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Jones AR, Enticott J, Ebeling PR, Mishra GD, Teede HT, Vincent AJ. Bone health in women with premature ovarian insufficiency/early menopause: a 23-year longitudinal analysis. Hum Reprod 2024; 39:1013-1022. [PMID: 38396142 PMCID: PMC11063537 DOI: 10.1093/humrep/deae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
STUDY QUESTION What is the frequency of, and predictors for, osteoporosis, fractures, and osteoporosis management (investigation, treatment) in women with premature ovarian insufficiency (POI; menopause <40 years) and early menopause (EM; menopause 40-44years)? SUMMARY ANSWER Over the 23-year follow-up duration, at a mean age of 68 years, women with POI/EM had higher osteoporosis/fracture risk and prevalence, higher osteoporosis screening and anti-osteoporosis medication use compared to women with usual age menopause; increasing age was predictive of increased risk of osteoporosis/fracture and menopause hormone therapy (MHT) prior to or at study entry (aged 45-50 years) was protective. WHAT IS KNOWN ALREADY Women with POI/EM have increased risk of osteoporosis and fractures with limited data regarding risk factors for reduced bone density and fractures. Clinical guidelines recommend screening with dual X-ray absorptiometry (DXA) and treatment with MHT for most women with POI/EM to reduce osteoporosis and fracture risk; however, studies indicate gaps in osteoporosis knowledge, guideline uptake, and management adherence by clinicians and women. STUDY DESIGN, SIZE, DURATION The Australian Longitudinal Study on Women's Health is a prospective longitudinal study of Australian women. This study uses the cohort of women born between 1946 and 1951, surveyed nine times between 1996 and 2019. Data from the Australian administrative health records, including hospital admissions data (fractures, osteoporosis), Medicare Benefits Schedule (DXA), and the Pharmaceutical Benefits Scheme (PBS; MHT, anti-osteoporosis medication, available only from 2002) were linked to survey data. PARTICIPANTS/MATERIALS, SETTING, METHODS Survey respondents with self-reported age of menopause were included. POI/EM was defined as menopause <45 years. T-test or chi-square were used for comparisons at baseline (P < 0.05 indicates significance). Generalized estimating equations for panel data explored predictors for the longitudinal outcomes of osteoporosis, fractures, DXA rates, MHT use, and anti-osteoporosis medication (in women with osteoporosis/fracture, from Survey 4 onwards only). Univariable regression was performed, and variables retained where P < 0.2, to form the multivariable model, and bootstrapping with 100 repetitions at 95% sampling of the original dataset to ensure robustness of results. MAIN RESULTS AND THE ROLE OF CHANCE Eight thousand six hundred and three women were included: 610 (7.1%) with POI/EM. Mean (SD) baseline age was 47.6 (1.45) years in the entire cohort and mean (SD) age of menopause was 38.2 (7.95) and 51.3 (3.04) years in women with POI/EM and usual age menopause, respectively (P < 0.001). Over the 23 years, of women with POI/EM, 303 (49.7%) had osteoporosis/fractures, 421 (69.0%) had DXA screening, 474 ever used MHT (77.7%), and 116 (39.1%) of those with osteoporosis/fractures used anti-osteoporosis medication. Of women with usual age menopause, 2929 (36.6%) had osteoporosis/fractures, 4920 (61.6%) had DXA screening, 4014 (50.2%) used MHT, and 964 (33.0%) of those with osteoporosis/fractures used anti-osteoporosis medication. Compared to women with menopause at age ≥45 years and after adjusting for other risk factors, women with POI/EM had increased risk of osteoporosis (odds ratio [OR] 1.37; 95% CI 1.07-1.77), fractures (OR 1.45; 1.15-1.81), DXA testing (OR 1.64; 1.42-1.90), MHT use (OR 6.87; 5.68-8.30), and anti-osteoporosis medication use (OR 1.50; 1.14-1.98). In women with POI/EM women, increasing age was associated with greater risk of osteoporosis/fracture (OR 1.09; 1.08-1.11), and MHT prior to or at study entry (aged 45-50 years), was protective (OR 0.65, 0.45-0.96). In women with POI/EM, age (OR 1.11; 1.10-1.12), fractures (OR 1.80, 1.38-2.34), current smoking (OR 0.60; 0.43-0.86), and inner (OR 0.68; 0.53-0.88) or outer regional (OR 0.63; 0.46-0.87) residential location were associated with DXA screening. In women with POI/EM, increasing age (OR 1.02; 1.01-1.02), and currently consuming alcohol (OR 1.17; 1.06-1.28), was associated with having ever used MHT. In the 299 women with POI/EM and osteoporosis/fractures, only 39.1% ever received treatment with an anti-osteoporosis medication. Increasing age (OR 1.07; 1.04-1.09) and lower BMI (OR 0.95; 0.92-0.98) were associated with greater likelihood of treatment with anti-osteoporosis medication. LIMITATIONS, REASONS FOR CAUTION Survey data including age of menopause were self-reported by participants; fracture questions were not included in the 2001 survey, and location or level of trauma of self-reported fractures was not asked. Additional risk/protective factors such as vitamin D status, calcium intake, and exercise were not able to be included. Due to sample size, POI and EM were combined for all analyses, and we were unable to differentiate between causes of POI/EM. PBS data were only available from 2004, and hospital admissions data were state-based, with all of Australia were only available from 2007. WIDER IMPLICATIONS OF THE FINDINGS This study supports previous literature indicating increased risk of osteoporosis and fractures in women with POI, and adds evidence for women with POI/EM, where there was a relative paucity of data. This is the first study to analyse a variety of clinical and demographic risk factors for osteoporosis and fractures in women with POI/EM, as well as analysing investigation and treatment rates. In these women, using MHT prior to or at study entry, aged 45-50 years, was protective for osteoporosis/fractures; however, having ever used MHT was not, highlighting the importance of early treatment with MHT in these women to preserve bone strength. Although women with POI/EM and osteoporosis or fractures were more likely to use anti-osteoporosis medications than those with usual age menopause, overall treatment rates are low at <40%, demonstrating a significant treatment gap that should be addressed to reduce future fracture risk. STUDY FUNDING/COMPETING INTEREST(S) This study was funded by The Australian NHMRC Centre of Research Excellence Women's Health in Reproductive Life (CRE-WHIRL, project number APP1171592). A.R.J. is the recipient of a National Health and Medical Research Council post-graduate research scholarship (grant number 1169192). P.R.E. is supported by a National Health and Medical Research Council grant 1197958. P.R.E. reports grants paid to their institution from Amgen, Sanofi, and Alexion, honoraria from Amgen paid to their institution, and honoraria from Alexion and Kyowa-Kirin. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- A R Jones
- Monash Centre for Health Research and Implementation, Monash University, Melbourne, VIC, Australia
- Department of Endocrinology, Monash Health, Melbourne, VIC, Australia
| | - J Enticott
- Monash Centre for Health Research and Implementation, Monash University, Melbourne, VIC, Australia
| | - P R Ebeling
- Department of Endocrinology, Monash Health, Melbourne, VIC, Australia
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - G D Mishra
- Australian Women and Girls’ Health Research Centre, School of Public Health, University of Queensland, Brisbane, QLD, Australia
| | - H T Teede
- Monash Centre for Health Research and Implementation, Monash University, Melbourne, VIC, Australia
- Department of Endocrinology, Monash Health, Melbourne, VIC, Australia
| | - A J Vincent
- Monash Centre for Health Research and Implementation, Monash University, Melbourne, VIC, Australia
- Department of Endocrinology, Monash Health, Melbourne, VIC, Australia
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Chen Z, Reynolds RH, Pardiñas AF, Gagliano Taliun SA, van Rheenen W, Lin K, Shatunov A, Gustavsson EK, Fogh I, Jones AR, Robberecht W, Corcia P, Chiò A, Shaw PJ, Morrison KE, Veldink JH, van den Berg LH, Shaw CE, Powell JF, Silani V, Hardy JA, Houlden H, Owen MJ, Turner MR, Ryten M, Al-Chalabi A. The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases. Neurobiol Dis 2023; 180:106082. [PMID: 36925053 DOI: 10.1016/j.nbd.2023.106082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.
