GWAS meta-analysis of cerebrospinal fluid Alzheimer's biomarkers reveals loci regulating lipids, brain volume and autophagy.
The 7 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Methods › Statistical analysis › Mendelian randomization ↔ Mandelian_Randomization.R, the whole file · a weak match · score 0.95 · MR Egger intercept, Inverse Variance Weighted, rsID, Weighted Median, Weighted Mode, clumped
- [2] § Methods › Statistical analysis › Colocalization ↔ Colocalization.R, the whole file · a weak match · score 0.85 · coloc.abf, QTL summary statistics, eQTL, lead variants, Colocalization, GTEx
- [3] § Results › CSF Aβ42 is causally associated with increased risk of AD ↔ Mandelian_Randomization.R, the whole file · a weak match · score 0.82 · Inverse Variance Weighted, MR Egger, Weighted Median, Weighted Mode, exposure, randomization
- [4] § Methods › Statistical analysis › Comparison with other AD-related endophenotypes ↔ GWAS_catalog_Search.R, the whole file · a weak match · score 0.60 · get_associations, GWAS catalog, metadata, lead variants, queried, risk
- [5] § Methods › Statistical analysis › Gene prioritization ↔ Colocalization.R, the whole file · a weak match · score 0.60 · QTL summary statistics, lead variant, Mb, downstream, colocalized, locus
- [6] § Methods › Genotyping and quality control ↔ ldscore/ldscore.py, lines 304–357 · score 0.57 · removed SNPs, allele frequency, Genotyping, kept, PLINK, filter
- [7] § Methods › Genotyping and quality control ↔ munge_sumstats.py, lines 56–144 · score 0.52 · imputation quality, allele frequency, MAF, Genotyping, SNPs, variants
Paper
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The authors' code
R · 32 lines · 2.1 KB · no license · 2 matches
- rm(list = ls())
- library(TwoSampleMR) #v0.6.21
- library(ieugwasr)
- ab42_input <- read_exposure_data('Summary stats file with rsID', sep = '\t', snp_col = 'rsID', beta_col = 'Beta', se_col = 'SE', effect_allele_col = 'effect_allele', other_allele_col = 'other_allele', pval_col = 'P')
- ##try to subset to genome-wide variants and try again
- ab42_input_sub <- ab42_input[ab42_input$pval.exposure < 5e-8,]
- ##now reclump
- ab42_clumped <- clump_data(ab42_input_sub)
- ##succeeded, 6 variants remain after clumping: "rs3818361" "rs8106813" "rs117310449" "rs6733839" "rs73558179" "rs12972970"
- ##now import outcome data
- ad_output <- read_outcome_data('Bellenguez_etal_2022/GRCh38/GCST90027158_buildGRCh38.tsv.gz', snps = ab42_clumped$SNP, sep = '\t', snp_col = 'variant_id', beta_col = 'beta', se_col = 'standard_error', effect_allele_col = 'effect_allele', other_allele_col = 'other_allele', eaf_col = 'effect_allele_frequency', pval_col = 'p_value') ##5 variants overlapping between datasets
- ab42_harmonised <- harmonise_data(exposure_dat = ab42_clumped, outcome_dat = ad_output)
- ab42_harmonised
- ab42_mr_output <- mr(ab42_harmonised)
- ab42_mr_output
- # id.exposure id.outcome outcome exposure method nsnp b se pval
- #1 8ouM9e SzfNwa outcome exposure MR Egger 5 -1.477011 0.3857676 3.138679e-02
- #2 8ouM9e SzfNwa outcome exposure Weighted median 5 -1.804159 0.1374088 2.220508e-39
- #3 8ouM9e SzfNwa outcome exposure Inverse variance weighted 5 -1.806293 0.2178966 1.135503e-16
- #4 8ouM9e SzfNwa outcome exposure Simple mode 5 -1.764206 0.2035272 9.746752e-04
- #5 8ouM9e SzfNwa outcome exposure Weighted mode 5 -1.798011 0.1861702 6.429873e-04
- egger_intercept <- mr_pleiotropy_test(ab42_harmonised) ##p = 0.3785061, not evidence for pleiotropy
- write.table(ab42_mr_output, 'output file name', quote = F, row.names = F, sep = '\t')
- tiff('ab42_mr_plot.tiff', width = 5, height = 5, units = 'in', compression = 'lzw', res = 300)
- mr_scatter_plot(ab42_mr_output, ab42_harmonised)
- dev.off()
Mandelian_Randomization.R at commit 3515bb2, no license · at the source
Overview
and 135 other authors
