Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

M. Fornage | K. Lunetta | S. Gabriel | M. Daly | E. Lander | R. Redon | T. Lehtimäki | R. Wilson | J. Haines | M. Pericak-Vance | G. Schellenberg | E. Wijsman | D. Witten | R. Gibbs | E. Boerwinkle | V. Salomaa | M. Perola | B. Neale | D. Muzny | K. Worley | W. Bush | E. Génin | R. Mayeux | J. Kaprio | B. Psaty | H. Soininen | K. Nho | J. Dartigues | E. Martin | A. Palotie | L. Farrer | A. Havulinna | M. Lathrop | T. Thornton | A. Goate | J. Lambert | P. Amouyel | Carlos Cruchaga | J. Dupuis | C. V. van Duijn | L. Cupples | P. Crane | C. Reitz | C. Tzourio | R. Schmidt | H. Schmidt | D. Campion | M. Hiltunen | S. Helisalmi | M. Ikram | N. Gupta | D. Howrigan | M. Kurki | J. Bis | X. Jian | L. Fulton | N. Amin | A. Naj | C. Bellenguez | A. DeStefano | G. Beecham | B. Grenier‐Boley | B. Vardarajan | B. Kunkle | K. Hamilton-Nelson | S. Seshadri | W. Salerno | S. Debette | Honghuang Lin | Yiyi Ma | J. Below | A. Renton | O. Quenez | J. Deleuze | Amanda Kuzma | G. Tosto | E. Marcora | S. J. van der Lee | L. Qu | Yuning Chen | C. Sarnowski | A. Remes | K. Mattila | Shahzad Ahmad | Yi Zhao | Daniel Lancour | Xiaoling Zhang | Michael Schmidt | F. Rajabli | C. Charbonnier | G. Nicolas | Jaeyoon Chung | Waleed Nasser | J. Farrell | Janowski Konrad | Devanshi Patel | Weixin Wang | S. Ahmad | J. Chung | Edoardo Marcora | R. Wilson | C. V. van Duijn | B. Psaty | D. Muzny | A. Kuzma | D. Lancour | D. Patel | Honghuang Lin | J. Konrad | M. Schmidt | A. Destefano | J. Haines | R. Schmidt

[1]  Hiep D. Nguyen,et al.  Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer’s Disease Sequencing Project , 2018, Dementia and Geriatric Cognitive Disorders.

[2]  H. Huang,et al.  Whole‐exome sequencing identifies a homozygous donor splice‐site mutation in STAG3 that causes primary ovarian insufficiency , 2018, Clinical genetics.

[3]  R. Redon,et al.  Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls , 2017, Neurobiology of Aging.

[4]  M. Fornage,et al.  The Alzheimer's Disease Sequencing Project: Study design and sample selection , 2017, Neurology: Genetics.

[5]  B. Schröder,et al.  Latest emerging functions of SPP/SPPL intramembrane proteases. , 2017, European journal of cell biology.

[6]  J. Haines,et al.  WHOLE-GENOME SEQUENCING IN FAMILIAL LATE-ONSET ALZHEIMER’S DISEASE IDENTIFIES RARE VARIATION IN AD CANDIDATE GENES , 2017, Alzheimer's & Dementia.

[7]  H. Hammes,et al.  Hyperglycaemic memory affects the neurovascular unit of the retina in a diabetic mouse model , 2017, Diabetologia.

[8]  P. Gleeson,et al.  Amyloid precursor protein traffics from the Golgi directly to early endosomes in an Arl5b‐ and AP4‐dependent pathway , 2017, Traffic.

[9]  Yaniv Erlich,et al.  Case–control association mapping by proxy using family history of disease , 2017, Nature Genetics.

[10]  Shane A. McCarthy,et al.  Reference-based phasing using the Haplotype Reference Consortium panel , 2016, Nature Genetics.

[11]  Anderson A Butler,et al.  Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction. , 2016, Epigenomics.

[12]  M. Gill,et al.  Common polygenic variation enhances risk prediction for Alzheimer's disease. , 2015, Brain : a journal of neurology.

