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1. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

Author: Stephen Watt, Louella Vasquez, Klaudia Walter, Alice L. Mann, Kousik Kundu, Lu Chen, Ying Sims, Simone Ecker, Frances Burden, Samantha Farrow, Ben Farr, Valentina Iotchkova, Heather Elding, Daniel Mead, Manuel Tardaguila, Hannes Ponstingl, David Richardson, Avik Datta, Paul Flicek, Laura Clarke, Kate Downes, Tomi Pastinen, Peter Fraser, Mattia Frontini, Biola-Maria Javierre, Mikhail Spivakov, and Nicole Soranzo
Subjects: Science
Abstract: PU.1 is a master regulator of myeloid development but its role in disease-relevant neutrophils is not well known. Here, the authors look at primary neutrophils from a human population and find that genetic variants affecting binding of PU.1 are associated with cell count and disease susceptibility.
Published: 2021
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2. Neutrophil lymphocyte ratio as an indicator for disease progression in Idiopathic Pulmonary Fibrosis

Author: Ling-Pei Ho, Rosie Barker, Harriet Bothwell, Andrea Pereira, Rachel K Hoyles, Rachel Benamore, Kritica Dwivedi, Andrew Achaiah, Amila Rathnapala, and Valentina Iotchkova
Subjects: Medicine, Diseases of the respiratory system, RC705-779
Abstract: Rationale Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease. Patients present at different stages and disease course is varied. Blood monocytes have been linked to all-cause mortality, and neutrophils to progression to IPF in patients with the indeterminate for usual interstitial pneumonia CT pattern.Objective To determine association between blood monocytes, neutrophils and lymphocytes levels (and their derived indexes), with lung function decline and mortality in IPF.Methods We performed a retrospective analysis of an IPF cohort (n=128) who had their first clinical visit at the Oxford Interstitial Lung Disease Service between 2013 and 2017. Association between blood monocytes, neutrophils, lymphocytes and derived indexes (within 4 months of visit) and decline in forced vital capacity (FVC) and all-cause mortality were assessed using Cox proportional hazard regression analysis. Kaplan-Meier analysis was used to assess time-to-event for 10% FVC decline and mortality for patients dichotomised to high and low leucocyte counts.Results Median length of follow-up was 31.0 months (IQR 16.2–42.4); 41.4% demonstrated FVC decline >10% per year and 43.8% died. In multivariate models (incorporating age, gender and initial FVC%), raised neutrophils, lymphopaenia and neutrophil:lymphocyte ratio were associated with FVC decline (p≤0.01); while both monocytes and neutrophil levels (and their derived indexes) were associated with all-cause mortality (p≤0.01). Kaplan-Meier analysis also showed association between neutrophils and its derived indexes but not monocyte, with FVC decline.Conclusion Blood neutrophil and lymphopaenia are more sensitive than monocytes as prognostic indicators of disease progression in those with established IPF.
Published: 2022
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3. Monocyte and neutrophil levels are potentially linked to progression to IPF for patients with indeterminate UIP CT pattern

Author: Ling-Pei Ho, Rosie Barker, Harriet Bothwell, Andrea Pereira, Rachel K Hoyles, Rachel Benamore, Kritica Dwivedi, Amila Rathnapala, and Valentina Iotchkova
Subjects: Medicine, Diseases of the respiratory system, RC705-779
Published: 2021
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4. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author: Simon Haworth, Chin Yang Shapland, Caroline Hayward, Bram P. Prins, Janine F. Felix, Carolina Medina-Gomez, Fernando Rivadeneira, Carol Wang, Tarunveer S. Ahluwalia, Martine Vrijheid, Mònica Guxens, Jordi Sunyer, Ioanna Tachmazidou, Klaudia Walter, Valentina Iotchkova, Andrew Jackson, Louise Cleal, Jennifer Huffmann, Josine L. Min, Lærke Sass, Paul R. H. J. Timmers, UK10K consortium, George Davey Smith, Simon E. Fisher, James F. Wilson, Tim J. Cole, Dietmar Fernandez-Orth, Klaus Bønnelykke, Hans Bisgaard, Craig E. Pennell, Vincent W. V. Jaddoe, George Dedoussis, Nicholas Timpson, Eleftheria Zeggini, Veronique Vitart, and Beate St Pourcain
Subjects: Science
Abstract: Size and shape of the brain are, among others, influenced by the dimensions of the skull. Here, the authors report genome-wide association studies for head circumference and intracranial volume in children and adults and the identification of nine common or low-frequency variants associated with these traits.
Published: 2019
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5. Multi-Modal Characterization of Monocytes in Idiopathic Pulmonary Fibrosis Reveals a Primed Type I Interferon Immune Phenotype

Author: Emily Fraser, Laura Denney, Agne Antanaviciute, Karl Blirando, Chaitanya Vuppusetty, Yuejuan Zheng, Emmanouela Repapi, Valentina Iotchkova, Stephen Taylor, Neil Ashley, Victoria St Noble, Rachel Benamore, Rachel Hoyles, Colin Clelland, Joseph M. D. Rastrick, Clare S. Hardman, Nasullah K. Alham, Rachel E. Rigby, Alison Simmons, Jan Rehwinkel, and Ling-Pei Ho
Subjects: monocytes, lung, fibrosis, idiopathic pulmonary fibrosis, macrophages, Immunologic diseases. Allergy, RC581-607
Abstract: Idiopathic pulmonary fibrosis (IPF) is the most severe form of chronic lung fibrosis. Circulating monocytes have been implicated in immune pathology in IPF but their phenotype is unknown. In this work, we determined the immune phenotype of monocytes in IPF using multi-colour flow cytometry, RNA sequencing and corresponding serum factors, and mapped the main findings to amount of lung fibrosis and single cell transcriptomic landscape of myeloid cells in IPF lungs. We show that monocytes from IPF patients displayed increased expression of CD64 (FcγR1) which correlated with amount of lung fibrosis, and an amplified type I IFN response ex vivo. These were accompanied by markedly raised CSF-1 levels, IL-6, and CCL-2 in serum of IPF patients. Interrogation of single cell transcriptomic data from human IPF lungs revealed increased proportion of CD64hi monocytes and “transitional macrophages” with higher expression of CCL-2 and type I IFN genes. Our study shows that monocytes in IPF patients are phenotypically distinct from age-matched controls, with a primed type I IFN pathway that may contribute to driving chronic inflammation and fibrosis. These findings strengthen the potential role of monocytes in the pathogenesis of IPF.
Published: 2021
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6. Neutrophil lymphocyte ratio as an indicator for disease progression in Idiopathic Pulmonary Fibrosis

Author: Andrew Achaiah, Amila Rathnapala, Andrea Pereira, Harriet Bothwell, Kritica Dwivedi, Rosie Barker, Valentina Iotchkova, Rachel Benamore, Rachel K Hoyles, and Ling-Pei Ho
Subjects: Pulmonary and Respiratory Medicine, Neutrophils, Disease Progression, Humans, Lymphocytes, Tomography, X-Ray Computed, Idiopathic Pulmonary Fibrosis, Retrospective Studies
Abstract: RationaleIdiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease. Patients present at different stages and disease course is varied. Blood monocytes have been linked to all-cause mortality, and neutrophils to progression to IPF in patients with the indeterminate for usual interstitial pneumonia CT pattern.ObjectiveTo determine association between blood monocytes, neutrophils and lymphocytes levels (and their derived indexes), with lung function decline and mortality in IPF.MethodsWe performed a retrospective analysis of an IPF cohort (n=128) who had their first clinical visit at the Oxford Interstitial Lung Disease Service between 2013 and 2017. Association between blood monocytes, neutrophils, lymphocytes and derived indexes (within 4 months of visit) and decline in forced vital capacity (FVC) and all-cause mortality were assessed using Cox proportional hazard regression analysis. Kaplan-Meier analysis was used to assess time-to-event for 10% FVC decline and mortality for patients dichotomised to high and low leucocyte counts.ResultsMedian length of follow-up was 31.0 months (IQR 16.2–42.4); 41.4% demonstrated FVC decline >10% per year and 43.8% died. In multivariate models (incorporating age, gender and initial FVC%), raised neutrophils, lymphopaenia and neutrophil:lymphocyte ratio were associated with FVC decline (p≤0.01); while both monocytes and neutrophil levels (and their derived indexes) were associated with all-cause mortality (p≤0.01). Kaplan-Meier analysis also showed association between neutrophils and its derived indexes but not monocyte, with FVC decline.ConclusionBlood neutrophil and lymphopaenia are more sensitive than monocytes as prognostic indicators of disease progression in those with established IPF.
Published: 2022

7. FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions [version 1; referees: 2 approved with reservations]

Author: Ian Dunham, Eugene Kulesha, Valentina Iotchkova, Sandro Morganella, and Ewan Birney
Subjects: Software Tool Article, Articles, Bioinformatics, Genome wide association, GWAS, Hypersensitive sites, regulatory elements
Abstract: Genome Wide Association Studies (GWAS) provide an unbiased discovery mechanism for numerous human diseases. However, a frustration in the analysis of GWAS is that the majority of variants discovered do not directly alter protein-coding genes. We have developed a simple analysis approach that detects the tissue-specific regulatory component of a set of GWAS SNPs by identifying enrichment of overlap with DNase I hotspots from diverse tissue samples. Functional element Overlap analysis of the Results of GWAS Experiments (FORGE) is available as a web tool and as standalone software and provides tabular and graphical summaries of the enrichments. Conducting FORGE analysis on SNP sets for 260 phenotypes available from the GWAS catalogue reveals numerous overlap enrichments with tissue-specific components reflecting the known aetiology of the phenotypes as well as revealing other unforeseen tissue involvements that may lead to mechanistic insights for disease.
Published: 2015
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8. Blood leukocyte levels as potential prognostic markers in IPF

Author: Ling-Pei Ho, Rachel K. Hoyles, Kritica Dwivedi, Rosia Barker, Armila Rathnapala, Andrew Achaiah, Harriet Bothwell, Valentina Iotchkova, and Andrea Pereira
Subjects: Oncology, medicine.medical_specialty, business.industry, Internal medicine, medicine, business
Published: 2021

9. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

Author: Hannes Ponstingl, Simone Ecker, Manuel Tardaguila, Samantha Farrow, Paul Flicek, Valentina Iotchkova, Ben Farr, Mattia Frontini, Lu Chen, Nicole Soranzo, Louella Vasquez, Peter Fraser, David J. Richardson, Alice L. Mann, Avik Datta, Daniel Mead, Heather Elding, Kate Downes, Klaudia Walter, Tomi Pastinen, Kousik Kundu, Biola-Maria Javierre, Mikhail Spivakov, Ying Sims, Stephen Watt, Frances Burden, Laura Clarke, Walter, Klaudia [0000-0003-4448-0301], Kundu, Kousik [0000-0002-1019-8351], Ecker, Simone [0000-0001-5648-1710], Iotchkova, Valentina [0000-0001-5057-0210], Mead, Daniel [0000-0001-7717-4330], Ponstingl, Hannes [0000-0001-7573-1703], Richardson, David [0000-0003-0247-9118], Flicek, Paul [0000-0002-3897-7955], Clarke, Laura [0000-0002-5989-6898], Fraser, Peter [0000-0002-0041-1227], Javierre, Biola-Maria [0000-0002-8682-6748], Spivakov, Mikhail [0000-0002-0383-3943], Soranzo, Nicole [0000-0003-1095-3852], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Male, Neutrophils, 45/43, General Physics and Astronomy, 631/250/262, 0302 clinical medicine, Transcriptional regulation, Promoter Regions, Genetic, Innate immunity, Multidisciplinary, article, 49/39, Middle Aged, Acquired immune system, Chromatin, Cell biology, Enhancer Elements, Genetic, Chromatin Immunoprecipitation Sequencing, Female, Adult, Science, Quantitative Trait Loci, Biology, Chromatin structure, General Biochemistry, Genetics and Molecular Biology, Autoimmune Diseases, 03 medical and health sciences, Young Adult, Immune system, Proto-Oncogene Proteins, 631/208/200, medicine, Humans, Enhancer, Gene, Aged, 45/91, Autoimmune disease, Innate immune system, General Chemistry, 631/337/100/101, medicine.disease, Gene regulation, 631/208/199, 030104 developmental biology, Gene Expression Regulation, Trans-Activators, Gene expression, 38/15, 030217 neurology & neurosurgery
Abstract: Funder: MS is funded by Medical Research Council (MC-A652-5QA20), Funder: This work was supported by the Wellcome Trust grant (206194) and EU FP7 High Impact Project BLUEPRINT (HEALTH-F5-2011-282510), Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with immune system traits and diseases. Here, we profile the binding of myeloid master regulator PU.1 in primary neutrophils across nearly a hundred volunteers. We show that variants associated with differential PU.1 binding underlie genetically-driven differences in cell count and susceptibility to autoimmune and inflammatory diseases. We integrate these results with other multi-individual genomic readouts, revealing coordinated effects of PU.1 binding variants on the local chromatin state, enhancer-promoter contacts and downstream gene expression, and providing a functional interpretation for 27 genes underlying immune traits. Collectively, these results demonstrate the functional role of PU.1 and its target enhancers in neutrophil transcriptional control and immune disease susceptibility.
Published: 2021