Atahualpa Castillo Morales16, Timothy J Hohman17, Logan Dumitrescu17, Ting-Chen Wang17, Niccolo’ Tesi3,4,18, Silke Kern19,20, Margda Waern19, Ingmar Skoog19,20, Argonde van Harten3,4, Yolande A L Pijnenburg3,4, Wiesje M van der Flier3,4, Pascual Sánchez-Juan21, Eloy Rodriguez-Rodriguez22,23, Luca Kleineidam24,25, Oliver Peters26,27, Anja Schneider24,25, Fahri Küçükali28,29, Céline Bellenguez30, Benjamin Grenier-Boley30, Sami Heikkinen31, Itziar de Rojas14,22, Dan Rujescu32, Norbert Scherbaum33, Lucrezia Hausner34, Emrah Düzel35,36, Timo Grimmer37, Jens Wiltfang38,39,40, Rik Vandenberghe41, Sebastiaan Engelborghs28,42, Stefanie Heilmann-Heimbach43, Matthias Schmid25,44, Thomas Tegos45, Nikolaos Scarmeas46,47, Oriol Dols-Icardo22,48, Fermin Moreno22,49,50, Jordi Pérez-Tur22,51, María J Bullido22,52,53,54, Raquel Sánchez-Valle55, Victoria Álvarez56,57, Pablo García-González14, Pablo Mir22,58, Luis M Real59,60, Gerard Piñol-Ripoll61,62, Jose María García-Alberca22,62,63, Harro Seelaar4, Inez Ramakers64, Janne Papma65,66, Marc Hulsman3,4,67, Christoph Laske68,69, Stefan Teipel70,71, Josef Priller26,72,73, Robert Perneczky74,75,76,77, Katharina Buerger74,78, Markus M Nöthen79, Piotr Lewczuk80,81, Johannes Kornhuber80, Harald Hampel82, Ina Giegling83, Oliver Goldhardt38, Janine Diehl-Schmid38, Victor Andrade7,84, Michael MT Heneka7,25, Lutz Frölich34, Jonathan Vogelgsang38,85, Caroline Graff86,87, Hakan Thonberg86,87, Abbe Ullgren86,87, Goran Papenberg88, Jean-François Deleuze89, Carole Dufouil90,91, Michael Wagner24,25, Frank Jessen25,92,93, Henne Holstege3,4,67,94, Cornelia van Duijn95,96,97, Thibaud Lebouvier98, Olivier Hannon99, Ville Leinonen100, Hilkka Soininen101, Sanna-Kaisa Herukka101,102, Vilmantas Giedraitis103, Malin Löwenmark103, Lena Kilander103, Patricia Genius10,11,12, Blanca Rodríguez10,11,12, Emma S Luckett104,105,106,107, Arcadi Navarro10,11,108,109, Amanda Cano14,22, Marta Marquié14,22, Kaj Blennow110,111, Henrik Zetterberg110,112,113, Alberto Lleo22,48, Mercè Boada14,22, Agustin Ruiz14,22,114, Virginia Man-Yee Lee115, Vivianna M Van Deerlin115, Yuetiva Deming113,116, Sterling C Johnson116, Corinne D Engelman117, Pau Pastor118, Ignacio Alvarez118, Elaine R Peskind119,120, Amanda J Heslegrave112,121, Andrew J Saykin122, Kwangsik Nho122, Suzanne E Schindler15,123,124, John C Morris15, David M Holtzman15, Eric McDade15, Alan E Renton125,126,127, Alison Goate125,126, Laura Ibanez1,2,124, Matthias Riemenschneider128, Marilyn S Albert129, Simon M Laws130, Tenielle Porter130, Eleanor K O’Brien130, Leslie M Shaw114, Betty M Tijms3,4, Martin Ingelsson131,132,133, Pieter Jelle Visser134,135,136, Mikko Hiltunen31, Kristel Sleegers28,29, Craig W Ritchie137,138, Rebecca Sims139, Michael Belloy2,15, Jean-Charles Lambert30, Natalia Vilor-Tejedor10,11,12,140, Maria Victoria Fernández14, Qingqin S Li141,142,143, Michael W Nagle6, Riccardo E Marioni5, Alfredo Ramirez7,24,25,144,145, Lars Bertram13, Sven J van der Lee3,4,146, Carlos Cruchaga1,2,124146 affiliations
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO USA
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC Location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Human Genetics and Causal Biology, Eisai Center for Genetics-Guided Dementia Discovery, Eisai Inc, Cambridge, MA USA
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Estudios en Neurociencias y Sistemas Complejos (ENyS), CONICET-HEC-UNAJ, Buenos Aires, Argentina
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- Department of Neurology, Washington University School of Medicine, St. Louis, MO USA
- UK Dementia Research Institute at Cardiff, Cardiff, UK
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN USA
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
- Department of Neuropsychiatry, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Reina Sofia Alzheimer Center, CIEN Foundation, ISCIII, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital, Santander, Spain
- Department of Cognitive Disorders and Old Age Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Psychiatry and Psychotherapy, Berlin, Germany
