19]  Benjamin A. Logsdon,et al.  Multi-tissue neocortical transcriptome-wide association study implicates 8 genes across 6 genomic loci in Alzheimer’s disease , 2020, Genome Medicine.

[20]  M. Hill,et al.  The multiplex model of the genetics of Alzheimer’s disease , 2020, Nature Neuroscience.

[21]  J. Dougherty,et al.  Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts , 2020, Biological Psychiatry.

[22]  A. Goate,et al.  Interpretation of risk loci from genome-wide association studies of Alzheimer's disease , 2020, The Lancet Neurology.

[23]  James B. Brewer,et al.  Brain cell type–specific enhancer–promoter interactome maps and disease-risk association , 2019, Science.

[24]  Ming Li,et al.  The genome-wide risk alleles for psychiatric disorders at 3p21.1 show convergent effects on mRNA expression, cognitive function, and mushroom dendritic spine , 2019, Molecular Psychiatry.

[25]  Bin Zhang,et al.  Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation , 2019, bioRxiv.

[26]  Sterling C. Johnson,et al.  Non-coding variability at the APOE locus contributes to the Alzheimer’s risk , 2019, Nature Communications.

[27]  O. Chiba-Falek,et al.  Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation , 2019, Alzheimer's & Dementia.

[28]  Lenka Maliskova,et al.  Mapping cis-Regulatory Chromatin Contacts in Neural Cells Links Neuropsychiatric Disorder Risk Variants to Target Genes , 2019, Nature Genetics.

[29]  Yun Joo Yoo,et al.  gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks , 2019, Bioinform..

[30]  Manolis Kellis,et al.  Single-cell transcriptomic analysis of Alzheimer’s disease , 2019, Nature.

[31]  David A. Knowles,et al.  Opportunities and challenges for transcriptome-wide association studies , 2019, Nature Genetics.

[32]  Nick C Fox,et al.  Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing , 2019, Nature Genetics.

[33]  Yongxia Huo,et al.  Functional genomics reveal gene regulatory mechanisms underlying schizophrenia risk , 2019, Nature Communications.

[34]  Timothy J. Hohman,et al.  Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk , 2019, Nature Genetics.

[35]  Prashant S. Emani,et al.  Comprehensive functional genomic resource and integrative model for the human brain , 2018, Science.

[36]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[37]  Judith A. Blake,et al.  Mouse Genome Database (MGD) 2019 , 2018, Nucleic Acids Res..

[38]  Y. Fang,et al.  Complement C7 is a novel risk gene for Alzheimer's disease in Han Chinese , 2018, National science review.

[39]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[40]  S. Beck,et al.  A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex , 2018, Nature Neuroscience.

[41]  A. Miyashita,et al.  Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping , 2018, BMC Medical Genomics.

[42]  Christopher D. Brown,et al.  Inferring the molecular mechanisms of noncoding Alzheimer’s disease-associated genetic variants , 2018, bioRxiv.

[43]  Christopher C. Overall,et al.  PU.1 regulates Alzheimer’s disease-associated genes in primary human microglia , 2018, Molecular Neurodegeneration.

[44]  Ashley R. Jones,et al.  Joint genome-wide association study of progressive supranuclear palsy identifies novel susceptibility loci and genetic correlation to neurodegenerative diseases , 2018, Molecular Neurodegeneration.

[45]  Y. Hurd,et al.  An atlas of chromatin accessibility in the adult human brain , 2018, Genome research.

[46]  Hongyu Zhao,et al.  A statistical framework for cross-tissue transcriptome-wide association analysis , 2018, bioRxiv.

[47]  Sina A. Gharib,et al.  Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood , 2018, Nature Communications.

[48]  Yong-Gang Yao,et al.  A systematic integrated analysis of brain expression profiles reveals YAP1 and other prioritized hub genes as important upstream regulators in Alzheimer's disease , 2018, Alzheimer's & Dementia.

[49]  W. Shi,et al.  Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB , 2017, Nature Communications.

[50]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[51]  Nicole M. Gaudelli,et al.  Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage , 2017, Nature.

[52]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[53]  Mary Goldman,et al.  Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics , 2016, Nature Communications.

[54]  Min Xu,et al.  Rare Genetic Variants of the Transthyretin Gene Are Associated with Alzheimer’s Disease in Han Chinese , 2017, Molecular Neurobiology.

[55]  K. Hao,et al.  A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease , 2017, Nature Neuroscience.

[56]  J. Haines,et al.  Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers , 2017, Acta Neuropathologica.