10. S79 Prevalence of the indeterminate for UIP CT feature and potential link between monocyte and neutrophil levels and progression to IPF – a single centre analysis

Author: Rachel K. Hoyles, Amila Rathnapala, Andrea Pereira, Andrew Achaiah, Rosie Barker, Kritica Dwivedi, LP Ho, Harriet Bothwell, and Valentina Iotchkova
Subjects: medicine.medical_specialty, Proportional hazards model, business.industry, Disease, Guideline, respiratory system, medicine.disease, Gastroenterology, respiratory tract diseases, Idiopathic pulmonary fibrosis, FEV1/FVC ratio, DLCO, Internal medicine, Cohort, Medicine, Indeterminate, business
Abstract: Introduction Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease with poor prognosis. Identifying patients early may allow intervention which could limit progression. The ‘indeterminate for UIP’ (iUIP) CT pattern could be a precursor to IPF. Aims To evaluate prevalence and progression of patients with ‘iUIP’ to a clinical diagnosis of IPF, and explore factors contributing to progression. Methods We performed a retrospective analysis of an IPF cohort seen in the Oxford ILD Service between 2013–2017. We analysed all HRCTs performed for each patient up to August 2019. HRCT images were re-categorised according to the 2018 IPF guideline to identify those with iUIP CT pattern. These were categorised as ‘non-progressors’ or ‘progressors’ depending on whether there has been change in CT scan in terms of extent of disease or change in pattern of disease to ‘definite’ or ‘probable’ UIP pattern.Radiological features, lung function trends, haematological data and patient demographics were examined to explore potential contribution to progression using a univariate Cox proportional hazard model. Results 230 individual patients with a clinical diagnosis of IPF were screened. 48 (21%) cases with iUIP pattern were identified. 32 patients had at least one follow-on CT scan. Of these evaluable cases, 23 (71%) demonstrated progression and 9 (29%) cases demonstrated no progression. Of the progressors; 26% (6 cases) demonstrated increase in extent of iUIP (over 3.1 ±0.8 yrs), 48% (11 cases) progressed to ‘probable UIP’ (over 3.8 ±1.6 yrs) and 26% progressed to ‘definite UIP’ (4.1 ±2.4 yrs). All those with ‘definite’ or ‘probable UIP’ were diagnosed as IPF by ILD MDT. Using Cox regression, CT-contemporaneous monocyte count >0.90 × 103/μL [HR 3.9 (1.3–12), p=0.017] and neutrophils >7.5 × 103/µl [HR 43 (4.2–430), p=0.001] were significantly associated with progression to IPF. There was also trend towards male gender, lower baseline FVC and TLCO, presence of GGO on CT and ex-smoker status in the progressor group. Conclusion 53% of evaluable iUIP patients progressed to a clinical diagnosis of IPF over 3.9 years (±1.9). Baseline monocyte (>0.90 × 103/μL) and neutrophil (>7.5 × 103/µl) counts were significantly associated with progression. These data provide a single-centre analysis of the evolution of patients with iUIP CT pattern, and first signal for potential factors associated with progression to IPF.
Published: 2021

11. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

Author: Giuseppe Matullo, John R. B. Perry, Meena Kumari, Gemma C Sharp, Tomáš Paus, E. Giralt-Steinhauer, Marta E. Alarcón-Riquelme, Koen F. Dekkers, F. Gagnon, Simonetta Guarrera, Cilla Söderhäll, Rosie M. Walker, Therese Tillin, M. Smarts, Juan E. Castillo-Fernandez, John M. Starr, Jean Shin, Dan Mason, T Esko, Christopher Shaw, Hannah R Elliott, Manon Bernard, David L. Corcoran, Yvonne Awaloff, Ahmad Al Khleifat, Bert Brunekreef, Clara Viberti, John Wright, Gibran Hemani, Kathryn L. Evans, Camilla Schmidt Morgen, Jouke J. Hottenga, Susan M. Ring, Terrie E. Moffitt, Silva Kasela, C. Hale, Idil Yet, Katri Räikkönen, René Luijk, Vanessa Schmoll, Kimberley Burrows, Annelot M. Dekker, D. VanHeemst, Jordana T. Bell, Jordi Jimenez-Conde, Carlotta Sacerdote, Salvatore Panico, Lili Milani, Nabila Kazmi, Torben Hansen, Aleksey Shatunov, J L Min, Richa Gupta, Henning Tiemeier, Grant W. Montgomery, Vincent W. V. Jaddoe, E.J.C. de Geus, Fernando Rivadeneira, Debbie A Lawlor, Carol A. Wang, Toni-Kim Clarke, Susanne Lucae, Nicholas J. Wareham, Jordi Sunyer, Felix R. Day, C. Soriano-Tarraga, Christoph Bock, Juan R. González, D. Aissi, J.B. van Meurs, Ian J. Deary, Ken K. Ong, Louise Arseneault, Eilis Hannon, Bastiaan T. Heijmans, Philip E. Melton, Ashok Kumar, Pierre-Emmanuel Morange, Zdenka Pausova, T.D. Spector, Nicholas G. Martin, J. Mill, Francesc Català-Moll, Alun D. Hughes, Leonard C. Schalkwyk, Giovanni Cugliari, Carlos Ruiz-Arenas, Elena Carnero-Montoro, Marine Germain, Yanni Zeng, Andrew M. McIntosh, Riccardo E. Marioni, Wilfried Karmaus, Ikram, Gonneke Willemsen, Miina Ollikainen, Karen M Ho, Craig E. Pennell, F.I. Rezwan, Darina Czamara, Ramona A. J. Zwamborn, Dorret I. Boomsma, Wendy L. McArdle, J. M. van Dongen, Guillermo Barturen, Matthew Suderman, Richie Poulton, Daniel Lawson, A. Metspalu, David-Alexandre Trégouët, Marian Beekman, Andrew D. Bretherick, Johanna Klughammer, Hongmei Zhang, M.H. van IJzendoorn, Nish Chaturvedi, Jari Lahti, Karen Sugden, Jan H. Veldink, Mariona Bustamante, Avshalom Caspi, Pooja R. Mandaviya, Judith M. Vonk, Tom R. Gaunt, Cheng-Jian Xu, John W. Holloway, Tian Lin, Tom G. Richardson, Caroline L Relton, Naomi R. Wray, Allan F. McRae, George Davey Smith, Erik Melén, Valentina Iotchkova, Ellen A. Nohr, Jaakko Kaprio, Göran Pershagen, Elisabeth B. Binder, A. al Chalabi, T.J. Gorrie-Stone, K. van Eijk, Gerard H. Koppelman, M. Lerro, Alexia Cardona, Sailalitha Bollepalli, P.E. Slagboom, Thorkild I. A. Sørensen, André G. Uitterlinden, Jaume Roquer, Peter M. Visscher, Janine F. Felix, Martin Kerick, Gail Davies, Rae-Chi Huang, Alfredo Iacoangeli, Alison D. Murray, Helsinki Institute of Life Science HiLIFE, Institute for Molecular Medicine Finland, Epigenetics of Complex Diseases and Traits, Department of Public Health, Department of Psychology and Logopedics, Biological Psychology, APH - Mental Health, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, APH - Methodology, Groningen Research Institute for Asthma and COPD (GRIAC), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Epidemiology, Internal Medicine, Pediatrics, Child and Adolescent Psychiatry / Psychology, and Clinical Child and Family Studies
Subjects: Multifactorial Inheritance, ADN, Quantitative Trait Loci, Genome-wide association study, VARIANTS, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, LINKS, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Quantitative Trait, Heritable, Genetic variation, Genetics, WIDE ASSOCIATION, GWAS, Humans, Genetic Predisposition to Disease, Genotip, METAANALYSIS, EQTL, 030304 developmental biology, Epigenesis, SNP ANALYSIS, 0303 health sciences, COMPLEX, dNaM, Chromosome Mapping, DNA, DNA Methylation, Phenotype, Genetic architecture, MODEL, Fenotip, Gene Expression Regulation, DNA methylation, MENDELIAN RANDOMIZATION, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 3111 Biomedicine, Metilació, Transcriptome, Genètica, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: DNA methylation quantitative trait locus (mQTL) analyses on 32,851 participants identify genetic variants associated with DNA methylation at 420,509 sites in blood, resulting in a database of >270,000 independent mQTLs. Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
Published: 2020

12. Incidence of symptomatic, image-confirmed venous thromboembolism following hospitalization for COVID-19 with 90-day follow-up

Author: Akshay Shah, Joshua Morton, Susan Shapiro, Paraskevi Untiveros, Gavinda Sangha, Nicola Curry, Valentina Iotchkova, Sarah Jaafar, and Richard A. Salisbury
Subjects: Diagnostic Imaging, Male, medicine.medical_specialty, Time Factors, medicine.drug_class, Low molecular weight heparin, 030204 cardiovascular system & hematology, law.invention, Thrombosis and Hemostasis, 03 medical and health sciences, 0302 clinical medicine, Randomized controlled trial, law, Internal medicine, medicine, Humans, 030212 general & internal medicine, Blood coagulation test, Aged, Retrospective Studies, Aged, 80 and over, business.industry, SARS-CoV-2, Medical record, Incidence (epidemiology), Incidence, COVID-19, Disease Management, Retrospective cohort study, Hematology, Venous Thromboembolism, Middle Aged, medicine.disease, Thrombosis, Hospitalization, England, Observational study, Female, Blood Coagulation Tests, Disease Susceptibility, Symptom Assessment, business, Biomarkers, Follow-Up Studies
Abstract: Key Points The rate of symptomatic VTE in patients after hospitalization for COVID-19 was 2.6% at 42 days after discharge. Bleeding is a significant cause of morbidity in addition to thrombosis in patients admitted with COVID-19., Although COVID-19 has been reported to be associated with high rates of venous thromboembolism (VTE), the risk of VTE and bleeding after hospitalization for COVID-19 remains unclear, and the optimal hospital VTE prevention strategy is not known. We collected retrospective observational data on thrombosis and bleeding in 303 consecutive adult patients admitted to the hospital for at least 24 hours for COVID-19. Patients presenting with VTE on admission were excluded. Data were collected until 90 days after admission or known death by using medical records and an established national VTE network. Maximal level of care was ward based in 78% of patients, with 22% requiring higher dependency care (12% noninvasive ventilation, 10% invasive ventilation). Almost all patients (97.0%) received standard thromboprophylaxis or were already receiving therapeutic anticoagulation (17.5%). Symptomatic image-confirmed VTE occurred in 5.9% of patients during index hospitalization, and in 7.2% at 90 days after admission (23.9% in patients requiring higher dependency care); half the events were isolated segmental or subsegmental defects on lung imaging. Bleeding occurred in 13 patients (4.3%) during index hospitalization (1.3% had major bleeding). The majority of bleeds occurred in patients on the general ward, and 6 patients were receiving treatment-dose anticoagulation, highlighting the need for caution in intensifying standard thromboprophylaxis strategies. Of 152 patients discharged from the hospital without an indication for anticoagulation, 97% did not receive thromboprophylaxis after discharge, and 3% received 7 days of treatment with low molecular weight heparin after discharge. The rate of symptomatic VTE in this group at 42 days after discharge was 2.6%, highlighting the need for large prospective randomized controlled trials of thromboprophylaxis after discharge in COVID-19., Visual Abstract
Published: 2020

13. Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

Author: Carol A. Wang, Simonetta Guarrera, Avshalom Caspi, Eilis Hannon, Marta E. Alarcón-Riquelme, P. Eline Slagboom, Pooja R. Mandaviya, Koen F. Dekkers, Cheng-Jian Xu, Jari Lahti, Juan E. Castillo-Fernandez, Dan Mason, Dylan Aïssi, Jan H. Veldink, Mariona Bustamante, Melissa C. Smart, Guillermo Barturen, Zdenka Pausova, Jenny van Dongen, Jordi Jimenez-Conde, Craig E. Pennell, Gibran Hemani, Tom R. Gaunt, Camilla Schmidt Morgen, Ken K. Ong, Toni-Kim Clarke, Alexia Cardona, Susanne Lucae, René Luijk, T.J. Gorrie-Stone, Phillip E. Melton, Thorkild I. A. Sørensen, André G. Uitterlinden, Jordana T. Bell, Jouke-Jan Hottenga, Meena Kumari, Francesc Català-Moll, Jonathan Mill, Tõnu Esko, Sailalitha Bollepalli, Dorret I. Boomsma, Torben Hansen, Hongmei Zhang, Yanni Zeng, John Wright, Wilfried Karmaus, Martin Kerick, Carolina Soriano-Tárraga, Jaakko Kaprio, Miina Ollikainen, Eco J. C. de Geus, Jordi Sunyer, Therese Tillin, Juan R. González, Yvonne Awaloff, Faisal I. Rezwan, Karen Sugden, Nicholas G. Martin, Karen M Ho, Andres Metspalu, Marine Germain, Kristel R. van Eijk, Ramona A. J. Zwamborn, George Davey Smith, Judith M. Vonk, Tian Lin, Henning Tiemeier, Grant W. Montgomery, Naomi R. Wray, Rae-Chi Huang, Alfredo Iacoangeli, Wendy L. McArdle, Jean Shin, Michael Lerro, Darina Czamara, Valentina Iotchkova, David-Alexandre Trégouët, Johanna Klughammer, Elena Carnero-Montoro, Pierre-Emmanuel Morange, Andrew M. McIntosh, Gemma C Sharp, Alun D. Hughes, Carlos Ruiz-Arenas, John M. Starr, Riccardo E. Marioni, Peter M. Visscher, Nabila Kazmi, Ian J. Deary, Kathryn L. Evans, Terrie E. Moffitt, Janine F. Felix, Tomáš Paus, Ashok Kumar, Jaume Roquer, Christopher Shaw, Hannah R Elliott, Susan M. Ring, Nish Chaturvedi, Giovanni Cugliari, Ahmad Al Khleifat, Joyce B. J. van Meurs, Kimberley Burrows, Bert Brunekreef, Debbie A Lawlor, Clara Viberti, Louise Arseneault, Silva Kasela, Cilla Söderhäll, Idil Yet, Manon Bernard, Christoph Bock, Vincent W. V. Jaddoe, Felix R. Day, Diana van Heemst, Alison D. Murray, Nicholas J. Wareham, Giuseppe Matullo, John R. B. Perry, Gerard H. Koppelman, M. Arfan Ikram, Ammar Al Chalabi, Gonneke Willemsen, Richie Poulton, Daniel Lawson, Andrew D. Bretherick, Vanessa Schmoll, Carlotta Sacerdote, Annelot M. Dekker, Lili Milani, Fernando Rivadeneira, Erik Melén, John W. Holloway, Gareth E. Davies, Tom G. Richardson, Caroline L Relton, Josine L. Min, Göran Pershagen, Elisabeth B. Binder, Marian Beekman, Chris Haley, Richa Gupta, Bastiaan T. Heijmans, Ellen A. Nohr, Allan F. McRae, Matthew Suderman, Rosie M. Walker, David L. Corcoran, Katri Räikkönen, Marinus H. van IJzendoorn, Eva Giralt-Steinhauer, Leonard C. Schalkwyk, Aleksey Shatunov, and Tim D. Spector
Subjects: Genetics, Regulation of gene expression, 0303 health sciences, Natural selection, dNaM, Biology, Genetic architecture, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, Genetic variation, DNA methylation, Trait, 030217 neurology & neurosurgery, DNA, 030304 developmental biology
Abstract: Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. Here we describe results of DNA methylation-quantitative trait loci (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTL of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We reveal that the genetic architecture of DNAm levels is highly polygenic and DNAm exhibits signatures of negative and positive natural selection. Using shared genetic control between distal DNAm sites we construct networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic factors are associated with both blood DNAm levels and complex diseases but in most cases these associations do not reflect causal relationships from DNAm to trait or vice versa indicating a more complex genotype-phenotype map than has previously been hypothesised.
Published: 2020

14. Type-1 IFN primed monocytes in pathogenesis of idiopathic pulmonary fibrosis

Author: Yuejuan Zheng, Jan Rehwinkel, Karl Blirando, Nasullah K Alham, Victoria St Noble, Emily Fraser, Emmanouela Repapi, Neil Ashley, Joseph M D Rastrick, Agne Antanaviciute, Colin Clelland, Rachel E. Rigby, Stephen S. Taylor, Rachel K. Hoyles, Ling-Pei Ho, Chaitanya Vuppusetty, Clare S. Hardman, Laura Denney, Valentina Iotchkova, and Rachel Benamore
Subjects: CD64, Lung, business.industry, Disease, respiratory system, medicine.disease, respiratory tract diseases, Pathogenesis, Idiopathic pulmonary fibrosis, Immune system, medicine.anatomical_structure, Fibrosis, Immunology, medicine, business, Ex vivo
Abstract: Idiopathic pulmonary fibrosis (IPF) is the most severe form of lung fibrosis. It is progressive, and has an extremely poor outcome and limited treatment options. The disease exclusively affects the lungs, and thus less attention has been focused on blood-borne immune cells. which could be a more effective therapeutic target than lung-based cells. Here, we questioned if circulating monocytes, which has been shown to be increased in IPF, bore abnormalities that might contribute to its pathogenesis. We found that levels of circulating monocytes correlated directly with the extent of fibrosis in the lungs, and increased further during acute clinical deterioration. Monocytes in IPF were phenotypically distinct, displaying increased expression of CD64, a type 1 IFN gene expression signature and a greater magnitude of type 1 IFN response when stimulated. These abnormalities were accompanied by markedly raised CSF-1 levels in the serum, prolonged survival of monocytesex vivo, and increased numbers of monocytes in lung tissue. Our study defines the key monocytic abnormalities in IPF, proposing type 1 IFN-primed monocytes as a potential driver of an aberrant repair response and fibrosis. It provides a rationale for targeting monocytes and identifies monocytic CD64 as a potential specific therapeutic target for IPF.
Published: 2020
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15. Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

Author: Laura Clarke, Hannes Ponstingl, Manuel Tardaguila, Lu Chen, Tomi Pastinen, Javierre B-M., Stephen B. Watt, Mattia Frontini, Nicole Soranzo, Mikhail Spivakov, Ben Farr, Louella Vasquez, Frances Burden, Alice L. Mann, David J. Richardson, Heather Elding, Ying Yan, Kousik Kundu, S. Farrow, Paul Flicek, Klaudia Walter, Avik Datta, Daniel Mead, Simone Ecker, Kate Downes, Valentina Iotchkova, and Peter Fraser
Subjects: Genetics, Autoimmune disease, Cell type, Myeloid, medicine.anatomical_structure, Immune system, Gene expression, medicine, Disease, Biology, Enhancer, medicine.disease, Chromatin
Abstract: Neutrophils play fundamental roles in innate inflammatory response, shape adaptive immunity1, and have been identified as a potentially causal cell type underpinning genetic associations with immune system traits and diseases2,3 The majority of these variants are non-coding and the underlying mechanisms are not fully understood. Here, we profiled the binding of one of the principal myeloid transcriptional regulators, PU.1, in primary neutrophils across nearly a hundred volunteers, and elucidate the coordinated genetic effects of PU.1 binding variation, local chromatin state, promoter-enhancer interactions and gene expression. We show that PU.1 binding and the associated chain of molecular changes underlie genetically-driven differences in cell count and autoimmune disease susceptibility. Our results advance interpretation for genetic loci associated with neutrophil biology and immune disease.
Published: 2019
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16. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

Author: Jenny van Dongen, Joost H.A. Martens, James E. Barrett, Lee M. Butcher, Edo Vellenga, Ian Dunham, Mattia Frontini, Andrew E. Teschendorff, John Ambrose, Robert Lowe, Dirk S. Paul, Guillaume Bourque, Sadia Saeed, Charles E. Breeze, Jonathan Laperle, Vardhman K. Rakyan, Willem H. Ouwehand, Ewan Birney, Filomena Matarese, Anke K. Bergmann, Hendrik G. Stunnenberg, Pierre-Étienne Jacques, Reiner Siebert, Javier Herrero, Stephan Beck, Kate Downes, Valentina Iotchkova, Paul, Dirk [0000-0002-8230-0116], Frontini, Mattia [0000-0001-8074-6299], Downes, Kate [0000-0003-0366-1579], Ouwehand, Willem [0000-0002-7744-1790], Apollo - University of Cambridge Repository, Biological Psychology, Guided Treatment in Optimal Selected Cancer Patients (GUTS), and Stem Cell Aging Leukemia and Lymphoma (SALL)
Subjects: Resource, Epigenomics, 0301 basic medicine, False discovery rate, Multiple Sclerosis, BLOOD, Statistics as Topic, Cell type specific, DNase I hypersensitive sites, Genome-wide association study, Computational biology, Biology, ENCODE, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Humans, REGULATORY DNA, Epigenetics, EPIGENETIC SIGNATURE, Molecular Biology, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Genetics, SJOGRENS-SYNDROME, epigenetics, histone marks, Stem Cells, ASSOCIATION, bioinformatics, DNA Methylation, epigenome-wide association study, CANCER, Disease etiology, FALSE DISCOVERY RATE, RHEUMATOID-ARTHRITIS, 030104 developmental biology, Organ Specificity, Karyotyping, DNA methylation, WIDE DNA METHYLATION, NAIVE CD4+T CELLS, Software, Genome-Wide Association Study, Signal Transduction
Abstract: Summary Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new standalone and web-based tool for the analysis and interpretation of EWAS data. eFORGE determines the cell type-specific regulatory component of a set of EWAS-identified differentially methylated positions. This is achieved by detecting enrichment of overlap with DNase I hypersensitive sites across 454 samples (tissues, primary cell types, and cell lines) from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects. Application of eFORGE to 20 publicly available EWAS datasets identified disease-relevant cell types for several common diseases, a stem cell-like signature in cancer, and demonstrated the ability to detect cell-composition effects for EWAS performed on heterogeneous tissues. Our approach bridges the gap between large-scale epigenomics data and EWAS-derived target selection to yield insight into disease etiology., Graphical Abstract, Highlights • Development of a tool for the analysis and interpretation of EWAS data • Identification of cell type-specific signals in heterogeneous EWAS data • Identification of cell-composition effects in EWAS • Compilation of eFORGE catalog of 20 published EWAS, Breeze et al. develop a tool for the analysis and interpretation of EWAS data. The eFORGE tool identifies cell type-specific, disease-relevant signals in heterogeneous EWAS data and can also identify cell-composition effects. Explore consortium data at the Cell Press IHEC webportal at http://www.cell.com/consortium/IHEC.
Published: 2016
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17. A multiple-phenotype imputation method for genetic studies

Author: Andrew Dahl, Nicole Soranzo, Andreas Kranis, Jonathan Marchini, Valentina Iotchkova, Richard Mott, Åsa Johansson, Ulf Gyllensten, and Amelie Baud
Subjects: Blood Platelets, Male, 0301 basic medicine, Mixed model, T-Lymphocytes, Population genetics, Genome-wide association study, Biology, Bioinformatics, Machine learning, computer.software_genre, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Bayes' theorem, 0302 clinical medicine, Animals, Outbred Strains, Genetics, Animals, Humans, SNP, Triticum, Genetic association, Models, Genetic, business.industry, Bayes Theorem, Rats, ComputingMethodologies_PATTERNRECOGNITION, Phenotype, 030104 developmental biology, Trait, Female, Artificial intelligence, business, Chickens, computer, Algorithms, 030217 neurology & neurosurgery, Imputation (genetics), Genome-Wide Association Study
Abstract: Genetic association studies have yielded a wealth of biological discoveries. However, these studies have mostly analyzed one trait and one SNP at a time, thus failing to capture the underlying complexity of the data sets. Joint genotype-phenotype analyses of complex, high-dimensional data sets represent an important way to move beyond simple genome-wide association studies (GWAS) with great potential. The move to high-dimensional phenotypes will raise many new statistical problems. Here we address the central issue of missing phenotypes in studies with any level of relatedness between samples. We propose a multiple-phenotype mixed model and use a computationally efficient variational Bayesian algorithm to fit the model. On a variety of simulated and real data sets from a range of organisms and trait types, we show that our method outperforms existing state-of-the-art methods from the statistics and machine learning literature and can boost signals of association.
Published: 2016

18. Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

Author: Kathleen M. Gorman, Esther Meyer, Detelina Grozeva, Egidio Spinelli, Amy McTague, Alba Sanchis-Juan, Keren J. Carss, Emily Bryant, Adi Reich, Amy L. Schneider, Ronit M. Pressler, Michael A. Simpson, Geoff D. Debelle, Evangeline Wassmer, Jenny Morton, Diana Sieciechowicz, Eric Jan-Kamsteeg, Alex R. Paciorkowski, Mary D. King, J. Helen Cross, Annapurna Poduri, Heather C. Mefford, Ingrid E. Scheffer, Tobias B. Haack, Gary McCullagh, John J. Millichap, Gemma L. Carvill, Jill Clayton-Smith, Eamonn R. Maher, F. Lucy Raymond, Manju A. Kurian, Jeremy F. McRae, Stephen Clayton, Tomas W. Fitzgerald, Joanna Kaplanis, Elena Prigmore, Diana Rajan, Alejandro Sifrim, Stuart Aitken, Nadia Akawi, Mohsan Alvi, Kirsty Ambridge, Daniel M. Barrett, Tanya Bayzetinova, Philip Jones, Wendy D. Jones, Daniel King, Netravathi Krishnappa, Laura E. Mason, Tarjinder Singh, Adrian R. Tivey, Munaza Ahmed, Uruj Anjum, Hayley Archer, Ruth Armstrong, Jana Awada, Meena Balasubramanian, Siddharth Banka, Diana Baralle, Angela Barnicoat, Paul Batstone, David Baty, Chris Bennett, Jonathan Berg, Birgitta Bernhard, A. Paul Bevan, Maria Bitner-Glindzicz, Edward Blair, Moira Blyth, David Bohanna, Louise Bourdon, David Bourn, Lisa Bradley, Angela Brady, Simon Brent, Carole Brewer, Kate Brunstrom, David J. Bunyan, John Burn, Natalie Canham, Bruce Castle, Kate Chandler, Elena Chatzimichali, Deirdre Cilliers, Angus Clarke, Susan Clasper, Virginia Clowes, Andrea Coates, Trevor Cole, Irina Colgiu, Amanda Collins, Morag N. Collinson, Fiona Connell, Nicola Cooper, Helen Cox, Lara Cresswell, Gareth Cross, Yanick Crow, Mariella D’Alessandro, Tabib Dabir, Rosemarie Davidson, Sally Davies, Dylan de Vries, John Dean, Charu Deshpande, Gemma Devlin, Abhijit Dixit, Angus Dobbie, Alan Donaldson, Dian Donnai, Deirdre Donnelly, Carina Donnelly, Angela Douglas, Sofia Douzgou, Alexis Duncan, Jacqueline Eason, Sian Ellard, Ian Ellis, Frances Elmslie, Karenza Evans, Sarah Everest, Tina Fendick, Richard Fisher, Frances Flinter, Nicola Foulds, Andrew Fry, Alan Fryer, Carol Gardiner, Lorraine Gaunt, Neeti Ghali, Richard Gibbons, Harinder Gill, Judith Goodship, David Goudie, Emma Gray, Andrew Green, Philip Greene, Lynn Greenhalgh, Susan Gribble, Rachel Harrison, Lucy Harrison, Victoria Harrison, Rose Hawkins, Liu He, Stephen Hellens, Alex Henderson, Sarah Hewitt, Lucy Hildyard, Emma Hobson, Simon Holden, Muriel Holder, Susan Holder, Georgina Hollingsworth, Tessa Homfray, Mervyn Humphreys, Jane Hurst, Ben Hutton, Stuart Ingram, Melita Irving, Lily Islam, Andrew Jackson, Joanna Jarvis, Lucy Jenkins, Diana Johnson, Elizabeth Jones, Dragana Josifova, Shelagh Joss, Beckie Kaemba, Sandra Kazembe, Rosemary Kelsell, Bronwyn Kerr, Helen Kingston, Usha Kini, Esther Kinning, Gail Kirby, Claire Kirk, Emma Kivuva, Alison Kraus, Dhavendra Kumar, V. K. Ajith Kumar, Katherine Lachlan, Wayne Lam, Anne Lampe, Caroline Langman, Melissa Lees, Derek Lim, Cheryl Longman, Gordon Lowther, Sally A. Lynch, Alex Magee, Eddy Maher, Alison Male, Sahar Mansour, Karen Marks, Katherine Martin, Una Maye, Emma McCann, Vivienne McConnell, Meriel McEntagart, Ruth McGowan, Kirsten McKay, Shane McKee, Dominic J. McMullan, Susan McNerlan, Catherine McWilliam, Sarju Mehta, Kay Metcalfe, Anna Middleton, Zosia Miedzybrodzka, Emma Miles, Shehla Mohammed, Tara Montgomery, David Moore, Sian Morgan, Hood Mugalaasi, Victoria Murday, Helen Murphy, Swati Naik, Andrea Nemeth, Louise Nevitt, Ruth Newbury-Ecob, Andrew Norman, Rosie O’Shea, Caroline Ogilvie, Kai-Ren Ong, Soo-Mi Park, Michael J. Parker, Chirag Patel, Joan Paterson, Stewart Payne, Daniel Perrett, Julie Phipps, Daniela T. Pilz, Martin Pollard, Caroline Pottinger, Joanna Poulton, Norman Pratt, Katrina Prescott, Sue Price, Abigail Pridham, Annie Procter, Hellen Purnell, Oliver Quarrell, Nicola Ragge, Raheleh Rahbari, Josh Randall, Julia Rankin, Lucy Raymond, Debbie Rice, Leema Robert, Eileen Roberts, Jonathan Roberts, Paul Roberts, Gillian Roberts, Alison Ross, Elisabeth Rosser, Anand Saggar, Shalaka Samant, Julian Sampson, Richard Sandford, Ajoy Sarkar, Susann Schweiger, Richard Scott, Ingrid Scurr, Ann Selby, Anneke Seller, Cheryl Sequeira, Nora Shannon, Saba Sharif, Charles Shaw-Smith, Emma Shearing, Debbie Shears, Eamonn Sheridan, Ingrid Simonic, Roldan Singzon, Zara Skitt, Audrey Smith, Kath Smith, Sarah Smithson, Linda Sneddon, Miranda Splitt, Miranda Squires, Fiona Stewart, Helen Stewart, Volker Straub, Mohnish Suri, Vivienne Sutton, Ganesh Jawahar Swaminathan, Elizabeth Sweeney, Kate Tatton-Brown, Cat Taylor, Rohan Taylor, Mark Tein, I. Karen Temple, Jenny Thomson, Marc Tischkowitz, Susan Tomkins, Audrey Torokwa, Becky Treacy, Claire Turner, Peter Turnpenny, Carolyn Tysoe, Anthony Vandersteen, Vinod Varghese, Pradeep Vasudevan, Parthiban Vijayarangakannan, Julie Vogt, Emma Wakeling, Sarah Wallwark, Jonathon Waters, Astrid Weber, Diana Wellesley, Margo Whiteford, Sara Widaa, Sarah Wilcox, Emily Wilkinson, Denise Williams, Nicola Williams, Louise Wilson, Geoff Woods, Christopher Wragg, Michael Wright, Laura Yates, Michael Yau, Chris Nellåker, Michael Parker, Helen V. Firth, Caroline F. Wright, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles, Saeed Al Turki, Carl Anderson, Richard Anney, Dinu Antony, Maria Soler Artigas, Muhammad Ayub, Senduran Balasubramaniam, Inês Barroso, Phil Beales, Jamie Bentham, Shoumo Bhattacharya, Ewan Birney, Douglas Blackwood, Martin Bobrow, Elena Bochukova, Patrick Bolton, Rebecca Bounds, Chris Boustred, Gerome Breen, Mattia Calissano, Keren Carss, Krishna Chatterjee, Lu Chen, Antonio Ciampi, Sebhattin Cirak, Peter Clapham, Gail Clement, Guy Coates, David Collier, Catherine Cosgrove, Tony Cox, Nick Craddock, Lucy Crooks, Sarah Curran, David Curtis, Allan Daly, Aaron Day-Williams, Ian N.M. Day, Thomas Down, Yuanping Du, Ian Dunham, Sarah Edkins, Peter Ellis, David Evans, Sadaf Faroogi, Ghazaleh Fatemifar, David R. Fitzpatrick, Paul Flicek, James Flyod, A. Reghan Foley, Christopher S. Franklin, Marta Futema, Louise Gallagher, Matthias Geihs, Daniel Geschwind, Heather Griffin, Xueqin Guo, Xiaosen Guo, Hugh Gurling, Deborah Hart, Audrey Hendricks, Peter Holmans, Bryan Howie, Liren Huang, Tim Hubbard, Steve E. Humphries, Pirro Hysi, David K. Jackson, Yalda Jamshidi, Tian Jing, Chris Joyce, Jane Kaye, Thomas Keane, Julia Keogh, John Kemp, Karen Kennedy, Anja Kolb-Kokocinski, Genevieve Lachance, Cordelia Langford, Daniel Lawson, Irene Lee, Monkol Lek, Jieqin Liang, Hong Lin, Rui Li, Yingrui Li, Ryan Liu, Jouko Lönnqvist, Margarida Lopes, Valentina Iotchkova, Daniel MacArthur, Jonathan Marchini, John Maslen, Mangino Massimo, Iain Mathieson, Gaëlle Marenne, Peter McGuffin, Andrew McIntosh, Andrew G. McKechanie, Andrew McQuillin, Sarah Metrustry, Hannah Mitchison, Alireza Moayyeri, James Morris, Francesco Muntoni, Kate Northstone, Michael O'Donnovan, Alexandros Onoufriadis, Stephen O'Rahilly, Karim Oualkacha, Michael J. Owen, Aarno Palotie, Kalliope Panoutsopoulou, Victoria Parker, Jeremy R. Parr, Lavinia Paternoster, Tiina Paunio, Felicity Payne, Olli Pietilainen, Vincent Plagnol, Lydia Quaye, Michael A. Quail, Karola Rehnström, Susan Ring, Graham R.S. Ritchie, Nicola Roberts, David B. Savage, Peter Scambler, Stephen Schiffels, Miriam Schmidts, Nadia Schoenmakers, Robert K. Semple, Eva Serra, Sally I. Sharp, So-Youn Shin, David Skuse, Kerrin Small, Lorraine Southam, Olivera Spasic-Boskovic, David St Clair, Jim Stalker, Elizabeth Stevens, Beate St Pourcian, Jianping Sun, Jaana Suvisaari, Ionna Tachmazidou, Martin D. Tobin, Ana Valdes, Margriet Van Kogelenberg, Peter M. Visscher, Louise V. Wain, James T.R. Walters, Guangbiao Wang, Jun Wang, Yu Wang, Kirsten Ward, Elanor Wheeler, Tamieka Whyte, Hywel Williams, Kathleen A. Williamson, Crispian Wilson, Kim Wong, ChangJiang Xu, Jian Yang, Fend Zhang, Pingbo Zhang, Timothy Aitman, Hana Alachkar, Sonia Ali, Louise Allen, David Allsup, Gautum Ambegaonkar, Julie Anderson, Richard Antrobus, Gavin Arno, Gururaj Arumugakani, Sofie Ashford, William Astle, Antony Attwood, Steve Austin, Chiara Bacchelli, Tamam Bakchoul, Tadbir K. Bariana, Helen Baxendale, David Bennett, Claire Bethune, Shahnaz Bibi, Marta Bleda, Harm Boggard, Paula Bolton-Maggs, Claire Booth, John R. Bradley, Angie Brady, Matthew Brown, Michael Browning, Christine Bryson, Siobhan Burns, Paul Calleja, Jenny Carmichael, Mark Caulfield, Elizabeth Chalmers, Anita Chandra, Patrick Chinnery, Manali Chitre, Colin Church, Emma Clement, Naomi Clements-Brod, Gerry Coghlan, Peter Collins, Nichola Cooper, Amanda Creaser-Myers, Rosa DaCosta, Louise Daugherty, Sophie Davies, John Davis, Minka De Vries, Patrick Deegan, Sri V.V. Deevi, Lisa Devlin, Eleanor Dewhurst, Rainer Doffinger, Natalie Dormand, Elizabeth Drewe, David Edgar, William Egner, Wendy N. Erber, Marie Erwood, Tamara Everington, Remi Favier, Helen Firth, Debra Fletcher, James C. Fox, Amy Frary, Kathleen Freson, Bruce Furie, Abigail Furnell, Daniel Gale, Alice Gardham, Michael Gattens, Pavandeep K. Ghataorhe, Rohit Ghurye, Simon Gibbs, Kimberley Gilmour, Paul Gissen, Sarah Goddard, Keith Gomez, Pavel Gordins, Stefan Gräf, Daniel Greene, Alan Greenhalgh, Andreas Greinacher, Sofia Grigoriadou, Scott Hackett, Charaka Hadinnapola, Rosie Hague, Matthias Haimel, Csaba Halmagyi, Tracey Hammerton, Daniel Hart, Grant Hayman, Johan W.M. Heemskerk, Robert Henderson, Anke Hensiek, Yvonne Henskens, Archana Herwadkar, Fengyuan Hu, Aarnoud Huissoon, Marc Humbert, Roger James, Stephen Jolles, Rashid Kazmi, David Keeling, Peter Kelleher, Anne M. Kelly, Fiona Kennedy, David Kiely, Nathalie Kingston, Ania Koziell, Deepa Krishnakumar, Taco W. Kuijpers, Dinakantha Kumararatne, Manju Kurian, Michael A. Laffan, Michele P. Lambert, Hana Lango Allen, Allan Lawrie, Sara Lear, Claire Lentaigne, Ri Liesner, Rachel Linger, Hilary Longhurst, Lorena Lorenzo, Rajiv Machado, Rob Mackenzie, Robert MacLaren, Eamonn Maher, Jesmeen Maimaris, Sarah Mangles, Ania Manson, Rutendo Mapeta, Hugh S. Markus, Jennifer Martin, Larahmie Masati, Mary Mathias, Vera Matser, Anna Maw, Elizabeth McDermott, Coleen McJannet, Stuart Meacham, Sharon Meehan, Karyn Megy, Michel Michaelides, Carolyn M. Millar, Shahin Moledina, Anthony Moore, Nicholas Morrell, Andrew Mumford, Sai Murng, Elaine Murphy, Sergey Nejentsev, Sadia Noorani, Paquita Nurden, Eric Oksenhendler, Willem H. Ouwehand, Sofia Papadia, Alasdair Parker, John Pasi, Chris Patch, Jeanette Payne, Andrew Peacock, Kathelijne Peerlinck, Christopher J. Penkett, Joanna Pepke-Zaba, David J. Perry, Val Pollock, Gary Polwarth, Mark Ponsford, Waseem Qasim, Isabella Quinti, Stuart Rankin, Karola Rehnstrom, Evan Reid, Christopher J. Rhodes, Michael Richards, Sylvia Richardson, Alex Richter, Irene Roberts, Matthew Rondina, Catherine Roughley, Kevin Rue-Albrecht, Crina Samarghitean, Saikat Santra, Ravishankar Sargur, Sinisa Savic, Sol Schulman, Harald Schulze, Marie Scully, Suranjith Seneviratne, Carrock Sewell, Olga Shamardina, Debbie Shipley, Ilenia Simeoni, Suthesh Sivapalaratnam, Kenneth Smith, Aman Sohal, Laura Southgate, Simon Staines, Emily Staples, Hans Stauss, Penelope Stein, Jonathan Stephens, Kathleen Stirrups, Sophie Stock, Jay Suntharalingam, R. Campbell Tait, Kate Talks, Yvonne Tan, Jecko Thachil, James Thaventhiran, Ellen Thomas, Moira Thomas, Dorothy Thompson, Adrian Thrasher, Catherine Titterton, Cheng-Hock Toh, Mark Toshner, Carmen Treacy, Richard Trembath, Salih Tuna, Wojciech Turek, Ernest Turro, Chris Van Geet, Marijke Veltman, Julie von Ziegenweldt, Anton Vonk Noordegraaf, Ivy Wanjiku, Timothy Q. Warner, Hugh Watkins, Andrew Webster, Steve Welch, Sarah Westbury, John Wharton, Deborah Whitehorn, Martin Wilkins, Lisa Willcocks, Catherine Williamson, Geoffrey Woods, John Wort, Nigel Yeatman, Patrick Yong, Tim Young, Ping Yu, Paediatric Infectious Diseases / Rheumatology / Immunology, ARD - Amsterdam Reproduction and Development, Pediatric surgery, APH - Aging & Later Life, Molecular cell biology and Immunology, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, and APH - Quality of Care
Subjects: 0301 basic medicine, Male, Adolescent, Loss of Heterozygosity, Context (language use), Postnatal microcephaly, Neurotransmission, medicine.disease_cause, Bioinformatics, Synaptic Transmission, Loss of heterozygosity, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Calcium Channels, N-Type, Report, Genetics, medicine, Humans, Child, Genetics (clinical), Mutation, Dyskinesias, business.industry, Infant, medicine.disease, Hypotonia, Pedigree, 030104 developmental biology, Dyskinesia, Child, Preschool, Calcium, Female, medicine.symptom, business, 030217 neurology & neurosurgery
Abstract: © 2019 American Society of Human Genetics The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.
Published: 2018