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Complex Genetics of Alzheimer’s Disease Lab, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, LabEx DISTALZ-U1167-RID-AGE Facteurs de Risque et Determiants moléculaires des maladies liées au vieillissement, Lille, France
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Martin-Luther-University Halle-Wittenberg, University Clinic and Outpatient Clinic for Psychiatry, Psychotherapy and Psychosomatics, Halle (Saale), Germany
- LVR-University Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
- Department of Geriatric Psychiatry, Central Institute for Mental Health Mannheim, Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
- Institute of Cognitive Neurology and Dementia Research (IKND), Otto-von-Guericke University, Magdeburg, Germany
- Center for Cognitive Disorders, Department of Psychiatry and Psychotherapy, Technical University of Munich, TUM School of Medicine and Health, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
- Medical Science Department, iBiMED, Aveiro, Portugal
- Department of Neurology, UZ Leuven, Leuven, Belgium
- Department of Neurology, Universitair Ziekenhuis Brussel and Neuroprotection and Neuromodulation (NEUR) Research Group, Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital of Bonn, Bonn, Germany
- 1st Department of Neurology, Medical school, Aristotle University of Thessaloniki, Thessaloniki, Greece
- 1st Department of Neurology, Aiginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Depatment of Neurology, Columbia University, New York, NY USA
- Sant Pau Memory Unit, Institut de Recerca Sant Pau, Department of Neurology, Hospital de la Santa Creu I Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Neurology, Hospital Universitario Donostia, San Sebastian, Spain
- Neurosciences Area, Instituto Biodonostia, San Sebastian, Spain
- Unitat de Genètica Molecular, Institut de Biomedicina de València-CSIC, Valencia, Spain
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Madrid, Spain
- Instituto de Investigacion Sanitaria ‘Hospital la Paz’ (IdIPaz), Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
- Alzheimer’s disease and other cognitive disorders unit. Service of Neurology. Hospital Clínic of Barcelona. Institut d’Investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain
- Laboratorio de Genética. Hospital Universitario Central de Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, Asturias, Spain
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología. Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología. Hospital Universitario de Valme, Sevilla, Spain
- Depatamento de Especialidades Quirúrgicas, Bioquímica e Inmunología. Facultad de Medicina. Universidad de Málaga, Málaga, Spain
- Unitat Trastorns Cognitius, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLLeida), Lleida, Spain
- Alzheimer Research Center & Memory Clinic, Andalusian Institute for Neuroscience, Málaga, Spain
- Maastricht University, Department of Psychiatry & Neuropsychologie, Alzheimer Center Limburg, Maastricht, the Netherlands
- Neurology department Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Internal Medicine Department, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Section for Dementia Research, Hertie Institute for Clinical Brain Research and Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Rostock, Germany
- Department of Psychosomatic Medicine, Rostock University Medical Center, Rostock, Germany
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar Technical University Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE Munich), Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy) Munich, Munich, Germany
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Institute of Human Genetics; University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurodegeneration Diagnostics, Medical University of Białystok, Białystok, Poland
- Sorbonne University, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, Paris, France
- Division of General Psychiatry, Dept. of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Department of Psychiatry, Harvard Medical School McLean Hospital, Belmont, MA USA