[57]  Joseph K. Pickrell,et al.  Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations , 2017, bioRxiv.

[58]  Eduard Korkotian,et al.  Loss of forebrain MTCH2 decreases mitochondria motility and calcium handling and impairs hippocampal-dependent cognitive functions , 2017, Scientific Reports.

[59]  Jing Zhao,et al.  The Genetic Architecture of Gene Expression in Peripheral Blood. , 2017, American journal of human genetics.

[60]  Vivien A. C. Schoonenberg,et al.  β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance , 2016, Cell.

[61]  Yong-Gang Yao,et al.  SZDB: A Database for Schizophrenia Genetic Research , 2016, Schizophrenia bulletin.

[62]  A. Ciechanover,et al.  The life cycle of the 26S proteasome: from birth, through regulation and function, and onto its death , 2016, Cell Research.

[63]  I. Tsarfaty,et al.  Mimp/Mtch2, an Obesity Susceptibility Gene, Induces Alteration of Fatty Acid Metabolism in Transgenic Mice , 2016, PloS one.

[64]  Pardis C Sabeti,et al.  Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay , 2016, Cell.

[65]  P. Visscher,et al.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets , 2016, Nature Genetics.

[66]  Y. Fang,et al.  CFH Variants Affect Structural and Functional Brain Changes and Genetic Risk of Alzheimer’s Disease , 2016, Neuropsychopharmacology.

[67]  Alison M. Goate,et al.  Alzheimer’s Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci , 2016, PloS one.

[68]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[69]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[70]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[71]  Carson C Chow,et al.  Second-generation PLINK: rising to the challenge of larger and richer datasets , 2014, GigaScience.

[72]  Daphne Koller,et al.  Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes , 2014, Science.

[73]  N. Andreasen,et al.  Pathways to Alzheimer's disease , 2014, Journal of internal medicine.

[74]  G. Ronnett,et al.  C1q/TNF-related Protein 4 (CTRP4) Is a Unique Secreted Protein with Two Tandem C1q Domains That Functions in the Hypothalamus to Modulate Food Intake and Body Weight* , 2013, The Journal of Biological Chemistry.

[75]  Nick C Fox,et al.  Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease , 2013, Nature Genetics.

[76]  Carol Moreno,et al.  Identifying multiple causative genes at a single GWAS locus , 2013, Genome research.

[77]  D. Koller,et al.  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals , 2013, Genome research.

[78]  H. Marzban,et al.  Spatial and Temporal Expression of Lysosomal Acid Phosphatase 2 (ACP2) Reveals Dynamic Patterning of the Mouse Cerebellar Cortex , 2013, The Cerebellum.

[79]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[80]  M. Weale,et al.  Conditional analysis identifies three novel major histocompatibility complex loci associated with psoriasis. , 2012, Human molecular genetics.

[81]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[82]  Bernardo L Sabatini,et al.  Synapses and Alzheimer's disease. , 2012, Cold Spring Harbor perspectives in biology.

[83]  P. Visscher,et al.  Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits , 2012, Nature Genetics.

[84]  Yang Luo,et al.  Identification of C1qTNF-related protein 4 as a potential cytokine that stimulates the STAT3 and NF-κB pathways and promotes cell survival in human cancer cells. , 2011, Cancer letters.

[85]  P. Visscher,et al.  GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.

[86]  Carol A. Miller,et al.  Down-regulation of DENN/MADD, a TNF receptor binding protein, correlates with neuronal cell death in Alzheimer's disease brain and hippocampal neurons , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[87]  Steven W. Taylor,et al.  The Subunit Composition of the Human NADH Dehydrogenase Obtained by Rapid One-step Immunopurification* , 2003, The Journal of Biological Chemistry.

[88]  J. Kelsoe,et al.  Identifying a series of candidate genes for mania and psychosis: a convergent functional genomics approach. , 2000, Physiological genomics.

[89]  C. Peters,et al.  Mice Deficient in Lysosomal Acid Phosphatase Develop Lysosomal Storage in the Kidney and Central Nervous System* , 1997, The Journal of Biological Chemistry.

[90]  Y. Zaltsman,et al.  Loss of Muscle MTCH2 Increases Whole-Body Energy Utilization and Protects from Diet-Induced Obesity. , 2017, Cell reports.

[91]  A. Niculescu,et al.  Convergent Functional Genomics: what we have learned and can learn about genes, pathways, and mechanisms , 2010, Neuropsychopharmacology.