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Affiliation(s)
- Zhongbo Chen
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK.
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Sarah A Gagliano Taliun
- Department of Medicine & Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada; Montréal Heart Institute, Montréal, Québec, Canada
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Kuang Lin
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Wim Robberecht
- Department of Neurology, University Hospital Leuven, Leuven, Belgium; Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease, Leuven, Belgium; Vesalius Research Center, Laboratory of Neurobiology, Leuven, Belgium
| | - Philippe Corcia
- ALS Center, Department of Neurology, CHRU Bretonneau, Tours, France
| | - Adriano Chiò
- Rita Levi Montalcini Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy; Azienda Ospedaliera Universitaria Città della Salute e della Scienza, Torino, Italy
| | - Pamela J Shaw
- Academic Neurology Unit, Department of Neuroscience, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, the Netherlands
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milano, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, 20122 Milano, Italy
| | - John A Hardy
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London (UCL), London, UK; Reta Lila Weston Institute, Queen Square Institute of Neurology, UCL, London, UK; UK Dementia Research Institute, Queen Square Institute of Neurology, UCL, London, UK; NIHR University College London Hospitals Biomedical Research Centre, London, UK; Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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3
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Adey BN, Cooper-Knock J, Al Khleifat A, Fogh I, van Damme P, Corcia P, Couratier P, Hardiman O, McLaughlin R, Gotkine M, Drory V, Silani V, Ticozzi N, Veldink JH, van den Berg LH, de Carvalho M, Pinto S, Mora Pardina JS, Povedano Panades M, Andersen PM, Weber M, Başak NA, Shaw CE, Shaw PJ, Morrison KE, Landers JE, Glass JD, Vourc’h P, Dobson RJB, Breen G, Al-Chalabi A, Jones AR, Iacoangeli A. Large-scale analyses of CAV1 and CAV2 suggest their expression is higher in post-mortem ALS brain tissue and affects survival. Front Cell Neurosci 2023; 17:1112405. [PMID: 36937187 PMCID: PMC10017967 DOI: 10.3389/fncel.2023.1112405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction: Caveolin-1 and Caveolin-2 (CAV1 and CAV2) are proteins associated with intercellular neurotrophic signalling. There is converging evidence that CAV1 and CAV2 (CAV1/2) genes have a role in amyotrophic lateral sclerosis (ALS). Disease-associated variants have been identified within CAV1/2 enhancers, which reduce gene expression and lead to disruption of membrane lipid rafts. Methods: Using large ALS whole-genome sequencing and post-mortem RNA sequencing datasets (5,987 and 365 tissue samples, respectively), and iPSC-derived motor neurons from 55 individuals, we investigated the role of CAV1/2 expression and enhancer variants in the ALS phenotype. Results: We report a differential expression analysis between ALS cases and controls for CAV1 and CAV2 genes across various post-mortem brain tissues and three independent datasets. CAV1 and CAV2 expression was consistently higher in ALS patients compared to controls, with significant results across the primary motor cortex, lateral motor cortex, and cerebellum. We also identify increased survival among carriers of CAV1/2 enhancer mutations compared to non-carriers within Project MinE and slower progression as measured by the ALSFRS. Carriers showed a median increase in survival of 345 days. Discussion: These results add to an increasing body of evidence linking CAV1 and CAV2 genes to ALS. We propose that carriers of CAV1/2 enhancer mutations may be conceptualised as an ALS subtype who present a less severe ALS phenotype with a longer survival duration and slower progression. Upregulation of CAV1/2 genes in ALS cases may indicate a causal pathway or a compensatory mechanism. Given prior research supporting the beneficial role of CAV1/2 expression in ALS patients, we consider a compensatory mechanism to better fit the available evidence, although further investigation into the biological pathways associated with CAV1/2 is needed to support this conclusion.
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Affiliation(s)
- Brett N. Adey
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Philip van Damme
- Department of Neurosciences, KU Leuven-University of Leuven, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
- VIB, Center for Brain and Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours, France
- Centre de référence sur la SLA, CHU de Tours, Tours, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges, France
- UMR 1094, Université de Limoges, Inserm, Limoges, France
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Russell McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem, Israel
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Mónica Povedano Panades
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L’Hospitalet de Llobregat, Barcelona, Spain
| | | | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, St. Gallen, Switzerland
| | - Nazli A. Başak
- Koc University School of Medicine, Translational Medicine Research Center, NDAL, Istanbul, Turkey
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Karen E. Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Jonathan D. Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, United States
| | - Patrick Vourc’h
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
- Service de Biochimie et Biologie molécularie, CHU de Tours, Tours, France
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre at University College London Hospitals, NHS Foundation Trust, London, United Kingdom
| | - Gerome Breen
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- King’s College Hospital, London, United Kingdom
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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Balendra R, Jones AR, Al Khleifat A, Chiwera T, Wicks P, Young CA, Shaw PJ, Turner MR, Leigh PN, Al-Chalabi A. Comparison Of King's Clinical Staging In Multinational Amyotrophic Lateral Sclerosis Cohorts. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:71-81. [PMID: 35852375 DOI: 10.1080/21678421.2022.2090847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background: Amyotrophic lateral sclerosis (ALS) shows considerable clinical heterogeneity, which affects clinical trials. A clinical staging system has been proposed for ALS with potential applications in patient care, research, trial design and health economic analyses. The King's system consists of five stages. We have previously shown that progressive clinical stages were reached at predictable proportions through the disease course, but this needs to be validated in other independent samples. Objectives: We aimed to compare King's clinical staging in ALS in four patient groups, located in different regions and countries and using different health care systems from the original study population in South London. Methods: Clinical data were extracted from two European phase 3 randomized controlled trials (MitoTarget and LiCALS) and from two databases predominately from the United States: the PRO-ACT Consortium Database and a database of patients from the PatientsLikeMe website. Clinical stage was estimated using an algorithm, and standardized time to each clinical stage was calculated in deceased patients. Results: 8,796 patients were included, of whom 1,959 had died by the end of follow-up. Stages occurred in the same order as in the original study for all cohorts. Median standardized times to stages (interquartile range) were Stage 2: 0.61 (0.47-0.75), Stage 3: 0.68 (0.56-0.81), Stage 4A: 0.82 (0.71-0.91), Stage 4B: 0.82 (0.69-0.92) and Stage 4 0.80 (0.67-0.91). Discussion: Timings for all stages were similar to those reported in the original study, except Stage 2 which occurred later in the clinical trial databases due to recruitment occurring after diagnosis.