- Division of Neurogeriatrics, Department NVS, Karolinska Institutet, Center for Alzheimer Research, Stockholm, Sweden
- Unit for Hereditary Dementias, Karolinska University Hospital-Solna, Stockholm, Sweden
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
- Inserm, Bordeaux Population Health Research Center, UMR 1219, Univ. Bordeaux, ISPED, CIC 1401-EC, Univ Bordeaux, Bordeaux, France
- CHU de Bordeaux, Pole santé publique, Bordeaux, France
- Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Centre for Artificial Intelligence in Precision Medicine, University of Oxford, Oxford, UK
- Univ.Lille, Inserm, CHULille, Lille Neuroscience & Cognition, UMR-S1172, Lille, France
- Université de Paris, EA 4468, APHP, Hôpital Broca, Paris, France
- Department of Neurosurgery, Kuopio University Hospital and Institute of Clinical Medicine-Neurosurgery, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, NeuroCenter, Kuopio University Hospital, Kuopio, Finland
- Department of Public Health and Caring Sciences/Clinical Geriatrics, Uppsala University, Uppsala, Sweden
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location VUmc, Amsterdam, Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
- Laboratory for Cognitive Neurology, KU Leuven, Leuven, Belgium
- Laboratory for Complex Genetics, KU Leuven, Leuven, Belgium
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
- Clinical neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- UK Dementia Research Institute at UCL, London, UK
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI USA
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases and Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI USA
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI USA
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
- Veterans Affairs Northwest Mental Illness Research, Education, and Clinical Center, Seattle, WA USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
- Indiana Alzheimer’s Disease Research Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Psychiatry, Saarland University, Homburg, Germany
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Centre for Precision Health, School of Medical Health Sciences, Edith Cowan University, Joondalup, WA Australia
- Krembil Brain Institute, University Health Network, Toronto, ON Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Departments of Medicine and Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON Canada
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, VUmc, Amsterdam, the Netherlands
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
- Scottish Brain Sciences, Scottish Gas Murrayfield Stadium, Edinburgh, UK
- School of Medicine, University of St Andrews, St Andrews, UK
- Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
- Department of Human Genetics, Radboud University Medical Center, Nijgmegen, the Netherlands
- Neuroscience, Janssen Research & Development LLC, Titusville, NJ USA
- JRD Data Science, Janssen Research & Development LLC, Titusville, NJ USA
- CHDI Management Inc., Princeton, NJ USA
- Department of Psychiatry, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, San Antonio, TX USA
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Disease (CECAD), University of Cologne, Cologne, Germany
- Section Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
Abstract
Cerebrospinal fluid amyloid beta 42, total tau, and phosphorylated tau 181 are well accepted markers of Alzheimer’s disease. These biomarkers better reflect disease pathogenesis compared to clinical diagnosis. Here, we perform a genome wide association study meta-analysis including 18,948 individuals of European ancestry and identify 12 genome-wide significant loci across all three biomarkers, eight of them novel. We replicate the association of biomarkers with APOE, CR1, GMNC/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 7 matches between paragraphs and lines of code.
