SynthesisPLoS genetics2015
Cell Specific eQTL Analysis without Sorting Cells.
Abstract readMeta-Analysis
In one paragraph
Synthesis in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
78citing papers in PubMed, 1 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia.Biological psychiatry · 2018Pooled it
- Genetic determinants of monocyte splicing are enriched for disease susceptibility loci.Nature communications · 2025Article
- Article
- Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction.bioRxiv : the preprint server for biology · 2024Article
- Fine-mapping and molecular characterisation of primary sclerosing cholangitis genetic risk loci.Nature communications · 2024Article
- HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data.Genome biology · 2024Article
- eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis.Cell genomics · 2024Article
- ACCURATE ESTIMATION OF RARE CELL-TYPE FRACTIONS FROM TISSUE OMICS DATA VIA HIERARCHICAL DECONVOLUTION.The annals of applied statistics · 2024Article
- Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders.American journal of human genetics · 2024Article
- PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs.Genome biology · 2024Article
- Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.American journal of human genetics · 2024Article
- eQTL studies: from bulk tissues to single cells.Journal of genetics and genomics = Yi chuan xue bao · 2023Review
- Methods and Insights from Single-Cell Expression Quantitative Trait Loci.Annual review of genomics and human genetics · 2023Review
- Single-cell genomics meets human genetics.Nature reviews. Genetics · 2023Review
- A computational method for cell type-specific expression quantitative trait loci mapping using bulk RNA-seq data.Nature communications · 2023Article
- Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy.Nature communications · 2023Article
- CeDAR: incorporating cell type hierarchy improves cell type-specific differential analyses in bulk omics data.Genome biology · 2023Article
- eQTL Studies: from Bulk Tissues to Single Cells.ArXiv · 2023Article
- Refined expression quantitative trait locus analysis on adenocarcinoma at the gastroesophageal junction reveals susceptibility and prognostic markers.Frontiers in genetics · 2023Article
- Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex.Genome medicine · 2022Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
58 authors.
Harm-Jan WestraUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Danny ArendsGroningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
Tõnu EskoEstonian Genome Center, University of Tartu, Tartu, Estonia; Divisions of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, United States of America; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America; Broad Institute, Cambridge, Massachusetts, United States of America.
Marjolein J PetersDepartment of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands.
Claudia SchurmannInterfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity & Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Katharina SchrammInstitute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany.
Johannes KettunenComputational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu, Finland; Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Hanieh YaghootkarGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
Benjamin P FairfaxWellcome Trust Centre for Human Genetics, Oxford, United Kingdom; Department of Oncology, Cancer and Haematology Centre, Churchill Hospital, Oxford, United Kingdom.
Anand Kumar AndiappanSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Yang LiUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
Jingyuan FuUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Juha KarjalainenUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Mathieu PlatteelUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Marijn VisschedijkUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
Rinse K WeersmaUniversity of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
Silva KaselaEstonian Genome Center, University of Tartu, Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Lili MilaniEstonian Genome Center, University of Tartu, Tartu, Estonia.
Liina TserelMolecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
Pärt PetersonMolecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
Eva ReinmaaEstonian Genome Center, University of Tartu, Tartu, Estonia.
Albert HofmanThe Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands.
André G UitterlindenDepartment of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands.
Fernando RivadeneiraDepartment of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands.
Georg HomuthInterfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Astrid PetersmannInstitute for Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
Roberto LorbeerInstitute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
Holger ProkischInstitute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany.
Thomas MeitingerInstitute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany; Munich Heart Alliance, Munich, Germany; German Center for Cardiovascular Research (DZHK), Germany.
Christian HerderInstitute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany.
Michael RodenInstitute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany; Department of Diabetology and Endocrinology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany.
Harald GrallertResearch Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
Samuli RipattiInstitute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland; Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom; Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland.
Markus PerolaEstonian Genome Center, University of Tartu, Tartu, Estonia; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Andrew R WoodGenetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
David MelzerInstitute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, United Kingdom.
Luigi FerrucciClinical Research Branch, National Institute on Aging NIA-ASTRA Unit, Harbor Hospital, Baltimore, Maryland, United States of America.
Andrew B SingletonLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America.
Dena G HernandezLaboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America; Department of Molecular Neuroscience and Reta Lila Laboratories, Institute of Neurology, UCL, London, United Kingdom.
Julian C KnightWellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
Rossella MelchiottiSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore; Doctoral School in Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Milan, Italy.
Bernett LeeSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Michael PoidingerSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Francesca ZolezziSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Anis LarbiSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
De Yun WangDepartment of Otolaryngology, National University of Singapore, Singapore.
Leonard H van den BergDepartment of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
Jan H VeldinkDepartment of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
Olaf RotzschkeSingapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
Seiko MakinoWellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
Veikko SalomaaDepartment of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Konstantin StrauchInstitute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Neuherberg, Germany.
Uwe VölkerInterfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Joyce B J van MeursDepartment of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands.
Andres MetspaluEstonian Genome Center, University of Tartu, Tartu, Estonia.
Cisca WijmengaUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Ritsert C JansenGroningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
Lude FrankeUniversity of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
Funding
Characterization of Normal Genomic VariabilityZIAAG000932 · NIA · NATIONAL INSTITUTE ON AGING · PI SINGLETON, ANDREW · 2009 to 2024
$11.3MWellcome Trust
Abstract
The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.
Indexed as
Polymorphism, Single NucleotideQuantitative Trait LociCell LineCrohn DiseaseGene Expression RegulationGenome-Wide Association StudyHumansLymphocytesNeutrophilsNod2 Signaling Adaptor ProteinPhenotypePrincipal Component AnalysisReproducibility of ResultsNOD2 protein, humanNod2 Signaling Adaptor Protein
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.