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Affiliation(s)
- Rubika Balendra
- UK Dementia Research Institute, University College London, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, UK
| | - Theresa Chiwera
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, UK
| | - Paul Wicks
- Wicks Digital Health, Wicks Digital Health, Lichfield, UK
| | - Carolyn A Young
- Department of Neurology, Walton Centre NHS Foundation Trust, Liverpool, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, OX3 9DU, UK
| | - P Nigel Leigh
- Department of Neuroscience, Brighton and Sussex Medical School, Trafford Centre for Biomedical Research, University of Sussex, Falmer, East Sussex, BN1 9RY, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, UK
- Department of Neurology, King's College Hospital, London, UK
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5
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Kabiljo R, Bowles H, Marriott H, Jones AR, Bouton CR, Dobson RJ, Quinn JP, Al Khleifat A, Swanson CM, Al-Chalabi A, Iacoangeli A. RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data. iScience 2022; 25:105289. [PMID: 36339261 PMCID: PMC9626663 DOI: 10.1016/j.isci.2022.105289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022] Open
Abstract
Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training. Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.
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Affiliation(s)
- Renata Kabiljo
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Harry Bowles
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Heather Marriott
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Clement R. Bouton
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Richard J.B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Institute of Health Informatics, University College London, London, UK
- NIHR Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London, UK
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
| | - Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9NU, UK
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
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6
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Jones AR, Iacoangeli A, Adey BN, Bowles H, Shatunov A, Troakes C, Garson JA, McCormick AL, Al-Chalabi A. Author Correction: A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Sci Rep 2022; 12:14171. [PMID: 35986057 PMCID: PMC9391455 DOI: 10.1038/s41598-022-18488-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK.
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Brett N Adey
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, King's College London, London, UK
| | - Harry Bowles
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Claire Troakes
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jeremy A Garson
- Division of Infection and Immunity, University College London, London, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 9NU, UK
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7
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Eitan C, Siany A, Barkan E, Olender T, van Eijk KR, Moisse M, Farhan SMK, Danino YM, Yanowski E, Marmor-Kollet H, Rivkin N, Yacovzada NS, Hung ST, Cooper-Knock J, Yu CH, Louis C, Masters SL, Kenna KP, van der Spek RAA, Sproviero W, Al Khleifat A, Iacoangeli A, Shatunov A, Jones AR, Elbaz-Alon Y, Cohen Y, Chapnik E, Rothschild D, Weissbrod O, Beck G, Ainbinder E, Ben-Dor S, Werneburg S, Schafer DP, Brown RH, Shaw PJ, Van Damme P, van den Berg LH, Phatnani H, Segal E, Ichida JK, Al-Chalabi A, Veldink JH, Hornstein E. Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3'UTR protect against ALS. Nat Neurosci 2022; 25:433-445. [PMID: 35361972 PMCID: PMC7614916 DOI: 10.1038/s41593-022-01040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 02/16/2022] [Indexed: 12/26/2022]
Abstract
The noncoding genome is substantially larger than the protein-coding genome but has been largely unexplored by genetic association studies. Here, we performed region-based rare variant association analysis of >25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole genomes and the whole genomes of 70,403 non-ALS controls. We identified interleukin-18 receptor accessory protein (IL18RAP) 3' untranslated region (3'UTR) variants as significantly enriched in non-ALS genomes and associated with a fivefold reduced risk of developing ALS, and this was replicated in an independent cohort. These variants in the IL18RAP 3'UTR reduce mRNA stability and the binding of double-stranded RNA (dsRNA)-binding proteins. Finally, the variants of the IL18RAP 3'UTR confer a survival advantage for motor neurons because they dampen neurotoxicity of human induced pluripotent stem cell (iPSC)-derived microglia bearing an ALS-associated expansion in C9orf72, and this depends on NF-κB signaling. This study reveals genetic variants that protect against ALS by reducing neuroinflammation and emphasizes the importance of noncoding genetic association studies.
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Affiliation(s)
- Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Aviad Siany
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Barkan
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kristel R van Eijk
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Yanowski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Natalia Rivkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Sarah Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Shu-Ting Hung
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Chien-Hsiung Yu
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Cynthia Louis
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Seth L Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Kevin P Kenna
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Rick A A van der Spek
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - William Sproviero
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Ahmad Al Khleifat
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Alfredo Iacoangeli
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Aleksey Shatunov
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Ashley R Jones
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
| | - Yael Elbaz-Alon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Elik Chapnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Daphna Rothschild
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Omer Weissbrod
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Beck
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sebastian Werneburg
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dorothy P Schafer
- Department of Neurobiology, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, USA
| | - Eran Segal
- Department of Computer Science And Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Ammar Al-Chalabi
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, United Kingdom
- King's College Hospital, Denmark Hill, London, United Kingdom
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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8
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Al Khleifat A, Iacoangeli A, van Vugt JJFA, Bowles H, Moisse M, Zwamborn RAJ, van der Spek RAA, Shatunov A, Cooper-Knock J, Topp S, Byrne R, Gellera C, López V, Jones AR, Opie-Martin S, Vural A, Campos Y, van Rheenen W, Kenna B, Van Eijk KR, Kenna K, Weber M, Smith B, Fogh I, Silani V, Morrison KE, Dobson R, van Es MA, McLaughlin RL, Vourc'h P, Chio A, Corcia P, de Carvalho M, Gotkine M, Panades MP, Mora JS, Shaw PJ, Landers JE, Glass JD, Shaw CE, Basak N, Hardiman O, Robberecht W, Van Damme P, van den Berg LH, Veldink JH, Al-Chalabi A. Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis. NPJ Genom Med 2022; 7:8. [PMID: 35091648 PMCID: PMC8799638 DOI: 10.1038/s41525-021-00267-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 10/21/2021] [Indexed: 02/01/2023] Open
Abstract
There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.
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Affiliation(s)
- Ahmad Al Khleifat
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Alfredo Iacoangeli
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Harry Bowles
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Matthieu Moisse
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Rick A A van der Spek
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Aleksey Shatunov
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Simon Topp
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Ross Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Cinzia Gellera
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano and Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milano, Italy
| | - Victoria López
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano and Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milano, Italy
| | - Ashley R Jones
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Sarah Opie-Martin
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Atay Vural
- Koc University, School of Medicine, Translational Medicine Research Center- NDAL, Istanbul, Turkey
| | - Yolanda Campos
- Mitochondrial pathology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Brendan Kenna
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Kristel R Van Eijk
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Kevin Kenna
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Bradley Smith
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Isabella Fogh
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano and Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milano, Italy
| | - Karen E Morrison
- Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Russell L McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Adriano Chio
- Rita Levi Montalcini, Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Citta della Salute e della Scienza, Torino, Italy
| | - Philippe Corcia
- Centre SLA, CHRU de Tours, Tours, France
- Federation des Centres SLA Tours and Limoges, LITORALS, Tours, France
| | - Mamede de Carvalho
- Physiology Institute, Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | | | - Monica P Panades
- Neurology Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan D Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Christopher E Shaw
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK
- King's College Hospital, Denmark Hill, London, UK
| | - Nazli Basak
- Koc University, School of Medicine, Translational Medicine Research Center- NDAL, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Republic of Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Republic of Ireland
| | - Wim Robberecht
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
- Neurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology; VIB Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
- Neurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ammar Al-Chalabi
- King's College London, Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, De Crespigny Park, London, UK.