19. Author Correction: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps

Author: Marcus E. Kleber, Lu Chen, Farmaki A-E., Tom R. Gaunt, C.M. van Duijn, Gianluigi Zaza, Charles Kooperberg, Abbas Dehghan, Oscar H. Franco, Jian'an Luan, Matthew T. Maurano, Mattia Frontini, Nicole Soranzo, Giovanni Malerba, George Dedoussis, Tao Jiang, Heather Elding, Michela Traglia, Raha Pazoki, Robert A. Scott, Maria Sabater-Lleal, Mattias Frånberg, J L Min, Daniela Toniolo, Valentina Iotchkova, Paul L. Auer, Adam S. Butterworth, E. C. M. van Leeuwen, Daniel Mead, Christopher S. Franklin, Anders Hamsten, Yasin Memari, André G. Uitterlinden, William J. Astle, Lorraine Southam, Claudia Langenberg, Jie Huang, Massimiliano Cocca, Fernando Rivadeneira, Alexander P. Reiner, Patrick Deelen, John A. Morris, Giovanni Gambaro, Ioanna Ntalla, Aaron Isaacs, Genevieve Lachance, Winfried März, N J Timpson, Perry Jrb., Kalliope Panoutsopoulou, Najaf Amin, Hugh Watkins, Albert Hofman, John C. Chambers, Lude Franke, Eleftheria Zeggini, Weihua Zhang, Shin S-Y., Caterina Barbieri, Deepti Jain, Bengt Sennblad, Angela Matchan, Jaspal S. Kooner, Klaudia Walter, Morris A. Swertz, Paolo Gasparini, and F van Dijk
Subjects: Cardiometabolic risk, Genetics & Heredity, Science & Technology, Published Erratum, MEDLINE, Computational biology, Biology, 06 Biological Sciences, Genetics, UK10K Consortium, Life Sciences & Biomedicine, Imputation (genetics), 11 Medical and Health Sciences, Developmental Biology
Abstract: Correction to: Nature Genetics https://doi.org/10.1038/ng.3668, published online 26 September 2016. In the version of the article published, the surname of author Aaron Isaacs is misspelled as Issacs.
Published: 2018

20. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author: Dietmar Fernández-Orth, Nicholas J. Timpson, George Dedoussis, Beate St Pourcain, George Davey Smith, Chin Yang Shapland, Tim J Cole, Andrew P. Jackson, Valentina Iotchkova, Jordi Sunyer, Caroline Hayward, Eleftheria Zeggini, Josine L. Min, Fernando Rivadeneira, Simon E. Fisher, Carolina Medina-Gomez, Tarunveer S. Ahluwalia, Ioanna Tachmazidou, Janine F. Felix, Veronique Vitart, Jennifer Huffmann, James F. Wilson, Mònica Guxens, Bram P. Prins, Martine Vrijheid, Hans Bisgaard, Simon Haworth, Craig E. Pennell, Lærke Sass, Vincent W. V. Jaddoe, Louise Cleal, Klaus Bønnelykke, Paul R. H. J. Timmers, Klaudia Walter, Carol A. Wang, and UK10K consortium
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, Cephalometry, Cranial growth, Biology, Article, White People, European descent, 03 medical and health sciences, 0302 clinical medicine, Gene Frequency, Intracranial volume, Internal medicine, Genetic variation, medicine, Humans, RNA, Messenger, Child, Allele frequency, Alleles, Aged, 030304 developmental biology, Aged, 80 and over, 0303 health sciences, Genome, Human, Skull, Gene Expression Regulation, Developmental, Genetic Variation, Middle Aged, Head circumference, Endocrinology, Developmental genetics, Genetic Loci, Female, Tumor Suppressor Protein p53, 030217 neurology & neurosurgery
Abstract: Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development., Size and shape of the brain are, among others, influenced by the dimensions of the skull. Here, the authors report genome-wide association studies for head circumference and intracranial volume in children and adults and the identification of nine common or low-frequency variants associated with these traits.
Published: 2018
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21. Whole-genome sequencing coupled to imputation discovers genetic signals for anthropometric traits

Author: Graham R. S. Ritchie, Massimiliano Cocca, Anette Varbo, Nicholas J. Timpson, George Dedoussis, Michael Boehnke, Marjolein N. Kooijman, Beate St Pourcain, Yasin Memari, André G. Uitterlinden, Andrew A Crawford, Eleftheria Zeggini, Fernando Rivadeneira, Satu Männistö, Caroline L Relton, Yali Xue, Petr Danecek, Kalliope Panoutsopoulou, Albert Hofman, George Davey Smith, María Soler Artigas, Michela Traglia, Josine L. Min, Weihua Zhang, Janine F. Felix, Christopher J Hammond, Claudia Langenberg, Jie Huang, Brian R. Walker, Narinder Bansal, Nigel W. Rayner, Emanuele Di Angelantonio, Kerrin S. Small, Konstantinos Hatzikotoulas, Cecilia M. Lindgren, Alisa K. Manning, Shane A. McCarthy, Susan M. Ring, Marcus E. Kleber, Abhishek Nag, Oliver Stegle, Paul Burton, Oscar H. Franco, William R. Scott, Carolina Medina-Gomez, Valentina Iotchkova, John R. B. Perry, Alireza Moayyeri, Lavinia Paternoster, Marianne Benn, Markus Perola, Katerina Trajanoska, Inês Barroso, Audrey E. Hendricks, Cinzia Sala, Carlo Sidore, Celia M. T. Greenwood, Jeremy Schwartzentruber, Richard Durbin, Cristina Bombieri, Klaudia Walter, Wei-Yu Lin, Hashem A. Shihab, Gialuigi Zaza, Jaspal S. Kooner, Magdalena Zoledziewska, Angela Matchan, Adam S. Butterworth, Pekka Jousilahti, Julia Steinberg, Anne Tybjærg-Hansen, John P. Kemp, Daniel Suveges, Nicole Soranzo, Chris Finan, Veikko Salomaa, Ioanna Ntalla, Nicholas J. Wareham, Adam E. Locke, Vincent W. V. Jaddoe, Ioanna Tachmazidou, Daniela Toniolo, Scott Wilson, Antonella Mulas, Aliki-Eleni Farmaki, Lorraine Southam, Martin D. Tobin, Tom R. Gaunt, Zhongsheng Chen, Paolo Gasparini, Andrew P. Morris, Giovanni Gambaro, John C. Chambers, Børge G. Nordestgaard, Sarah Metrustry, Benjamin Lehne, Jian'an Luan, Giovanni Malerba, Robert A. Scott, Mark I. McCarthy, Michal Szpak, Francesco Cucca, Tim D. Spector, Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, University of Helsinki, Institute for Molecular Medicine Finland, Quantitative Genetics, Tachmazidou, Ioanna, Süveges, Dániel, Min, Josine L., Ritchie, Graham R. S., Steinberg, Julia, Walter, Klaudia, Iotchkova, Valentina, Schwartzentruber, Jeremy, Huang, Jie, Memari, Yasin, Mccarthy, Shane, Crawford, Andrew A., Bombieri, Cristina, Cocca, Massimiliano, Farmaki, Aliki-Eleni, Gaunt, Tom R., Jousilahti, Pekka, Kooijman, Marjolein N., Lehne, Benjamin, Malerba, Giovanni, Männistö, Satu, Matchan, Angela, Medina-Gomez, Carolina, Metrustry, Sarah J., Nag, Abhishek, Ntalla, Ioanna, Paternoster, Lavinia, Rayner, Nigel W., Sala, Cinzia, Scott, William R., Shihab, Hashem A., Southam, Lorraine, St Pourcain, Beate, Traglia, Michela, Trajanoska, Katerina, Zaza, Gialuigi, Zhang, Weihua, Artigas, María S., Bansal, Narinder, Benn, Marianne, Chen, Zhongsheng, Danecek, Petr, Lin, Wei-Yu, Locke, Adam, Luan, Jian'An, Manning, Alisa K., Mulas, Antonella, Sidore, Carlo, Tybjaerg-Hansen, Anne, Varbo, Anette, Zoledziewska, Magdalena, Finan, Chri, Hatzikotoulas, Konstantino, Hendricks, Audrey E., Kemp, John P., Moayyeri, Alireza, Panoutsopoulou, Kalliope, Szpak, Michal, Wilson, Scott G., Boehnke, Michael, Cucca, Francesco, Di Angelantonio, Emanuele, Langenberg, Claudia, Lindgren, Cecilia, Mccarthy, Mark I., Morris, Andrew P., Nordestgaard, Børge G., Scott, Robert A., Tobin, Martin D., Wareham, Nicholas J., Burton, Paul, Chambers, John C., Smith, George Davey, Dedoussis, George, Felix, Janine F., Franco, Oscar H., Gambaro, Giovanni, Gasparini, Paolo, Hammond, Christopher J., Hofman, Albert, Jaddoe, Vincent W. V., Kleber, Marcu, Kooner, Jaspal S., Perola, Marku, Relton, Caroline, Ring, Susan M., Rivadeneira, Fernando, Salomaa, Veikko, Spector, Timothy D., Stegle, Oliver, Toniolo, Daniela, Uitterlinden, André G., Barroso, Inê, Greenwood, Celia M. T., Perry, John R. B., Walker, Brian R., Butterworth, Adam S., Xue, Yali, Durbin, Richard, Small, Kerrin S., Soranzo, Nicole, Timpson, Nicholas J., Zeggini, Eleftheria, McCarthy, Shane [0000-0002-2715-4187], Bansal, Narinder [0000-0002-6925-1719], Luan, Jian'an [0000-0003-3137-6337], Di Angelantonio, Emanuele [0000-0001-8776-6719], Langenberg, Claudia [0000-0002-5017-7344], Wareham, Nicholas [0000-0003-1422-2993], Barroso, Ines [0000-0001-5800-4520], Perry, John [0000-0001-6483-3771], Butterworth, Adam [0000-0002-6915-9015], Soranzo, Nicole [0000-0003-1095-3852], and Apollo - University of Cambridge Repository
Subjects: Male, 0301 basic medicine, DXA trait, Lipodystrophy, next-generation whole-genome sequencing, GoT2D Consortium, LOCI, Genome-wide association study, imputation, anthropometry, DXA traits, genetic association study, UK Biobank, UK10K, Body Height, Cohort Studies, DNA Methylation, Databases, Genetic, Female, Genetic Variation, Humans, Meta-Analysis as Topic, Obesity, Physical Chromosome Mapping, Quantitative Trait Loci, Sequence Analysis, DNA, Sex Characteristics, Syndrome, United Kingdom, Anthropometry, Genome, Human, Genome-Wide Association Study, Genetics, Genetics (clinical), Settore MED/03 - GENETICA MEDICA, DISEASE, HOMEOBOX GENE, WIDE ASSOCIATION, Genetics & Heredity, Genome, 1184 Genetics, developmental biology, physiology, 11 Medical And Health Sciences, RARE VARIANTS, OBESITY, LOW-FREQUENCY, Life Sciences & Biomedicine, Sequence Analysis, arcOGEN Consortium, Human, ADULT HUMAN HEIGHT, Understanding Society Scientific Group, Computational biology, TARGETED DISRUPTION, Quantitative trait locus, Biology, Article, Databases, 03 medical and health sciences, Genetic, Genetic variation, Journal Article, UK10K Consortium, Allele, Genetic association, Whole genome sequencing, Science & Technology, SpiroMeta Consortium, DNA, 06 Biological Sciences, Sex Characteristic, 030104 developmental biology, Human genome, 3111 Biomedicine, Cohort Studie, KNOCKOUT MICE, Imputation (genetics)
Abstract: Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of twelve anthropometric traits associated with height, body mass and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. Seventy-one percent of signals reside within genes and fine-mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits, and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically-relevant discoveries across the frequency spectrum.
Published: 2017

22. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Author: Nicholas J. Timpson, Klaudia Walter, Josine L. Min, Ioanna Tachmazidou, Giovanni Malerba, So Youn Shin, Lu Chen, Marta Futema, Lorraine Southam, Valentina Iotchkova, Jie Huang, Yasin Memari, Shane McCarthy, Petr Danecek, Dawn Muddyman, Massimo Mangino, Cristina Menni, John R. B. Perry, Susan M. Ring, Amadou Gaye, George Dedoussis, Aliki Eleni Farmaki, Paul Burton, Philippa J. Talmud, Giovanni Gambaro, Tim D. Spector, George Davey Smith, Richard Durbin, J. Brent Richards, Steve E. Humphries, Eleftheria Zeggini, Nicole Soranzo, Saeed Al Turki, Carl Anderson, Richard Anney, Dinu Antony, Maria Soler Artigas, Muhammad Ayub, Senduran Balasubramaniam, Jeffrey C. Barrett, Inês Barroso, Phil Beales, Jamie Bentham, Shoumo Bhattacharya, Ewan Birney, Douglas Blackwood, Martin Bobrow, Elena Bochukova, Patrick Bolton, Rebecca Bounds, Chris Boustred, Gerome Breen, Mattia Calissano, Keren Carss, Krishna Chatterjee, Antonio Ciampi, Sebhattin Cirak, Peter Clapham, Gail Clement, Guy Coates, David Collier, Catherine Cosgrove, Tony Cox, Nick Craddock, Lucy Crooks, Sarah Curran, David Curtis, Allan Daly, Aaron Day Williams, Ian N. M. Day, Thomas Down, Yuanping Du, Ian Dunham, Sarah Edkins, Peter Ellis, David Evans, Sadaf Faroogi, Ghazaleh Fatemifar, David R. Fitzpatrick, Paul Flicek, James Flyod, A. Reghan Foley, Christopher S. Franklin, Louise Gallagher, Tom Gaunt, Matthias Geihs, Daniel Geschwind, Celia Greenwood, Heather Griffin, Detelina Grozeva, Xueqin Guo, Xiaosen Guo, Hugh Gurling, Deborah Hart, Audrey Hendricks, Peter Holmans, Bryan Howie, Liren Huang, Tim Hubbard, Matthew E. Hurles, Pirro Hysi, David K. Jackson, Yalda Jamshidi, Tian Jing, Chris Joyce, Jane Kaye, Thomas Keane, Julia Keogh, John Kemp, Karen Kennedy, Anja Kolb Kokocinski, Genevieve Lachance, Cordelia Langford, Daniel Lawson, Irene Lee, Monkol Lek, Jieqin Liang, Hong Lin, Rui Li, Yingrui Li, Ryan Liu, Jouko Lönnqvist, Margarida Lopes, Valentina Lotchkova, Daniel MacArthur, Jonathan Marchini, John Maslen, Mangino Massimo, Iain Mathieson, Gaëlle Marenne, Peter McGuffin, Andrew McIntosh, Andrew G. McKechanie, Andrew McQuillin, Sarah Metrustry, Josine Min, Hannah Mitchison, Alireza Moayyeri, James Morris, Francesco Muntoni, Kate Northstone, Michael O'Donnovan, Alexandros Onoufriadis, Stephen O'Rahilly, Karim Oualkacha, Michael J. Owen, Aarno Palotie, Kalliope Panoutsopoulou, Victoria Parker, Jeremy R. Parr, Lavinia Paternoster, Tiina Paunio, Felicity Payne, John Perry, Olli Pietilainen, Vincent Plagnol, Lydia Quaye, Michael A. Quail, Lucy Raymond, Karola Rehnström, Brent Richards, Susan Ring, Graham R. S. Ritchie, Nicola Roberts, David B. Savage, Peter Scambler, Stephen Schiffels, Miriam Schmidts, Nadia Schoenmakers, Robert K. Semple, Eva Serra, Sally I. Sharp, Hasheem Shihab, David Skuse, Kerrin Small, Olivera Spasic Boskovic, Tim Spector, David St Clair, Jim Stalker, Elizabeth Stevens, Beate St Pourcian, Jianping Sun, Gabriela Surdulescu, Jaana Suvisaari, Ionna Tachmazidou, Nicholas Timpson, Martin D. Tobin, Ana Valdes, Margriet Van Kogelenberg, Parthiban Vijayarangakannan, Peter M. Visscher, Louise V. Wain, James T. R. Walters, Guangbiao Wang, Jun Wang, Yu Wang, Kirsten Ward, Elanor Wheeler, Tamieka Whyte, Hywel Williams, Kathleen A. Williamson, Crispian Wilson, Scott G. Wilson, Kim Wong, ChangJiang Xu, Jian Yang, Fend Zhang, Pingbo Zhang, Hou Feng Zheng, COCCA, MASSIMILIANO, Nicholas J., Timpson, Klaudia, Walter, Josine L., Min, Ioanna, Tachmazidou, Giovanni, Malerba, So Youn, Shin, Lu, Chen, Marta, Futema, Lorraine, Southam, Valentina, Iotchkova, Cocca, Massimiliano, Jie, Huang, Yasin, Memari, Shane, Mccarthy, Petr, Danecek, Dawn, Muddyman, Massimo, Mangino, Cristina, Menni, John R. B., Perry, Susan M., Ring, Amadou, Gaye, George, Dedoussi, Aliki Eleni, Farmaki, Paul, Burton, Philippa J., Talmud, Giovanni, Gambaro, Tim D., Spector, George Davey, Smith, Richard, Durbin, J., Brent Richard, Steve E., Humphrie, Eleftheria, Zeggini, Nicole, Soranzo, Saeed Al, Turki, Carl, Anderson, Richard, Anney, Dinu, Antony, Maria Soler, Artiga, Muhammad, Ayub, Senduran, Balasubramaniam, Jeffrey C., Barrett, Inês, Barroso, Phil, Beale, Jamie, Bentham, Shoumo, Bhattacharya, Ewan, Birney, Douglas, Blackwood, Martin, Bobrow, Elena, Bochukova, Patrick, Bolton, Rebecca, Bound, Chris, Boustred, Gerome, Breen, Mattia, Calissano, Keren, Car, Krishna, Chatterjee, Antonio, Ciampi, Sebhattin, Cirak, Peter, Clapham, Gail, Clement, Guy, Coate, David, Collier, Catherine, Cosgrove, Tony, Cox, Nick, Craddock, Lucy, Crook, Sarah, Curran, David, Curti, Allan, Daly, Aaron Day, William, Ian N. M., Day, Thomas, Down, Yuanping, Du, Ian, Dunham, Sarah, Edkin, Peter, Elli, David, Evan, Sadaf, Faroogi, Ghazaleh, Fatemifar, David R., Fitzpatrick, Paul, Flicek, James, Flyod, A., Reghan Foley, Christopher S., Franklin, Louise, Gallagher, Tom, Gaunt, Matthias, Geih, Daniel, Geschwind, Celia, Greenwood, Heather, Griffin, Detelina, Grozeva, Xueqin, Guo, Xiaosen, Guo, Hugh, Gurling, Deborah, Hart, Audrey, Hendrick, Peter, Holman, Bryan, Howie, Liren, Huang, Tim, Hubbard, Matthew E., Hurle, Pirro, Hysi, David K., Jackson, Yalda, Jamshidi, Tian, Jing, Chris, Joyce, Jane, Kaye, Thomas, Keane, Julia, Keogh, John, Kemp, Karen, Kennedy, Anja Kolb, Kokocinski, Genevieve, Lachance, Cordelia, Langford, Daniel, Lawson, Irene, Lee, Monkol, Lek, Jieqin, Liang, Hong, Lin, Rui, Li, Yingrui, Li, Ryan, Liu, Jouko, Lönnqvist, Margarida, Lope, Valentina, Lotchkova, Daniel, Macarthur, Jonathan, Marchini, John, Maslen, Mangino, Massimo, Iain, Mathieson, Gaëlle, Marenne, Peter, Mcguffin, Andrew, Mcintosh, Andrew G., Mckechanie, Andrew, Mcquillin, Sarah, Metrustry, Josine, Min, Hannah, Mitchison, Alireza, Moayyeri, James, Morri, Francesco, Muntoni, Kate, Northstone, Michael, O'Donnovan, Alexandros, Onoufriadi, Stephen, O'Rahilly, Karim, Oualkacha, Michael J., Owen, Aarno, Palotie, Kalliope, Panoutsopoulou, Victoria, Parker, Jeremy R., Parr, Lavinia, Paternoster, Tiina, Paunio, Felicity, Payne, John, Perry, Olli, Pietilainen, Vincent, Plagnol, Lydia, Quaye, Michael A., Quail, Lucy, Raymond, Karola, Rehnström, Brent, Richard, Susan, Ring, Graham R. S., Ritchie, Nicola, Robert, David B., Savage, Peter, Scambler, Stephen, Schiffel, Miriam, Schmidt, Nadia, Schoenmaker, Robert K., Semple, Eva, Serra, Sally I., Sharp, Hasheem, Shihab, David, Skuse, Kerrin, Small, Olivera Spasic, Boskovic, Tim, Spector, David St, Clair, Jim, Stalker, Elizabeth, Steven, Beate St, Pourcian, Jianping, Sun, Gabriela, Surdulescu, Jaana, Suvisaari, Ionna, Tachmazidou, Nicholas, Timpson, Martin D., Tobin, Ana, Valde, Margriet Van, Kogelenberg, Parthiban, Vijayarangakannan, Peter M., Visscher, Louise V., Wain, James T. R., Walter, Guangbiao, Wang, Jun, Wang, Yu, Wang, Kirsten, Ward, Elanor, Wheeler, Tamieka, Whyte, Hywel, William, Kathleen A., Williamson, Crispian, Wilson, Scott G., Wilson, Kim, Wong, Changjiang, Xu, Jian, Yang, Fend, Zhang, Pingbo, Zhang, and Hou Feng, Zheng
Subjects: Very low-density lipoprotein, Population, vldl, apoc3, General Physics and Astronomy, Genome-wide association study, 030204 cardiovascular system & hematology, Biology, rare mutations, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, genome-wide association study (GWAS), plasma lipids, 0302 clinical medicine, Polymorphism (computer science), Genetic variation, Settore MED/14 - NEFROLOGIA, Allele, education, Allele frequency, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, cholesterol, General Chemistry, Minor allele frequency
Abstract: The analysis of rich catalogues of genetic variation from population-based sequencing provides an opportunity to screen for functional effects. Here we report a rare variant in APOC3 (rs138326449-A, minor allele frequency ~0.25% (UK)) associated with plasma triglyceride (TG) levels (−1.43 s.d. (s.e.=0.27 per minor allele (P-value=8.0 × 10−8)) discovered in 3,202 individuals with low read-depth, whole-genome sequence. We replicate this in 12,831 participants from five additional samples of Northern and Southern European origin (−1.0 s.d. (s.e.=0.173), P-value=7.32 × 10−9). This is consistent with an effect between 0.5 and 1.5 mmol l−1 dependent on population. We show that a single predicted splice donor variant is responsible for association signals and is independent of known common variants. Analyses suggest an independent relationship between rs138326449 and high-density lipoprotein (HDL) levels. This represents one of the first examples of a rare, large effect variant identified from whole-genome sequencing at a population scale., Population-based genome sequencing provides an increasingly rich resource for the identification of low-frequency, large effect variants associated with clinically important phenotypes. Timpson et al. use UK10K data to identify a variant of the APOC3 gene strongly associated with plasma triglyceride levels.
Published: 2014

23. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Author: Valentina Iotchkova, J L Min, Ritchie Grs., Ewan Birney, Klaudia Walter, Sandro Morganella, N J Timpson, Ian Dunham, Nicole Soranzo, and Matthias Geihs
Subjects: 0303 health sciences, Computer science, Genome-wide association study, Genomics, Computational biology, Quantitative trait locus, ENCODE, Data science, Phenotype, 03 medical and health sciences, 0302 clinical medicine, Regulatory sequence, Genetic variation, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Genetic association
Abstract: Loci discovered by genome-wide association studies (GWAS) predominantly map outside protein-coding genes. The interpretation of functional consequences of non-coding variants can be greatly enhanced by catalogs of regulatory genomic regions in cell lines and primary tissues. However, robust and readily applicable methods are still lacking to systematically evaluate the contribution of these regions to genetic variation implicated in diseases or quantitative traits. Here we propose a novel approach that leverages GWAS findings with regulatory or functional annotations to classify features relevant to a phenotype of interest. Within our framework, we account for major sources of confounding that current methods do not offer. We further assess enrichment statistics for 27 GWAS traits within regulatory regions from the ENCODE and Roadmap projects. We characterise unique enrichment patterns for traits and annotations, driving novel biological insights. The method is implemented in standalone software and R package to facilitate its application by the research community.
Published: 2016
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24. Significant impact of miRNA–target gene networks on genetics of human complex traits