[13]  P. Deyn,et al.  Mutations in ABCA7 in a Belgian cohort of Alzheimer's disease patients: a targeted resequencing study , 2015, The Lancet Neurology.

[14]  P. S. St George-Hyslop,et al.  Rare coding mutations identified by sequencing of Alzheimer disease genome‐wide association studies loci , 2015, Annals of neurology.

[15]  Sara M. Willems,et al.  The impact of low-frequency and rare variants on lipid levels , 2015, Nature Genetics.

[16]  H. Stefánsson,et al.  Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease , 2015, Nature Genetics.

[17]  Nengjun Yi,et al.  A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model , 2015, Human Heredity.

[18]  Yufeng Shen,et al.  Coding mutations in SORL1 and Alzheimer disease , 2015, Annals of neurology.

[19]  Ouagazzal Abdel-mouttalib Nociceptin/orphanin-FQ modulation of learning and memory. , 2015, Vitamins and hormones.

[20]  K. Chu,et al.  Distinct Expression of Long Non-Coding RNAs in an Alzheimer's Disease Model. , 2015, Journal of Alzheimer's disease : JAD.

[21]  G. Calo’,et al.  Nociceptin/orphanin FQ-NOP receptor system in inflammatory and immune-mediated diseases. , 2015, Vitamins and hormones.

[22]  J. Haines,et al.  A rare mutation in UNC5C predisposes to late-onset Alzheimer's disease and increases neuronal cell death , 2014, Nature Medicine.

[23]  K. Lunetta,et al.  Two rare AKAP9 variants are associated with Alzheimer's disease in African Americans , 2014, Alzheimer's & Dementia.

[24]  K. Lunetta,et al.  PLXNA4 is associated with Alzheimer disease and modulates tau phosphorylation , 2014, Annals of neurology.

[25]  Nick C Fox,et al.  Gene-Wide Analysis Detects Two New Susceptibility Genes for Alzheimer's Disease , 2014, PLoS ONE.

[26]  John Farrell,et al.  A search for age-related macular degeneration risk variants in Alzheimer disease genes and pathways , 2014, Neurobiology of Aging.

[27]  M. Nöthen,et al.  Follow-up of loci from the International Genomics of Alzheimer's Disease Project identifies TRIP4 as a novel susceptibility gene , 2014, Translational Psychiatry.

[28]  Mustafa Tekin,et al.  The promise of whole-exome sequencing in medical genetics , 2013, Journal of Human Genetics.

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

[30]  T. Willnow,et al.  Sorting receptor SORLA – a trafficking path to avoid Alzheimer disease , 2013, Journal of Cell Science.

[31]  A. Singleton,et al.  TREM2 variants in Alzheimer's disease. , 2013, The New England journal of medicine.

[32]  A. Hofman,et al.  Variant of TREM2 associated with the risk of Alzheimer's disease. , 2013, The New England journal of medicine.

[33]  R. Cancedda,et al.  An intronic ncRNA-dependent regulation of SORL1 expression affecting Aβ formation is upregulated in post-mortem Alzheimer's disease brain samples , 2012, Disease Models & Mechanisms.

[34]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[35]  M. Rieder,et al.  Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. , 2012, American journal of human genetics.

[36]  Ole A. Andreassen,et al.  A mutation in APP protects against Alzheimer’s disease and age-related cognitive decline , 2012, Nature.

[37]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[38]  R. Corominas,et al.  Candidate pathway association study in cocaine dependence: The control of neurotransmitter release , 2012, The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry.

[39]  D. G. Clark,et al.  Common variants in MS4A4/MS4A6E, CD2uAP, CD33, and EPHA1 are associated with late-onset Alzheimer’s disease , 2011, Nature Genetics.

[40]  Nick C Fox,et al.  Common variants in ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer’s disease , 2011, Nature Genetics.

[41]  Sandro Sorbi,et al.  Meta-analysis of the association between variants in SORL1 and Alzheimer disease. , 2011, Archives of neurology.

[42]  Thomas Lumley,et al.  META-ANALYSIS OF A RARE-VARIANT ASSOCIATION TEST. , 2011 .

[43]  V. Yang,et al.  Mammalian Krüppel-like factors in health and diseases. , 2010, Physiological reviews.