- King's College Hospital, Denmark Hill, London, UK.
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9
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Al Khleifat A, Iacoangeli A, Jones AR, van Vugt JJFA, Moisse M, Shatunov A, Zwamborn RAJ, van der Spek RAA, Cooper-Knock J, Topp S, van Rheenen W, Kenna B, Van Eijk KR, Kenna K, Byrne R, López V, Opie-Martin S, Vural A, Campos Y, Weber M, Smith B, Fogh I, Silani V, Morrison KE, Dobson R, van Es MA, McLaughlin RL, Vourc’h P, Chio A, Corcia P, de Carvalho M, Gotkine M, Panades MP, Mora JS, Shaw PJ, Landers JE, Glass JD, Shaw CE, Basak N, Hardiman O, Robberecht W, Van Damme P, van den Berg LH, Veldink JH, Al-Chalabi A. Telomere length analysis in amyotrophic lateral sclerosis using large-scale whole genome sequence data. Front Cell Neurosci 2022; 16:1050596. [PMID: 36589292 PMCID: PMC9799999 DOI: 10.3389/fncel.2022.1050596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the loss of upper and lower motor neurons, leading to progressive weakness of voluntary muscles, with death following from neuromuscular respiratory failure, typically within 3 to 5 years. There is a strong genetic contribution to ALS risk. In 10% or more, a family history of ALS or frontotemporal dementia is obtained, and the Mendelian genes responsible for ALS in such families have now been identified in about 50% of cases. Only about 14% of apparently sporadic ALS is explained by known genetic variation, suggesting that other forms of genetic variation are important. Telomeres maintain DNA integrity during cellular replication, differ between sexes, and shorten naturally with age. Sex and age are risk factors for ALS and we therefore investigated telomere length in ALS. Methods Samples were from Project MinE, an international ALS whole genome sequencing consortium that includes phenotype data. For validation we used donated brain samples from motor cortex from people with ALS and controls. Ancestry and relatedness were evaluated by principal components analysis and relationship matrices of DNA microarray data. Whole genome sequence data were from Illumina HiSeq platforms and aligned using the Isaac pipeline. TelSeq was used to quantify telomere length using whole genome sequence data. We tested the association of telomere length with ALS and ALS survival using Cox regression. Results There were 6,580 whole genome sequences, reducing to 6,195 samples (4,315 from people with ALS and 1,880 controls) after quality control, and 159 brain samples (106 ALS, 53 controls). Accounting for age and sex, there was a 20% (95% CI 14%, 25%) increase of telomere length in people with ALS compared to controls (p = 1.1 × 10-12), validated in the brain samples (p = 0.03). Those with shorter telomeres had a 10% increase in median survival (p = 5.0×10-7). Although there was no difference in telomere length between sporadic ALS and familial ALS (p=0.64), telomere length in 334 people with ALS due to expanded C9orf72 repeats was shorter than in those without expanded C9orf72 repeats (p = 5.0×10-4). Discussion Although telomeres shorten with age, longer telomeres are a risk factor for ALS and worsen prognosis. Longer telomeres are associated with ALS.
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Affiliation(s)
- Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- Ahmad Al Khleifat,
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Joke J. F. A. van Vugt
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- VIB Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Aleksey Shatunov
- Institute of Medicine, North-Eastern Federal University, Yakutsk, Russia
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
| | - Ramona A. J. Zwamborn
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Rick A. A. van der Spek
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Brendan Kenna
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Kristel R. Van Eijk
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Kevin Kenna
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Ross Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Victoria López
- Computational Biology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Atay Vural
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
| | - Yolanda Campos
- Computational Biology Unit, Instituto de Salud Carlos III, Madrid, Spain
| | - Markus Weber
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Bradley Smith
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Karen E. Morrison
- Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Michael A. van Es
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Adriano Chio
- Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Citta della Salute e della Scienza, Turin, Italy
| | - Philippe Corcia
- Centre SLA, CHRU de Tours, Tours, France
- Federation des Centres SLA Tours and Limoges, LITORALS, Tours, France
| | - Mamede de Carvalho
- Physiology Institute, Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | - Marc Gotkine
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Jonathan D. Glass
- Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, United States
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- King’s College Hospital, London, United Kingdom
| | - Nazli Basak
- School of Medicine, Translational Medicine Research Center-NDAL, Koc University, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, KU Leuven—University of Leuven, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H. van den Berg
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Jan H. Veldink
- Department of Neurology, University Medical Center (UMC) Utrecht Brain Center, Utrecht University, Utrecht, Netherlands
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
- King’s College Hospital, London, United Kingdom
- *Correspondence: Ammar Al-Chalabi,
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10
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Kwok A, Camacho IS, Winter S, Knight M, Meade RM, Van der Kamp MW, Turner A, O'Hara J, Mason JM, Jones AR, Arcus VL, Pudney CR. A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability. Front Mol Biosci 2021; 8:778244. [PMID: 34926581 PMCID: PMC8681860 DOI: 10.3389/fmolb.2021.778244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
It is now over 30 years since Demchenko and Ladokhin first posited the potential of the tryptophan red edge excitation shift (REES) effect to capture information on protein molecular dynamics. While there have been many key efforts in the intervening years, a biophysical thermodynamic model to quantify the relationship between the REES effect and protein flexibility has been lacking. Without such a model the full potential of the REES effect cannot be realized. Here, we present a thermodynamic model of the tryptophan REES effect that captures information on protein conformational flexibility, even with proteins containing multiple tryptophan residues. Our study incorporates exemplars at every scale, from tryptophan in solution, single tryptophan peptides, to multitryptophan proteins, with examples including a structurally disordered peptide, de novo designed enzyme, human regulatory protein, therapeutic monoclonal antibodies in active commercial development, and a mesophilic and hyperthermophilic enzyme. Combined, our model and data suggest a route forward for the experimental measurement of the protein REES effect and point to the potential for integrating biomolecular simulation with experimental data to yield novel insights.