NeuroGenomicsAndInformatics/GWAS-project
3515bb22c1cdc4258801726824ae43c62f6473de, 1 December 2025Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
8 files
- Colocalization.R, R, 79 lines
- Effect_size_comparison.R
, R, 163 lines - GNOVA_plot.R, R, 45 lines
- GWAS_catalog_Search.R, R, 42 lines
- Mandelian_Randomization.
R , R, 32 lines - Pathway_Analysis.R, R, 244 lines
- Prepare_file_for_MTAG.R, R, 60 lines
- README.md, Text, 192 lines
Zenodo 17780074
Availability: 1 check, the latest on 29 September 2026: the link answers (HTTP 200)
- 29 September 2026: the link answers (HTTP 200)
8 files
- Colocalization.R, R, 79 lines
- Effect_size_comparison.R
, R, 163 lines - GNOVA_plot.R, R, 45 lines
- GWAS_catalog_Search.R, R, 42 lines
- Mandelian_Randomization.
R , R, 32 lines - Pathway_Analysis.R, R, 244 lines
- Prepare_file_for_MTAG.R, R, 60 lines
- README.md, Text, 191 lines
bulik/ldsc
2fdeeb3b44379408794154993dbd6101b8946b7e, 16 January 2026Availability: 1 check, the latest on 26 September 2026: the link answers
- 26 September 2026: the link answers
27 files
- ContinuousAnnotations/
quantile_M.pl , Perl, 241 lines - ContinuousAnnotations/
quantile_h2g.r , R, 76 lines - ldsc.py, Python, 660 lines
- ldscore/
__init__.py , Python, 1 line - ldscore/
irwls.py , Python, 196 lines - ldscore/
jackknife.py , Python, 514 lines - ldscore/
ldscore.py , Python, 415 lines - ldscore/
parse.py , Python, 292 lines - ldscore/
regressions.py , Python, 743 lines - ldscore/
sumstats.py , Python, 581 lines - make_annot.py, Python, 56 lines
- munge_sumstats.py, Python, 745 lines
- setup.py, Python, 20 lines
- test/
parse_test/ , MATLAB, 1 linetest.l2.M - test/
parse_test/ , MATLAB, 1 linetest1.l2.M - test/
parse_test/ , MATLAB, 1 linetest2.l2.M - test/
parse_test/ , MATLAB, 1 linetest_bad.l2.M - test/
simulate.py , Python, 81 lines - test/
test_irwls.py , Python, 69 lines - test/
test_jackknife.py , Python, 267 lines - test/
test_ldscore.py , Python, 111 lines - test/
test_munge_sumstats.py , Python, 358 lines - test/
test_parse.py , Python, 129 lines - test/
test_regressions.py , Python, 342 lines - test/
test_sumstats.py , Python, 487 lines - LICENSE, License, 675 lines
- README.md, Text, 122 lines
xtonyjiang/GNOVA
5e0c460662cd257bb7887e9430f8a46c0ee6321f, 4 June 2024Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
10 files
- calculate.py, Python, 150 lines
- gnova.py, Python, 85 lines
- ldsc_thin.py, Python, 257 lines
- ldscore/
__init__.py , Python, 1 line - ldscore/
ldscore.py , Python, 414 lines, 1 match - ldscore/
parse.py , Python, 281 lines - munge_sumstats.py, Python, 723 lines, 1 match
- prep.py, Python, 114 lines
- LICENSE, License, 674 lines
- README.md, Text, 81 lines
jigyasha-timsina/gwas-project
3515bb22c1cdc4258801726824ae43c62f6473de, 1 December 2025Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
8 files
- Colocalization.R, R, 79 lines, 2 matches
- Effect_size_comparison.R
, R, 163 lines - GNOVA_plot.R, R, 45 lines
- GWAS_catalog_Search.R, R, 42 lines, 1 match
- Mandelian_Randomization.