Author: Naomasa Suita, Toshihiro Tanaka, Eiryo Kawakami, Nicole Soranzo, Johji Inazawa, Valentina Iotchkova, Masahiro Kanai, Tomoki Muramatsu, and Yukinori Okada
Subjects: Adult, Risk, 0301 basic medicine, Multifactorial Inheritance, Hydrolases, Gene regulatory network, Down-Regulation, Context (language use), Genome-wide association study, Biology, Kidney, Polymorphism, Single Nucleotide, Article, Arthritis, Rheumatoid, 03 medical and health sciences, Protein-Arginine Deiminase Type 2, microRNA, Humans, Gene Regulatory Networks, Genetic Predisposition to Disease, Molecular Targeted Therapy, Gene, Epigenomics, Genetic association, Genetics, Multidisciplinary, Body Height, 3. Good health, MicroRNAs, 030104 developmental biology, PADI2, Protein-Arginine Deiminases, Genome-Wide Association Study
Abstract: The impact of microRNA (miRNA) on the genetics of human complex traits, especially in the context of miRNA-target gene networks, has not been fully assessed. Here, we developed a novel analytical method, MIGWAS, to comprehensively evaluate enrichment of genome-wide association study (GWAS) signals in miRNA–target gene networks. We applied the method to the GWAS results of the 18 human complex traits from >1.75 million subjects and identified significant enrichment in rheumatoid arthritis (RA), kidney function and adult height (P P = 1.7 × 10−4). Interestingly, these results were consistent with current literature-based knowledge of the traits on miRNA obtained through the NCBI PubMed database search (adjusted P = 0.024). Our method provided a list of miRNA and target gene pairs with excess genetic association signals, part of which included drug target genes. We identified a miRNA (miR-4728-5p) that downregulates PADI2, a novel RA risk gene considered as a promising therapeutic target (rs761426, adjusted P = 2.3 × 10−9). Our study indicated the significant impact of miRNA–target gene networks on the genetics of human complex traits and provided resources which should contribute to drug discovery and nucleic acid medicine.
Published: 2016
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25. MultiMeta: an R package for meta-analysing multi-phenotype genome-wide association studies

Author: Nicole Soranzo, Paolo Gasparini, Dragana Vuckovic, and Valentina Iotchkova
Subjects: 0303 health sciences, 03 medical and health sciences, R package, 0302 clinical medicine, Multivariate analysis, Genome-wide association study, Computational biology, Biology, Phenotype, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Summary: As new methods for multivariate analysis of Genome Wide Association Studies (GWAS) become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting. Availability: The R package MultiMeta can be downloaded from CRAN Contact: dragana.vuckovic@burlo.trieste.it
Published: 2015
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26. MultiMeta: An R package for meta-analyzing multi-phenotype genome-wide association studies

Author: Valentina Iotchkova, Nicole Soranzo, Paolo Gasparini, Dragana Vuckovic, Vuckovic, Dragana, Gasparini, Paolo, Soranzo, N., and Iotchkova, V.
Subjects: Statistics and Probability, Multivariate analysis, Genetic Loci, Genome-Wide Association Study, Humans, Multivariate Analysis, Phenotype, Meta-Analysis as Topic, Software, Biochemistry, Molecular Biology, Computational Theory and Mathematics, Computer Science Applications1707 Computer Vision and Pattern Recognition, Computational Mathematics, Computer science, Locus (genetics), Genome-wide association study, computer.software_genre, Computational Theory and Mathematic, Multivariate Analysi, Applications Notes, Computer Science Applications, R package, Computational Mathematic, Data mining, computer, Human
Abstract: Summary: As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n-dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Published: 2015

27. Data of GWAS associated SNPs in regulatory regions

Author: Ian Dunham, Eugene Kulesha, Valentina Iotchkova, Sandro Morganella, Ewan Birney, Ian Dunham, Eugene Kulesha, Valentina Iotchkova, Sandro Morganella, and Ewan Birney
Published: 2015
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28. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Author: Tomi Pastinen, Guillaume Bourque, Paul Flicek, Bing Ge, Farzin Pourfarzad, Frederik Otzen Bagger, Simone Ecker, Lu Chen, Augusto Rendon, Stephen Watt, John J. Lambourne, Heather Elding, Mattia Frontini, Nicole Soranzo, Karola Rehnström, Roderic Guigó, Marie-Laure Yaspo, Willem H. Ouwehand, Frances Burden, Avik Datta, Dirk S. Paul, Kim Berentsen, Filomena Matarese, Xiaojian Shao, Laura Clarke, Alice L. Mann, Hendrik G. Stunnenberg, Francesco Paolo Casale, Stephan Busche, Vyacheslav Amstislavskiy, Matthew T. Maurano, Warren A. Cheung, Shu-Huang Chen, Marc Sultan, Emmanouil T. Dermitzakis, Thomas Risch, Eva M. Janssen-Megens, Lorenzo Bomba, Diego Garrido-Martín, Nilofar Sharifi, Tony Kwan, David Bujold, Louella Vasquez, Klaudia Walter, Bowon Kim, Stylianos E. Antonarakis, Irina Colgiu, Marie-Michelle Simon, John A. Morris, Ying Yan, Daniel Rico, Oliver Stegle, Stephan Beck, Vera Pancaldi, Steven P. Wilder, Ernesto Lowy, Hans Lehrach, José M. Fernández, Shuang-Yin Wang, Kousik Kundu, Daniel Mead, Sofie Ashford, Maxime Caron, Oliver Delaneau, Sophia Rowlston, Joost H.A. Martens, Adriana Redensek, Samantha Farrow, Valentina Iotchkova, Kate Downes, Amit Mandoli, David J. Richardson, Alfonso Valencia, Ehsan Habibi, Cornelis A. Albers, Taco W. Kuijpers, Kundu, Kousik [0000-0002-1019-8351], Lambourne, John [0000-0003-2460-0759], Bagger, Frederik [0000-0003-0636-8845], Rendon Restrepo, Augusto [0000-0001-8994-0039], Frontini, Mattia [0000-0001-8074-6299], Ouwehand, Willem [0000-0002-7744-1790], Paul, Dirk [0000-0002-8230-0116], Downes, Kate [0000-0003-0366-1579], Soranzo, Nicole [0000-0003-1095-3852], Apollo - University of Cambridge Repository, Other departments, Paediatric Infectious Diseases / Rheumatology / Immunology, AII - Amsterdam institute for Infection and Immunity, Landsteiner Laboratory, Delaneau, Olivier, Dermitzakis, Emmanouil, and Antonarakis, Stylianos
Subjects: Epigenomics, Male, 0301 basic medicine, Transcription, Genetic, Neutrophils, Transription, QTL, T-Lymphocytes, Monocyte, Monocytes, Transcriptome, T-cell, Histone code, ddc:576.5, histone modification, Genetics, DNA methylation, Neutrophil, neutrophil, Middle Aged, 3. Good health, Histone Code, Immune System Diseases, monocyte, Female, Allele specific, Molecular Developmental Biology, Histone modification, Adult, Resource, Quantitative Trait Loci, Quantitative trait locus, Biology, General Biochemistry, Genetics and Molecular Biology, allele specific, Young Adult, transription, 03 medical and health sciences, t-cell, Humans, Genetic Predisposition to Disease, Epigenetics, Molecular Biology, Aged, Genetic association, EWAS, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Biochemistry, Genetics and Molecular Biology(all), Hematopoietic Stem Cells, Human genetics, Immune, Alternative Splicing, 030104 developmental biology, immune
Abstract: Summary Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk., Graphical Abstract, Highlights • Genome, transcriptome, and epigenome reference panel in three human immune cell types • Identified 4,418 genes associated with epigenetic changes independent of genetics • Described genome-epigenome coordination defining cell-type-specific regulatory events • Functionally mapped disease mechanisms at 345 unique autoimmune disease loci, As part of the IHEC consortium, this study integrates genetic, epigenetic, and transcriptomic profiling in three immune cell types from nearly 200 people to characterize the distinct and cooperative contributions of diverse genomic inputs to transcriptional variation. Explore the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC.

29. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

Author: Suthesh Sivapalaratnam, Matthias Haimel, Stephen Kaptoge, Nilofar Sharifi, John J. Lambourne, Karyn Megy, Bing Ge, Jared O'Connell, William J. Astle, Luigi Grassi, Martijn van der Ent, Stuart Meacham, Stephen F. Garner, Eleanor Wheeler, John Danesh, Tony Kwan, Jennifer G. Sambrook, Tao Jiang, Louise C. Daugherty, Dirk S. Paul, Eva M. Janssen-Megens, Klaudia Walter, Stephen Watt, Alfonso Valencia, Joost H.A. Martens, Jonathan Marchini, S.M. Sheard, Mihir A Kamat, Ying Yang, Stephan Beck, Anita Kaan, Guillaume Bourque, Louella Vasquez, Jose A. Guerrero, Emanuele Di Angelantonio, Daniel Mead, David J. Roberts, Mattia Frontini, Nicole Soranzo, Myrto Kostadima, John Bradley, Heather Elding, Shuang-Yin Wang, Lu Chen, Salih Tuna, Kousik Kundu, Olivier Delaneau, Kathleen Freson, Diego Garrido-Martín, Dave Allen, David Bujold, Amit Mandoli, Lorenzo Bomba, Taco W. Kuijpers, Valentina Iotchkova, Alice L. Mann, James R Staley, Heleen J. Bouman, Kate Downes, Roderic Guigó, Carmel Moore, Kim Berentsen, Tomi Pastinen, Hendrik G. Stunnenberg, Willem H. Ouwehand, Fernando Riveros-Mckay, Romina Petersen, Enrique Carrillo-de-Santa-Pau, Steven P. Wilder, David Juan, Bowon Kim, Dace Ruklisa, Daniel Rico, Adam S. Butterworth, Vascular Medicine, Paediatric Infectious Diseases / Rheumatology / Immunology, AII - Amsterdam institute for Infection and Immunity, Landsteiner Laboratory, and Other departments
Subjects: 0301 basic medicine, COMPLEX DISEASES, Platelet disorder, Autoimmune diseases, Population, Genome-wide association study, Quantitative trait locus, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, blood, Mendelian randomization, autoimmune diseases, genetics, Allele, Complex disease, education, Mendelian randomisation, Molecular Biology, cardiovasular diseases, Genetic association, Genetics, education.field_of_study, epigenetics, hematology, Biochemistry, Genetics and Molecular Biology(all), complex disease, Hematology, hematopoiesis, cardiovascular diseases, 3. Good health, Hematopoiesis, 030104 developmental biology, Cardiovascular diseases, Epigenetics, Common disease-common variant
Abstract: Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (

30. Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome

Author: Yasuhide Hayashi, Jan-Henning Klusmann, M Labuhn, Udo Oppermann, Alison Kennedy, Sören Matzk, David Samulowski, Marie-Laure Yaspo, Takashi Taga, Irene Roberts, Raj Bhayadia, C Scheer, Leila N. Varghese, Mitchell J. Weiss, Dirk Heckl, Kelly J. Perkins, Thomas Risch, Vyacheslav Amstislavskiy, John D. Crispino, Etsuro Ito, Peter J. Campbell, Seishi Ogawa, Jeffrey W. Taub, Bilyana Stoilova, Stefan N. Constantinescu, Adrian Schwarzer, Dirk Reinhardt, Paresh Vyas, Kenichi Yoshida, Elli Papaemmanuil, Marlen Metzner, Valentina Iotchkova, Catherine Garnett, David Cruz Hernandez, UCL - SSS/DDUV/SIGN - Cell signalling, and UCL - (SLuc) Service d'hématologie
Subjects: 0301 basic medicine, Cancer Research, Myeloid, Transcription, Genetic, Chromosomes, Human, Pair 21, Down syndrome, Preleukemia, Medizin, cancer transformation, preleukemia, CRISPR screen, Cytokine Receptor Common beta Subunit, 0302 clinical medicine, Mice, Inbred NOD, GATA1 Transcription Factor, Exome, Gene Expression Regulation, Leukemic, Myeloid leukemia, GATA1, 3. Good health, medicine.anatomical_structure, Cell Transformation, Neoplastic, Phenotype, Oncology, Leukemia, Myeloid, 030220 oncology & carcinogenesis, Disease Progression, Cytokine receptor, Mice, Transgenic, Biology, Article, Leukemoid Reaction, 03 medical and health sciences, stomatognathic system, medicine, Biomarkers, Tumor, Animals, Humans, Genetic Predisposition to Disease, Acute myeloid leukemia, business.industry, Cell Biology, medicine.disease, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, HEK293 Cells, Cancer cell, Mutation, Cancer research, Down Syndrome, business, Trisomy, 030215 immunology
Abstract: Summary Myeloid leukemia in Down syndrome (ML-DS) clonally evolves from transient abnormal myelopoiesis (TAM), a preleukemic condition in DS newborns. To define mechanisms of leukemic transformation, we combined exome and targeted resequencing of 111 TAM and 141 ML-DS samples with functional analyses. TAM requires trisomy 21 and truncating mutations in GATA1; additional TAM variants are usually not pathogenic. By contrast, in ML-DS, clonal and subclonal variants are functionally required. We identified a recurrent and oncogenic hotspot gain-of-function mutation in myeloid cytokine receptor CSF2RB. By a multiplex CRISPR/Cas9 screen in an in vivo murine TAM model, we tested loss-of-function of 22 recurrently mutated ML-DS genes. Loss of 18 different genes produced leukemias that phenotypically, genetically, and transcriptionally mirrored ML-DS.
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31. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Author: Huang, J, Howie, B, Mccarthy, S, Memari, Y, Walter, K, Min, Jl, Danecek, P, Malerba, Giovanni, Trabetti, Elisabetta, Zheng, Hf, Gambaro, G, Richards, Jb, Durbin, R, Timpson, Nj, Marchini, J, Soranzo, N, Al Turki, S, Amuzu, A, Anderson, Ca, Anney, R, Antony, D, Artigas, Ms, Ayub, M, Bala, S, Barrett, Jc, Barroso, I, Beales, P, Benn, M, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, Pf, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Casas, Jp, Chambers, Jc, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, Da, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Day, In, Day Williams, A, Dedoussis, G, Down, T, Du, Y, van Duijn, Cm, Dunham, I, Edkins, S, Ekong, R, Ellis, P, Evans, Dm, Farooqi, Is, Fitzpatrick, Dr, Flicek, P, Floyd, J, Foley, Ar, Franklin, Cs, Futema, M, Gallagher, L, Gasparini, P, Gaunt, Tr, Geihs, M, Geschwind, D, Greenwood, C, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, Ae, Holmans, P, Huang, L, Hubbard, T, Humphries, Se, Hurles, Me, Hysi, P, Iotchkova, V, Isaacs, A, Jackson, Dk, Jamshidi, Y, Johnson, J, Joyce, C, Karczewski, Kj, Kaye, J, Keane, T, Kemp, Jp, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, Kleber, Me, van Kogelenberg, M, Kolb Kokocinski, A, Kooner, Js, Lachance, G, Langenberg, C, Langford, C, Lawson, D, Lee, I, van Leeuwen, Em, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lönnqvist, J, Lopes, Lr, Lopes, M, Luan, J, Macarthur, Dg, Mangino, M, Marenne, G, März, W, Maslen, J, Matchan, A, Mathieson, I, Mcguffin, P, Mcintosh, Am, Mckechanie, Ag, Mcquillin, A, Metrustry, S, Migone, N, Mitchison, Hm, Moayyeri, A, Morris, J, Morris, R, Muddyman, D, Muntoni, F, Nordestgaard, Bg, Northstone, K, O'Donovan, Mc, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, Mj, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, Jr, Paternoster, L, Paunio, T, Payne, F, Payne, Sj, Perry, Jr, Pietilainen, O, Plagnol, V, Pollitt, Rc, Povey, S, Quail, Ma, Quaye, L, Raymond, L, Rehnström, K, Ridout, Ck, Ring, S, Ritchie, Gr, Roberts, N, Robinson, Rl, Savage, Db, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, Rh, Scott, Ra, Semple, Rk, Serra, E, Sharp, Si, Shaw, A, Shihab, Ha, Shin, Sy, Skuse, D, Small, Ks, Smee, C, Smith, Gd, Southam, L, Spasic Boskovic, O, Spector, Td, St Clair, D, St Pourcain, B, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Tachmazidou, I, Taylor, R, Tian, J, Tobin, Md, Toniolo, D, Traglia, M, Tybjaerg Hansen, A, Valdes, Am, Vandersteen, Am, Varbo, A, Vijayarangakannan, P, Visscher, Pm, Wain, Lv, Walters, Jt, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whincup, P, Whyte, T, Williams, Hj, Williamson, Ka, Wilson, C, Wilson, Sg, Wong, K, Xu, C, Yang, J, Zaza, Gianluigi, Zeggini, E, Zhang, F, Zhang, P, Zhang, W., Clinicum, Department of Psychiatry, Jie, Huang, Bryan, Howie, Shane, Mccarthy, Yasin, Memari, Klaudia, Walter, Josine L., Min, Petr, Danecek, Giovanni, Malerba, Elisabetta, Trabetti, Hou Feng, Zheng, Saeed Al, Turki, Antoinette, Amuzu, Carl A., Anderson, Richard, Anney, Dinu, Antony, María Soler, Artiga, Muhammad, Ayub, Senduran, Bala, Jeffrey C., Barrett, Inês, Barroso, Phil, Beale, Marianne, Benn, Jamie, Bentham, Shoumo, Bhattacharya, Ewan, Birney, Douglas, Blackwood, Martin, Bobrow, Elena, Bochukova, Patrick F., Bolton, Rebecca, Bound, Chris, Boustred, Gerome, Breen, Mattia, Calissano, Keren, Car, Juan Pablo, Casa, John C., Chamber, Ruth, Charlton, Krishna, Chatterjee, Lu, Chen, Antonio, Ciampi, Sebahattin, Cirak, Peter, Clapham, Gail, Clement, Guy, Coate, Cocca, Massimiliano, David A., Collier, Catherine, Cosgrove, Tony, Cox, Nick, Craddock, Lucy, Crook, Sarah, Curran, David, Curti, Allan, Daly, Ian N. M., Day, Aaron Day, William, George, Dedoussi, Thomas, Down, Yuanping, Du, Cornelia M., van Duijn, Ian, Dunham, Sarah, Edkin, Rosemary, Ekong, Peter, Elli, David M., Evan, I., Sadaf Farooqi, David R., Fitzpatrick, Paul, Flicek, James, Floyd, A., Reghan Foley, Christopher S., Franklin, Marta, Futema, Louise, Gallagher, Gasparini, Paolo, Tom R., Gaunt, Matthias, Geih, Daniel, Geschwind, Celia, Greenwood, Heather, Griffin, Detelina, Grozeva, Xiaosen, Guo, Xueqin, Guo, Hugh, Gurling, Deborah, Hart, Audrey E., Hendrick, Peter, Holman, Liren, Huang, Tim, Hubbard, Steve E., Humphrie, Matthew E., Hurle, Pirro, Hysi, Valentina, Iotchkova, Aaron, Isaac, David K., Jackson, Yalda, Jamshidi, Jon, Johnson, Chris, Joyce, Konrad J., Karczewski, Jane, Kaye, Thomas, Keane, John P., Kemp, Karen, Kennedy, Alastair, Kent, Julia, Keogh, Farrah, Khawaja, Marcus E., Kleber, Margriet van, Kogelenberg, Anja Kolb, Kokocinski, Jaspal S., Kooner, Genevieve, Lachance, Claudia, Langenberg, Cordelia, Langford, Daniel, Lawson, Irene, Lee, Elisabeth M., van Leeuwen, Monkol, Lek, Rui, Li, Yingrui, Li, Jieqin, Liang, Hong, Lin, Ryan, Liu, Jouko, Lönnqvist, Luis R., Lope, Margarida, Lope, Jian'An, Luan, Daniel G., Macarthur, Massimo, Mangino, Gaëlle, Marenne, Winfried, März, John, Maslen, Angela, Matchan, Iain, Mathieson, Peter, Mcguffin, Andrew M., Mcintosh, Andrew G., Mckechanie, Andrew, Mcquillin, Sarah, Metrustry, Nicola, Migone, Hannah M., Mitchison, Alireza, Moayyeri, James, Morri, Richard, Morri, Dawn, Muddyman, Francesco, Muntoni, Børge G., Nordestgaard, Kate, Northstone, Michael C., O'Donovan, Stephen, O'Rahilly, Alexandros, Onoufriadi, Karim, Oualkacha, Michael J., Owen, Aarno, Palotie, Kalliope, Panoutsopoulou, Victoria, Parker, Jeremy R., Parr, Lavinia, Paternoster, Tiina, Paunio, Felicity, Payne, Stewart J., Payne, John R. B., Perry, Olli, Pietilainen, Vincent, Plagnol, Rebecca C., Pollitt, Sue, Povey, Michael A., Quail, Lydia, Quaye, Lucy, Raymond, Karola, Rehnström, Cheryl K., Ridout, Susan, Ring, Graham R. S., Ritchie, Nicola, Robert, Rachel L., Robinson, David B., Savage, Peter, Scambler, Stephan, Schiffel, Miriam, Schmidt, Nadia, Schoenmaker, Richard H., Scott, Robert A., Scott, Robert K., Semple, Eva, Serra, Sally I., Sharp, Adam, Shaw, Hashem A., Shihab, So Youn, Shin, David, Skuse, Kerrin S., Small, Carol, Smee, George Davey, Smith, Lorraine, Southam, Olivera Spasic, Boskovic, Timothy D., Spector, David St, Clair, Beate St, Pourcain, Jim, Stalker, Elizabeth, Steven, Jianping, Sun, Gabriela, Surdulescu, Jaana, Suvisaari, Petros, Syrri, Ioanna, Tachmazidou, Rohan, Taylor, Jing, Tian, Martin D., Tobin, Daniela, Toniolo, Michela, Traglia, Anne Tybjaerg, Hansen, Ana M., Valde, Anthony M., Vandersteen, Anette, Varbo, Parthiban, Vijayarangakannan, Peter M., Visscher, Louise V., Wain, James T. R., Walter, Guangbiao, Wang, Jun, Wang, Yu, Wang, Kirsten, Ward, Eleanor, Wheeler, Peter, Whincup, Tamieka, Whyte, Hywel J., William, Kathleen A., Williamson, Crispian, Wilson, Scott G., Wilson, Kim, Wong, Changjiang, Xu, Jian, Yang, Gianluigi, Zaza, Eleftheria, Zeggini, Feng, Zhang, Pingbo, Zhang, Weihua, Zhang, Giovanni, Gambaro, J., Brent Richard, Richard, Durbin, Nicholas J., Timpson, Jonathan, Marchini, and Nicole, Soranzo
Subjects: Computer science, General Physics and Astronomy, Genome-wide association study, 0302 clinical medicine, Gene Frequency, Haplotype, Genetics,Biological sciences, Settore MED/14 - NEFROLOGIA, Aged, 80 and over, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, TWINSUK, Middle Aged, single-nucleotide polymorphism, Whole-genome sequencing, WGS imputation panel, single-nucleotide polymorphism, Biological sciences, Italy, MAP, Adult, Adolescent, Genotype, WGS imputation panel, Population, Single-nucleotide polymorphism, FORMAT, Computational biology, GENOTYPE IMPUTATION, Polymorphism, Single Nucleotide, Article, White People, General Biochemistry, Genetics and Molecular Biology, Young Adult, 03 medical and health sciences, Humans, GENOME-WIDE ASSOCIATION, 1000 Genomes Project, education, Allele frequency, Alleles, Aged, 030304 developmental biology, Whole-genome sequencing, Models, Statistical, Models, Genetic, Genome, Human, Genetic Variation, General Chemistry, United Kingdom, Minor allele frequency, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Haplotypes, 3111 Biomedicine, 030217 neurology & neurosurgery, Imputation (genetics)
Abstract: Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants., Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods.
Published: 2015

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31 results on '"Valentina Iotchkova"'

1. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

2. Neutrophil lymphocyte ratio as an indicator for disease progression in Idiopathic Pulmonary Fibrosis

3. Monocyte and neutrophil levels are potentially linked to progression to IPF for patients with indeterminate UIP CT pattern

4. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

5. Multi-Modal Characterization of Monocytes in Idiopathic Pulmonary Fibrosis Reveals a Primed Type I Interferon Immune Phenotype

6. Neutrophil lymphocyte ratio as an indicator for disease progression in Idiopathic Pulmonary Fibrosis

7. FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions [version 1; referees: 2 approved with reservations]

8. Blood leukocyte levels as potential prognostic markers in IPF

9. Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

10. S79 Prevalence of the indeterminate for UIP CT feature and potential link between monocyte and neutrophil levels and progression to IPF – a single centre analysis

11. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation

12. Incidence of symptomatic, image-confirmed venous thromboembolism following hospitalization for COVID-19 with 90-day follow-up

13. Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

14. Type-1 IFN primed monocytes in pathogenesis of idiopathic pulmonary fibrosis

15. Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

16. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

17. A multiple-phenotype imputation method for genetic studies

18. Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia

19. Author Correction: Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps

20. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

21. Whole-genome sequencing coupled to imputation discovers genetic signals for anthropometric traits

22. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

23. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

24. Significant impact of miRNA–target gene networks on genetics of human complex traits

25. MultiMeta: an R package for meta-analysing multi-phenotype genome-wide association studies

26. MultiMeta: An R package for meta-analyzing multi-phenotype genome-wide association studies

27. Data of GWAS associated SNPs in regulatory regions

28. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

29. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

30. Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome

31. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

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31 results on '"Valentina Iotchkova"'

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