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Affiliation(s)
- A Kwok
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - I S Camacho
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - S Winter
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - R M Meade
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - M W Van der Kamp
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | | | - J M Mason
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - A R Jones
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - V L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - C R Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,BLOC Laboratories Limited, Bath, United Kingdom
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11
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Johnson JO, Chia R, Miller DE, Li R, Kumaran R, Abramzon Y, Alahmady N, Renton AE, Topp SD, Gibbs JR, Cookson MR, Sabir MS, Dalgard CL, Troakes C, Jones AR, Shatunov A, Iacoangeli A, Al Khleifat A, Ticozzi N, Silani V, Gellera C, Blair IP, Dobson-Stone C, Kwok JB, Bonkowski ES, Palvadeau R, Tienari PJ, Morrison KE, Shaw PJ, Al-Chalabi A, Brown RH, Calvo A, Mora G, Al-Saif H, Gotkine M, Leigh F, Chang IJ, Perlman SJ, Glass I, Scott AI, Shaw CE, Basak AN, Landers JE, Chiò A, Crawford TO, Smith BN, Traynor BJ. Association of Variants in the SPTLC1 Gene With Juvenile Amyotrophic Lateral Sclerosis. JAMA Neurol 2021; 78:1236-1248. [PMID: 34459874 PMCID: PMC8406220 DOI: 10.1001/jamaneurol.2021.2598] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Importance Juvenile amyotrophic lateral sclerosis (ALS) is a rare form of ALS characterized by age of symptom onset less than 25 years and a variable presentation. Objective To identify the genetic variants associated with juvenile ALS. Design, Setting, and Participants In this multicenter family-based genetic study, trio whole-exome sequencing was performed to identify the disease-associated gene in a case series of unrelated patients diagnosed with juvenile ALS and severe growth retardation. The patients and their family members were enrolled at academic hospitals and a government research facility between March 1, 2016, and March 13, 2020, and were observed until October 1, 2020. Whole-exome sequencing was also performed in a series of patients with juvenile ALS. A total of 66 patients with juvenile ALS and 6258 adult patients with ALS participated in the study. Patients were selected for the study based on their diagnosis, and all eligible participants were enrolled in the study. None of the participants had a family history of neurological disorders, suggesting de novo variants as the underlying genetic mechanism. Main Outcomes and Measures De novo variants present only in the index case and not in unaffected family members. Results Trio whole-exome sequencing was performed in 3 patients diagnosed with juvenile ALS and their parents. An additional 63 patients with juvenile ALS and 6258 adult patients with ALS were subsequently screened for variants in the SPTLC1 gene. De novo variants in SPTLC1 (p.Ala20Ser in 2 patients and p.Ser331Tyr in 1 patient) were identified in 3 unrelated patients diagnosed with juvenile ALS and failure to thrive. A fourth variant (p.Leu39del) was identified in a patient with juvenile ALS where parental DNA was unavailable. Variants in this gene have been previously shown to be associated with autosomal-dominant hereditary sensory autonomic neuropathy, type 1A, by disrupting an essential enzyme complex in the sphingolipid synthesis pathway. Conclusions and Relevance These data broaden the phenotype associated with SPTLC1 and suggest that patients presenting with juvenile ALS should be screened for variants in this gene.
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Affiliation(s)
- Janel O. Johnson
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Ruth Chia
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Danny E. Miller
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, University of Washington, Seattle
| | - Rachel Li
- Department of Pediatrics, Children’s Hospital of Richmond at VCU, Richmond, Virginia
| | - Ravindran Kumaran
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Yevgeniya Abramzon
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Nada Alahmady
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Alan E. Renton
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Simon D. Topp
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- UK Dementia Research Institute at King’s College London, London, United Kingdom
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Mark R. Cookson
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Marya S. Sabir
- Neurodegenerative Diseases Research Unit, Laboratory of Neurogenetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Claire Troakes
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ashley R. Jones
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Nicola Ticozzi
- Istituto Auxologico Italiano, IRCCS, Department of Neurology–Stroke Unit and Laboratory of Neuroscience, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Vincenzo Silani
- Istituto Auxologico Italiano, IRCCS, Department of Neurology–Stroke Unit and Laboratory of Neuroscience, Milan, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico ‘Carlo Besta,’ Milan, Italy
| | - Ian P. Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, Australia
- School of Medical Sciences, University of New South Wales, Kensington, Australia
| | - John B. Kwok
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, Australia
- School of Medical Sciences, University of New South Wales, Kensington, Australia
| | - Emily S. Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, University of Washington, Seattle
| | - Robin Palvadeau
- Suna and Inan Kırac Foundation, Neurodegeneration Research Laboratory, KUTTAM, School of Medicine, Koc University, Istanbul, Turkey
| | - Pentti J. Tienari
- Department of Neurology, Helsinki University Hospital and Translational Immunology Programme, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Karen E. Morrison
- Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester
| | - Andrea Calvo
- ALS Center, ‘Rita Levi Montalcini’ Department of Neuroscience, University of Turin, Turin, Italy
| | | | - Hind Al-Saif
- Department of Neurology, Children’s Hospital of Richmond at VCU, Richmond, Virginia
| | - Marc Gotkine
- Department of Neurology, The Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Fawn Leigh
- Department of Neurology, Seattle Children’s Hospital, University of Washington, Seattle
| | - Irene J. Chang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle
| | - Seth J. Perlman
- Department of Neurology, Seattle Children’s Hospital, University of Washington, Seattle
| | - Ian Glass
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, University of Washington, Seattle
| | - Anna I. Scott
- Department of Laboratories, Seattle Children’s Hospital, Seattle, Washington
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Christopher E. Shaw
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- UK Dementia Research Institute at King’s College London, London, United Kingdom
| | - A. Nazli Basak
- Suna and Inan Kırac Foundation, Neurodegeneration Research Laboratory, KUTTAM, School of Medicine, Koc University, Istanbul, Turkey
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester
| | - Adriano Chiò
- ALS Center, ‘Rita Levi Montalcini’ Department of Neuroscience, University of Turin, Turin, Italy
- Neurology 1, AOU Città della Salute e della Scienza, Turin, Italy
| | - Thomas O. Crawford
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University, Baltimore, Maryland
| | - Bradley N. Smith
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
- National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
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12
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Jones AR, Iacoangeli A, Adey BN, Bowles H, Shatunov A, Troakes C, Garson JA, McCormick AL, Al-Chalabi A. A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. Sci Rep 2021; 11:14283. [PMID: 34253796 PMCID: PMC8275748 DOI: 10.1038/s41598-021-93742-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
There is increasing evidence that endogenous retroviruses (ERVs) play a significant role in central nervous system diseases, including amyotrophic lateral sclerosis (ALS). Studies of ALS have consistently identified retroviral enzyme reverse transcriptase activity in patients. Evidence indicates that ERVs are the cause of reverse transcriptase activity in ALS, but it is currently unclear whether this is due to a specific ERV locus or a family of ERVs. We employed a combination of bioinformatic methods to identify whether specific ERVs or ERV families are associated with ALS. Using the largest post-mortem RNA-sequence datasets available we selectively identified ERVs that closely resembled full-length proviruses. In the discovery dataset there was one ERV locus (HML6_3p21.31c) that showed significant increased expression in post-mortem motor cortex tissue after multiple-testing correction. Using six replication post-mortem datasets we found HML6_3p21.31c was consistently upregulated in ALS in motor cortex and cerebellum tissue. In addition, HML6_3p21.31c showed significant co-expression with cytokine binding and genes involved in EBV, HTLV-1 and HIV type-1 infections. There were no significant differences in ERV family expression between ALS and controls. Our results support the hypothesis that specific ERV loci are involved in ALS pathology.