R , R, 32 lines, 2 matches - Pathway_Analysis.R, R, 244 lines
- Prepare_file_for_MTAG.R, R, 60 lines
- README.md, Text, 192 lines
Code availability
We used publicly available software for all analyses in this study. This included: PLINK 2 version 2.00a3.6LM for all single variant analysis, METAL (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 5 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 54 scripts, each with its path and the digest of its content;
- 7 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
Datasets cited
- dss.niagads.org/
datasets/ , at dss.niagads.org; found in “Data availability”ng00191 - ebi.ac.uk/
gwas/ , at EMBL-EBI; found in “Data availability”studies
Data Availability Statement
The GWAS meta-analysis summary statistics generated in this study have been deposited in the NIAGADS database under accession code NG00191 (https://
We used publicly available software for all analyses in this study. This included: PLINK 2 version 2.00a3.6LM for all single variant analysis, METAL (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 155 authors, 2 keywords, 14 MeSH terms, 5 funders, 88 references.
Cite
This paper
Timsina, J., Jiang, C., McCartney, D. L., Tao, F., Dalmasso, M. C., Najar, J., Anastasi, F., Ohlei, O., Puerta Fuentes, R., Yang, C., Bradley, J., Western, D., Ali, M., Wang, C., Yang, C., Wu, Y., Liu, M., Budde, J., Williams, J., . . . Cruchaga, C. (2026). GWAS meta-analysis of cerebrospinal fluid Alzheimer's biomarkers reveals loci regulating lipids, brain volume and autophagy. Nature communications, 17(1), 7385. https://
BibTeX
@article{timsina2026gwas
author = {Timsina, Jigyasha and Jiang, Chenyang and McCartney, Daniel L and Tao, Feifei and Dalmasso, Maria Carolina and Najar, Jenna and Anastasi, Federica and Ohlei, Olena and Puerta Fuentes, Raquel and Yang, Chenyu and Bradley, Joseph and Western, Daniel and Ali, Muhammad and Wang, Ciyang and Yang, Chengran and Wu, Ying and Liu, Menghan and Budde, John and Williams, Julie and Mahoney, Rebecca and Castillo Morales, Atahualpa and Hohman, Timothy J and Dumitrescu, Logan and Wang, Ting-Chen and Tesi, Niccolo’ and Kern, Silke and Waern, Margda and Skoog, Ingmar and van Harten, Argonde and Pijnenburg, Yolande A L and van der Flier, Wiesje M and Sánchez-Juan, Pascual and Rodriguez-Rodriguez, Eloy and Kleineidam, Luca and Peters, Oliver and Schneider, Anja and Küçükali, Fahri and Bellenguez, Céline and Grenier-Boley, Benjamin and Heikkinen, Sami and de Rojas, Itziar and Rujescu, Dan and Scherbaum, Norbert and Hausner, Lucrezia and Düzel, Emrah and Grimmer, Timo and Wiltfang, Jens and Vandenberghe, Rik and Engelborghs, Sebastiaan and Heilmann-Heimbach, Stefanie and Schmid, Matthias and Tegos, Thomas and Scarmeas, Nikolaos and Dols-Icardo, Oriol and Moreno, Fermin and Pérez-Tur, Jordi and Bullido, María J and Sánchez-Valle, Raquel and Álvarez, Victoria and García-González, Pablo and Mir, Pablo and Real, Luis M and Piñol-Ripoll, Gerard and García-Alberca, Jose María and Seelaar, Harro