[44]  Michael Boehnke,et al.  LocusZoom: regional visualization of genome-wide association scan results , 2010, Bioinform..

[45]  Sudha Seshadri,et al.  Genome-wide analysis of genetic loci associated with Alzheimer disease. , 2010, JAMA.

[46]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[47]  O. Saitoh,et al.  A genetic variation in the dysbindin gene (DTNBP1) is associated with memory performance in healthy controls , 2010 .

[48]  M. Rowan,et al.  Inherent Anti-amyloidogenic Activity of Human Immunoglobulin γ Heavy Chains* , 2009, The Journal of Biological Chemistry.

[49]  L. Kiemeney,et al.  Corrigendum: Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer , 2009, Nature Genetics.

[50]  P. Bosco,et al.  Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease , 2009, Nature Genetics.

[51]  K. Ohi,et al.  Association between the dysbindin gene (DTNBP1) and cognitive functions in Japanese subjects , 2009, Psychiatry and clinical neurosciences.

[52]  C. Catsman-Berrevoets,et al.  Mutation in the AP4M1 gene provides a model for neuroaxonal injury in cerebral palsy. , 2009, American journal of human genetics.

[53]  K. Frazer,et al.  Common vs. rare allele hypotheses for complex diseases. , 2009, Current opinion in genetics & development.

[54]  Kathleen A. Kennedy,et al.  A New Triggering Receptor Expressed on Myeloid Cells (Trem) Family Member, Trem-Like 4, Binds to Dead Cells and Is a DNAX Activation Protein 12-Linked Marker for Subsets of Mouse Macrophages and Dendritic Cells1 , 2009, The Journal of Immunology.

[55]  Nick C Fox,et al.  Letter abstract - Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's Disease , 2009 .

[56]  J. Pandey Immunoglobulin GM genes as functional risk and protective factors for the development of Alzheimer's disease. , 2009, Journal of Alzheimer's disease : JAD.

[57]  H. Koeppen,et al.  Human plasma contains cross-reactive Abeta conformer-specific IgG antibodies. , 2008, Biochemistry.

[58]  M. Raftery,et al.  NSF, Unc-18-1, dynamin-1 and HSP90 are inclusion body components in neuronal intranuclear inclusion disease identified by anti-SUMO-1-immunocapture , 2008, Acta Neuropathologica.

[59]  W. Bodmer,et al.  Common and rare variants in multifactorial susceptibility to common diseases , 2008, Nature Genetics.

[60]  K. Lunetta,et al.  The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease , 2007, Nature Genetics.

[61]  J. Goodrich,et al.  Non-coding-RNA regulators of RNA polymerase II transcription , 2006, Nature Reviews Molecular Cell Biology.

[62]  M. Raiteri,et al.  Trafficking of presynaptic AMPA receptors mediating neurotransmitter release: Neuronal selectivity and relationships with sensitivity to cyclothiazide , 2006, Neuropharmacology.

[63]  L. Fratiglioni,et al.  Role of genes and environments for explaining Alzheimer disease. , 2006, Archives of general psychiatry.

[64]  G. Abecasis,et al.  Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies , 2006, Nature Genetics.

[65]  N. Varin‐Blank,et al.  Characterization of VIK-1: a new Vav-interacting Kruppel-like protein , 2005, Oncogene.

[66]  W. Engel,et al.  Mutation in the gene encoding lysosomal acid phosphatase (Acp2) causes cerebellum and skin malformation in mouse , 2004, Neurogenetics.

[67]  H. Braak,et al.  Neuropathological stageing of Alzheimer-related changes , 2004, Acta Neuropathologica.

[68]  J. Pritchard Are rare variants responsible for susceptibility to complex diseases? , 2001, American journal of human genetics.

[69]  A. Kakita,et al.  A quantitative study on the expression of synapsin II and N-ethylmaleimide-sensitive fusion protein in schizophrenic patients , 2001, Neuroscience Letters.

[70]  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.

[71]  S. Mirra,et al.  Making the diagnosis of Alzheimer's disease. A primer for practicing pathologists. , 1993, Archives of pathology & laboratory medicine.