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Affiliation(s)
- Ashley R. Jones
- grid.13097.3c0000 0001 2322 6764Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9NU UK
| | - Alfredo Iacoangeli
- grid.13097.3c0000 0001 2322 6764Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9NU UK ,grid.13097.3c0000 0001 2322 6764Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK ,grid.451056.30000 0001 2116 3923National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
| | - Brett N. Adey
- grid.13097.3c0000 0001 2322 6764Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK ,grid.13097.3c0000 0001 2322 6764Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK ,grid.13097.3c0000 0001 2322 6764NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, King’s College London, London, UK
| | - Harry Bowles
- grid.13097.3c0000 0001 2322 6764Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9NU UK ,grid.13097.3c0000 0001 2322 6764Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK ,grid.451056.30000 0001 2116 3923National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK ,grid.451056.30000 0001 2116 3923National Institute for Health Research Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Aleksey Shatunov
- grid.13097.3c0000 0001 2322 6764Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9NU UK
| | - Claire Troakes
- grid.13097.3c0000 0001 2322 6764MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Jeremy A. Garson
- grid.83440.3b0000000121901201Division of Infection and Immunity, University College London, London, UK
| | - Adele L. McCormick
- grid.12896.340000 0000 9046 8598School of Life Sciences, University of Westminster, London, UK
| | - Ammar Al-Chalabi
- grid.13097.3c0000 0001 2322 6764Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE5 9NU UK
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13
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Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, Kwok JB, Mather KA, Mellick GD, Sachdev PS, Wallace L, Henders AK, Zwamborn RAJ, Hop PJ, Lunnon K, Pishva E, Roubroeks JAY, Soininen H, Tsolaki M, Mecocci P, Lovestone S, Kłoszewska I, Vellas B, Furlong S, Garton FC, Henderson RD, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson G, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Anderson TJ, Bentley SR, Dalrymple-Alford J, Fowder J, Gratten J, Halliday G, Hickie IB, Kennedy M, Lewis SJG, Montgomery GW, Pearson J, Pitcher TL, Silburn P, Zhang F, Visscher PM, Yang J, Stevenson AJ, Hillary RF, Marioni RE, Harris SE, Deary IJ, Jones AR, Shatunov A, Iacoangeli A, van Rheenen W, van den Berg LH, Shaw PJ, Shaw CE, Morrison KE, Al-Chalabi A, Veldink JH, Hannon E, Mill J, Wray NR, McRae AF. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol 2021; 22:90. [PMID: 33771206 PMCID: PMC8004462 DOI: 10.1186/s13059-021-02275-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. RESULTS We use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson's disease (and none with Alzheimer's disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. CONCLUSIONS We identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
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Grants
- U24 AG021886 NIA NIH HHS
- U01 AG016976 NIA NIH HHS
- Department of Health
- U01 AG024904 NIA NIH HHS
- 108890/Z/15/Z Wellcome Trust
- 503480 Medical Research Council
- TURNER/OCT15/972-797 Motor Neurone Disease Association
- U01 AG032984 NIA NIH HHS
- R01 HL105756 NHLBI NIH HHS
- 082604/2/07/Z Wellcome Trust
- R01 AG033193 NIA NIH HHS
- National Health and Medical Research Council
- Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge
- Medical Research Council (UK)
- Economic and Social Research Council
- National Institute for Health Research (NIHR)
- the European Community’s Health Seventh Framework Programme
- Horizon 2020 Programme
- MND Association and the Wellcome Trust.
- European Research Council (ERC)
- EU Joint Programme – Neurodegenerative Disease Research ()
- EU Joint Programme - Neurodegenerative Disease Research (JPND)
- Australian Research Council
- Mater Foundation
- ForeFront - NHMRC
- Australian National Health and Medical Research Council
- University of Otago Research Grant, together with financial support from the Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd
- National Health and Medical Research Council and the Dementia Collaborative Research Centres program (DCRC2), as well as funding from the Science and Industry Endowment Fund (SIEF) and the Cooperative Research Centre (CRC) for Mental Health – funded throug
- EU Joint Programme - Neurodegenerative Disease Research (JPND), co-funded through the Australian National Health and Medical Research (NHMRC) Council, Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge,
- EU Joint Programme - Neurodegenerative Disease Research (JPND), United Kingdom Medical Research Council, Economic and Social Research Council, Motor Neuro Disease Association (GB), National Institute for Health Research (NIHR) Biomedical Research Centre at
- EU Joint Programme - Neurodegenerative Disease Research (JPND), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health, Unit
- National Health and Medical Research Council, Australian Research Council, Mater Foundation,
- Australian National Health and Medical Research Council (
- University of Otago Research Grant, Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd., National Health and Medical Research Counc
- EFPIA companies and SMEs as part of InnoMed (Innovative Medicines in Europe), an Integrated Project funded by the European Union of the Sixth Framework program
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Simon M Laws
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Costanza L Vallerga
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Internal Medicine, Erasmus MC, University Medical Center, 3015GD, Rotterdam, The Netherlands
| | | | - Ian P Blair
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - John B Kwok
- Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW, 2031, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, 2031, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ramona A J Zwamborn
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul J Hop
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Patrizia Mecocci
- Department of Medicine, Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | | | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, 3195, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, 6150, Australia
- Notre Dame University, Fremantle, WA, 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, 2139, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tim J Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Steven R Bentley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - John Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand
- School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - Javed Fowder
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Jacob Gratten
- Mater Research, Translational Research Institute, Brisbane, Australia
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Glenda Halliday
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian B Hickie
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Martin Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simon J G Lewis
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - John Pearson
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Toni L Pitcher
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Peter Silburn
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Cristopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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14
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Iacoangeli A, Fogh I, Selvackadunco S, Topp SD, Shatunov A, van Rheenen W, Al-Khleifat A, Opie-Martin S, Ratti A, Calvo A, Van Damme P, Robberecht W, Chio A, Dobson RJ, Hardiman O, Shaw CE, van den Berg LH, Andersen PM, Smith BN, Silani V, Veldink JH, Breen G, Troakes C, Al-Chalabi A, Jones AR. SCFD1 expression quantitative trait loci in amyotrophic lateral sclerosis are differentially expressed. Brain Commun 2021; 3:fcab236. [PMID: 34708205 PMCID: PMC8545614 DOI: 10.1093/braincomms/fcab236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/05/2021] [Accepted: 08/12/2021] [Indexed: 11/14/2022] Open
Abstract
Evidence indicates that common variants found in genome-wide association studies increase risk of disease through gene regulation via expression Quantitative Trait Loci. Using multiple genome-wide methods, we examined if Single Nucleotide Polymorphisms increase risk of Amyotrophic Lateral Sclerosis through expression Quantitative Trait Loci, and whether expression Quantitative Trait Loci expression is consistent across people who had Amyotrophic Lateral Sclerosis and those who did not. In combining public expression Quantitative Trait Loci data with Amyotrophic Lateral Sclerosis genome-wide association studies, we used Summary-data-based Mendelian Randomization to confirm that SCFD1 was the only gene that was genome-wide significant in mediating Amyotrophic Lateral Sclerosis risk via expression Quantitative Trait Loci (Summary-data-based Mendelian Randomization beta = 0.20, standard error = 0.04, P-value = 4.29 × 10-6). Using post-mortem motor cortex, we tested whether expression Quantitative Trait Loci showed significant differences in expression between Amyotrophic Lateral Sclerosis (n = 76) and controls (n = 25), genome-wide. Of 20 757 genes analysed, the two most significant expression Quantitative Trait Loci to show differential in expression between Amyotrophic Lateral Sclerosis and controls involve two known Amyotrophic Lateral Sclerosis genes (SCFD1 and VCP). Cis-acting SCFD1 expression Quantitative Trait Loci downstream of the gene showed significant differences in expression between Amyotrophic Lateral Sclerosis and controls (top expression Quantitative Trait Loci beta = 0.34, standard error = 0.063, P-value = 4.54 × 10-7). These SCFD1 expression Quantitative Trait Loci also significantly modified Amyotrophic Lateral Sclerosis survival (number of samples = 4265, hazard ratio = 1.11, 95% confidence interval = 1.05-1.17, P-value = 2.06 × 10-4) and act as an Amyotrophic Lateral Sclerosis trans-expression Quantitative Trait Loci hotspot for a wider network of genes enriched for SCFD1 function and Amyotrophic Lateral Sclerosis pathways. Using gene-set analyses, we found the genes that correlate with this trans-expression Quantitative Trait Loci hotspot significantly increase risk of Amyotrophic Lateral Sclerosis (beta = 0.247, standard deviation = 0.017, P = 0.001) and schizophrenia (beta = 0.263, standard deviation = 0.008, P-value = 1.18 × 10-5), a disease that genetically correlates with Amyotrophic Lateral Sclerosis. In summary, SCFD1 expression Quantitative Trait Loci are a major factor in Amyotrophic Lateral Sclerosis, not only influencing disease risk but are differentially expressed in post-mortem Amyotrophic Lateral Sclerosis. SCFD1 expression Quantitative Trait Loci show distinct expression profiles in Amyotrophic Lateral Sclerosis that correlate with a wider network of genes that also confer risk of the disease and modify the disease's duration.