and Ramakers, Inez and Papma, Janne and Hulsman, Marc and Laske, Christoph and Teipel, Stefan and Priller, Josef and Perneczky, Robert and Buerger, Katharina and Nöthen, Markus M and Lewczuk, Piotr and Kornhuber, Johannes and Hampel, Harald and Giegling, Ina and Goldhardt, Oliver and Diehl-Schmid, Janine and Andrade, Victor and Heneka, Michael MT and Frölich, Lutz and Vogelgsang, Jonathan and Graff, Caroline and Thonberg, Hakan and Ullgren, Abbe and Papenberg, Goran and Deleuze, Jean-François and Dufouil, Carole and Wagner, Michael and Jessen, Frank and Holstege, Henne and van Duijn, Cornelia and Lebouvier, Thibaud and Hannon, Olivier and Leinonen, Ville and Soininen, Hilkka and Herukka, Sanna-Kaisa and Giedraitis, Vilmantas and Löwenmark, Malin and Kilander, Lena and Genius, Patricia and Rodríguez, Blanca and Luckett, Emma S and Navarro, Arcadi and Cano, Amanda and Marquié, Marta and Blennow, Kaj and Zetterberg, Henrik and Lleo, Alberto and Boada, Mercè and Ruiz, Agustin and Lee, Virginia Man-Yee and Van Deerlin, Vivianna M and Deming, Yuetiva and Johnson, Sterling C and Engelman, Corinne D and Pastor, Pau and Alvarez, Ignacio and Peskind, Elaine R and Heslegrave, Amanda J and Saykin, Andrew J and Nho, Kwangsik and Schindler, Suzanne E and Morris, John C and Holtzman, David M and McDade, Eric and Renton, Alan E and Goate, Alison and Ibanez, Laura and Riemenschneider, Matthias and Albert, Marilyn S and Laws, Simon M and Porter, Tenielle and O’Brien, Eleanor K and Shaw, Leslie M and Tijms, Betty M and Ingelsson, Martin and Visser, Pieter Jelle and Hiltunen, Mikko and Sleegers, Kristel and Ritchie, Craig W and Sims, Rebecca and Belloy, Michael and Lambert, Jean-Charles and Vilor-Tejedor, Natalia and Fernández, Maria Victoria and Li, Qingqin S and Nagle, Michael W and Marioni, Riccardo E and Ramirez, Alfredo and Bertram, Lars and van der Lee, Sven J and Cruchaga, Carlos},
title = {{GWAS meta-analysis of cerebrospinal fluid Alzheimer's biomarkers reveals loci regulating lipids, brain volume and autophagy}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {7385},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/
url = {https://
pmid = {42014397},
pmcid = {PMC13402690}
}
RIS
TY - JOUR
AU - Timsina, Jigyasha
AU - Jiang, Chenyang
AU - McCartney, Daniel L
AU - Tao, Feifei
AU - Dalmasso, Maria Carolina
AU - Najar, Jenna
AU - Anastasi, Federica
AU - Ohlei, Olena
AU - Puerta Fuentes, Raquel
AU - Yang, Chenyu
AU - Bradley, Joseph
AU - Western, Daniel
AU - Ali, Muhammad
AU - Wang, Ciyang
AU - Yang, Chengran
AU - Wu, Ying
AU - Liu, Menghan
AU - Budde, John
AU - Williams, Julie
AU - Mahoney, Rebecca
AU - Castillo Morales, Atahualpa
AU - Hohman, Timothy J
AU - Dumitrescu, Logan
AU - Wang, Ting-Chen
AU - Tesi, Niccolo’
AU - Kern, Silke
AU - Waern, Margda
AU - Skoog, Ingmar
AU - van Harten, Argonde
AU - Pijnenburg, Yolande A L
AU - van der Flier, Wiesje M
AU - Sánchez-Juan, Pascual
AU - Rodriguez-Rodriguez, Eloy
AU - Kleineidam, Luca
AU - Peters, Oliver
AU - Schneider, Anja
AU - Küçükali, Fahri
AU - Bellenguez, Céline
AU - Grenier-Boley, Benjamin
AU - Heikkinen, Sami
AU - de Rojas, Itziar
AU - Rujescu, Dan
AU - Scherbaum, Norbert
AU - Hausner, Lucrezia
AU - Düzel, Emrah
AU - Grimmer, Timo
AU - Wiltfang, Jens
AU - Vandenberghe, Rik
AU - Engelborghs, Sebastiaan
AU - Heilmann-Heimbach, Stefanie
AU - Schmid, Matthias
AU - Tegos, Thomas
AU - Scarmeas, Nikolaos
AU - Dols-Icardo, Oriol
AU - Moreno, Fermin
AU - Pérez-Tur, Jordi
AU - Bullido, María J
AU - Sánchez-Valle, Raquel
AU - Álvarez, Victoria
AU - García-González, Pablo
AU - Mir, Pablo
AU - Real, Luis M
AU - Piñol-Ripoll, Gerard
AU - García-Alberca, Jose María
AU - Seelaar, Harro
AU - Ramakers, Inez
AU - Papma, Janne
AU - Hulsman, Marc
AU - Laske, Christoph
AU - Teipel, Stefan
AU - Priller, Josef
AU - Perneczky, Robert
AU - Buerger, Katharina
AU - Nöthen, Markus M
AU - Lewczuk, Piotr
AU - Kornhuber, Johannes
AU - Hampel, Harald
AU - Giegling, Ina
AU - Goldhardt, Oliver
AU - Diehl-Schmid, Janine
AU - Andrade, Victor
AU - Heneka, Michael MT
AU - Frölich, Lutz
AU - Vogelgsang, Jonathan
AU - Graff, Caroline
AU - Thonberg, Hakan
AU - Ullgren, Abbe
AU - Papenberg, Goran
AU - Deleuze, Jean-François
AU - Dufouil, Carole
AU - Wagner, Michael
AU - Jessen, Frank
AU - Holstege, Henne
AU - van Duijn, Cornelia
AU - Lebouvier, Thibaud
AU - Hannon, Olivier
AU - Leinonen, Ville
AU - Soininen, Hilkka
AU - Herukka, Sanna-Kaisa
AU - Giedraitis, Vilmantas
AU - Löwenmark, Malin
AU - Kilander, Lena
AU - Genius, Patricia
AU - Rodríguez, Blanca
AU - Luckett, Emma S
AU - Navarro, Arcadi
AU - Cano, Amanda
AU - Marquié, Marta
AU - Blennow, Kaj
AU - Zetterberg, Henrik
AU - Lleo, Alberto
AU - Boada, Mercè
AU - Ruiz, Agustin
AU - Lee, Virginia Man-Yee
AU - Van Deerlin, Vivianna M
AU - Deming, Yuetiva
AU - Johnson, Sterling C
AU - Engelman, Corinne D
AU - Pastor, Pau
AU - Alvarez, Ignacio
AU - Peskind, Elaine R
AU - Heslegrave, Amanda J
AU - Saykin, Andrew J
AU - Nho, Kwangsik
AU - Schindler, Suzanne E
AU - Morris, John C
AU - Holtzman, David M
AU - McDade, Eric
AU - Renton, Alan E
AU - Goate, Alison
AU - Ibanez, Laura
AU - Riemenschneider, Matthias
AU - Albert, Marilyn S
AU - Laws, Simon M
AU - Porter, Tenielle
AU - O’Brien, Eleanor K
AU - Shaw, Leslie M
AU - Tijms, Betty M
AU - Ingelsson, Martin
AU - Visser, Pieter Jelle
AU - Hiltunen, Mikko
AU - Sleegers, Kristel
AU - Ritchie, Craig W
AU - Sims, Rebecca
AU - Belloy, Michael
AU - Lambert, Jean-Charles
AU - Vilor-Tejedor, Natalia
AU - Fernández, Maria Victoria
AU - Li, Qingqin S
AU - Nagle, Michael W
AU - Marioni, Riccardo E
AU - Ramirez, Alfredo
AU - Bertram, Lars
AU - van der Lee, Sven J
AU - Cruchaga, Carlos
TI - GWAS meta-analysis of cerebrospinal fluid Alzheimer's biomarkers reveals loci regulating lipids, brain volume and autophagy
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/
VL - 17
IS - 1
SP - 7385
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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}
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