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Affiliation(s)
- Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK.,Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Sashika Selvackadunco
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simon D Topp
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ahmad Al-Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Sarah Opie-Martin
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Antonia Ratti
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Andrea Calvo
- Department of Neuroscience 'Rita Levi Montalcini', ALS Centre, University of Turin, Torino, Italy.,Neuroscience Institute of Torino (NIT), University of Torino, Torino, Piemonte, Italy
| | | | - Philip Van Damme
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium.,Department of Neurosciences, Laboratory of Neurobiology, VIB Center for Brain and Disease Research, Leuven, Belgium
| | - Wim Robberecht
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Adriano Chio
- Department of Neuroscience 'Rita Levi Montalcini', ALS Centre, University of Turin, Torino, Italy.,Neuroscience Institute of Torino (NIT), University of Torino, Torino, Piemonte, Italy
| | - Richard J Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, University of Dublin Trinity College, Dublin, Ireland.,Department of Neurology, Beaumont Hospital, Dublin 9, Ireland
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Peter M Andersen
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
| | - Vincenzo Silani
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano, IRCCS, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy.,Aldo Ravelli Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Claire Troakes
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK.,Department of Neurology, King's College Hospital, London, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience King's College London, 5 Cutcombe Road, London SE5 9RT, UK
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15
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Opie-Martin S, Wootton RE, Budu-Aggrey A, Shatunov A, Jones AR, Iacoangeli A, Al Khleifat A, Davey-Smith G, Al-Chalabi A. Relationship between smoking and ALS: Mendelian randomisation interrogation of causality. J Neurol Neurosurg Psychiatry 2020; 91:1312-1315. [PMID: 32848012 DOI: 10.1136/jnnp-2020-323316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/29/2020] [Accepted: 05/10/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Smoking has been widely studied as a susceptibility factor for amyotrophic lateral sclerosis (ALS), but results are conflicting and at risk of confounding bias. We used the results of recently published large genome-wide association studies and Mendelian randomisation methods to reduce confounding to assess the relationship between smoking and ALS. METHODS Two genome-wide association studies investigating lifetime smoking (n=463 003) and ever smoking (n=1 232 091) were identified and used to define instrumental variables for smoking. A genome-wide association study of ALS (20 806 cases; 59 804 controls) was used as the outcome for inverse variance weighted Mendelian randomisation, and four other Mendelian randomisation methods, to test whether smoking is causal for ALS. Analyses were bidirectional to assess reverse causality. RESULTS There was no strong evidence for a causal or reverse causal relationship between smoking and ALS. The results of Mendelian randomisation using the inverse variance weighted method were: lifetime smoking OR 0.94 (95% CI 0.74 to 1.19), p value 0.59; ever smoking OR 1.10 (95% CI 1 to 1.23), p value 0.05. CONCLUSIONS Using multiple methods, large sample sizes and sensitivity analyses, we find no evidence with Mendelian randomisation techniques that smoking causes ALS. Other smoking phenotypes, such as current smoking, may be suitable for future Mendelian randomisation studies.
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Affiliation(s)
- Sarah Opie-Martin
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Robyn E Wootton
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.,School of Psychological Science, University of Bristol, Bristol, UK.,NIHR Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Ashley Budu-Aggrey
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - George Davey-Smith
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK .,Department of Neurology, King's College Hospital, London SE5 9RS, United Kingdom
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16
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Iacoangeli A, Lin T, Al Khleifat A, Jones AR, Opie-Martin S, Coleman JRI, Shatunov A, Sproviero W, Williams KL, Garton F, Restuadi R, Henders AK, Mather KA, Needham M, Mathers S, Nicholson GA, Rowe DB, Henderson R, McCombe PA, Pamphlett R, Blair IP, Schultz D, Sachdev PS, Newhouse SJ, Proitsi P, Fogh I, Ngo ST, Dobson RJB, Wray NR, Steyn FJ, Al-Chalabi A. Genome-wide Meta-analysis Finds the ACSL5-ZDHHC6 Locus Is Associated with ALS and Links Weight Loss to the Disease Genetics. Cell Rep 2020; 33:108323. [PMID: 33113361 PMCID: PMC7610013 DOI: 10.1016/j.celrep.2020.108323] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/28/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
We meta-analyze amyotrophic lateral sclerosis (ALS) genome-wide association study (GWAS) data of European and Chinese populations (84,694 individuals). We find an additional significant association between rs58854276 spanning ACSL5-ZDHHC6 with ALS (p = 8.3 × 10−9), with replication in an independent Australian cohort (1,502 individuals; p = 0.037). Moreover, B4GALNT1, G2E3-SCFD1, and TRIP11-ATXN3 are identified using a gene-based analysis. ACSL5 has been associated with rapid weight loss, as has another ALS-associated gene, GPX3. Weight loss is frequent in ALS patients and is associated with shorter survival. We investigate the effect of the ACSL5 and GPX3 single-nucleotide polymorphisms (SNPs), using longitudinal body composition and weight data of 77 patients and 77 controls. In patients’ fat-free mass, although not significant, we observe an effect in the expected direction (rs58854276: −2.1 ± 1.3 kg/A allele, p = 0.053; rs3828599: −1.0 ± 1.3 kg/A allele, p = 0.22). No effect was observed in controls. Our findings support the increasing interest in lipid metabolism in ALS and link the disease genetics to weight loss in patients. Cross-ethnic meta-analysis finds an association between the ACSL5-ZDHHC6 locus and ALS The ACSL5-ZDHHC6 association is replicated in an independent Australian cohort ACSL5-ZDHHC6 lead SNP is in ACSL5 and is an eQTL of ZDHHC6 in brain tissues ACSL5 SNPs might have an effect on fat-free mass in ALS patients
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Affiliation(s)
- Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, King's College London, London, UK; Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Sarah Opie-Martin
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Jonathan R I Coleman
- National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sidney NSW 2109, Australia
| | - Fleur Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine, University of New South Wales, Sydney NSW, Australia; Neuroscience Research Australia, Randwick NSW, Australia
| | - Merilee Needham
- Fiona Stanley Hospital, 11 Robin Warren Drive, Murdoch Perth WA 6150, Australia; Notre Dame University, 32 Mouat Street, Fremantle WA 6160, Australia; Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale VIC 3195, Australia
| | - Garth A Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney NSW 2139, Australia
| | - Dominic B Rowe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Robert Henderson
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney NSW, Australia
| | - Ian P Blair
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - David Schultz
- Flinders Medical Centre, Bedford Park SA 5042, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, UNSW Medicine, University of New South Wales, Sydney NSW, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Sydney NSW Australia
| | - Stephen J Newhouse
- Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Institute of Health Informatics, University College London, London, UK
| | - Petroula Proitsi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Shyuan T Ngo
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD, Australia
| | - Richard J B Dobson
- Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute for Health Research Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; Institute of Health Informatics, University College London, London, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Brisbane QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane QLD, Australia
| | - Frederik J Steyn
- Centre for Clinical Research, The University of Queensland, Brisbane QLD, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane QLD, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane QLD, Australia
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, London, UK; King's College Hospital, Bessemer Road, London SE5 9RS, UK
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17
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Jones AR, Tovée MJ, Cutler LR, Parkinson KN, Ells LJ, Araujo-Soares V, Pearce MS, Mann KD, Scott D, Harris JM, Adamson AJ. Development of the MapMe intervention body image scales of known weight status for 4-5 and 10-11 year old children. J Public Health (Oxf) 2019; 40:582-590. [PMID: 29190364 PMCID: PMC6266708 DOI: 10.1093/pubmed/fdx129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022] Open
Abstract
Background Parents tend to visually assess children to determine their weight status and typically underestimate child body size. A visual tool may aid parents to more accurately assess child weight status and so support strategies to reduce childhood overweight. Body image scales (BIS) are visual images of people ranging from underweight to overweight but none exist for children based on UK criteria. Our aim was to develop sex- and age-specific BIS for children, based on British growth reference (UK90) criteria. Methods BIS were developed using 3D surface body scans of children, their associated weight status using UK90 criteria from height and weight measurements, and qualitative work with parents and health professionals. Results Height, weight and 3D body scans were collected (211: 4–5 years; 177: 10–11 years). Overall, 12 qualitative sessions were held with 37 participants. Four BIS (4–5-year-old girls and boys, 10–11-year-old girls and boys) were developed. Conclusions This study has created the first sex- and age-specific BIS, based on UK90 criteria. The BIS have potential for use in child overweight prevention and management strategies, and in future research. This study also provides a protocol for the development of further BIS appropriate to other age groups and ethnicities.
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Affiliation(s)
- A R Jones
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - M J Tovée
- School of Psychology, University of Lincoln, Lincoln, UK.,Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - L R Cutler
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - K N Parkinson
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - L J Ells
- School of Health and Social Care, Health and Social Care Institute, Teesside University, Middlesbrough, UK
| | - V Araujo-Soares
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - M S Pearce
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - K D Mann
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - D Scott
- Department of Public Health and Wellbeing, Northumbria University, Newcastle upon Tyne, UK
| | - J M Harris
- School of Psychology and Neuroscience. University of St Andrews, Fife, UK
| | - A J Adamson
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
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18
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Iacoangeli A, Al Khleifat A, Jones AR, Sproviero W, Shatunov A, Opie-Martin S, Morrison KE, Shaw PJ, Shaw CE, Fogh I, Dobson RJ, Newhouse SJ, Al-Chalabi A. C9orf72 intermediate expansions of 24-30 repeats are associated with ALS. Acta Neuropathol Commun 2019; 7:115. [PMID: 31315673 PMCID: PMC6637621 DOI: 10.1186/s40478-019-0724-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
The expansion of a hexanucleotide repeat GGGGCC in C9orf72 is the most common known cause of ALS accounting for ~ 40% familial cases and ~ 7% sporadic cases in the European population. In most people, the repeat length is 2, but in people with ALS, hundreds to thousands of repeats may be observed. A small proportion of people have an intermediate expansion, of the order of 20 to 30 repeats in size, and it remains unknown whether intermediate expansions confer risk of ALS in the same way that massive expansions do. We investigated the association of this intermediate repeat with ALS by performing a meta-analysis of four previously published studies and a new British/Alzheimer's Disease Neuroimaging Initiative dataset of 1295 cases and 613 controls. The final dataset comprised 5071 cases and 3747 controls. Our meta-analysis showed association between ALS and intermediate C9orf72 repeats of 24 to 30 repeats in size (random-effects model OR = 4.2, 95% CI = 1.23-14.35, p-value = 0.02). Furthermore, we showed a different frequency of the repeat between the northern and southern European populations (Fisher's exact test p-value = 5 × 10- 3). Our findings provide evidence for the association between intermediate repeats and ALS (p-value = 2 × 10- 4) with direct relevance for research and clinical practice by showing that an expansion of 24 or more repeats should be considered pathogenic.
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19
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Chen Z, Chen JA, Shatunov A, Jones AR, Kravitz SN, Huang AY, Lawrence L, Lowe JK, Lewis CM, Payan CAM, Lieb W, Franke A, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Bensimon G, Leigh PN, Bronstein JM, Coppola G, Geschwind DH, Al-Chalabi A. Genome-wide survey of copy number variants finds MAPT duplications in progressive supranuclear palsy. Mov Disord 2019; 34:1049-1059. [PMID: 31059154 DOI: 10.1002/mds.27702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/01/2019] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Progressive supranuclear palsy is a neurodegenerative tauopathy manifesting clinically as a progressive akinetic-rigid syndrome. In this study, we sought to identify genetic variants influencing PSP susceptibility through a genome-wide association analysis of a cohort of well-characterized patients who had participated in the Neuroprotection and Natural History in Parkinson Plus Syndromes and Blood Brain Barrier in Parkinson Plus Syndromes studies. METHODS We genotyped single-nucleotide polymorphisms in 283 PSP cases from the United Kingdom, Germany, and France and compared these with genotypes from 4472 controls. Copy number variants were identified from genotyping data. RESULTS We observed associations on chromosome 17 within or close to the MAPT gene and explored the genetic architecture at this locus. We confirmed the previously reported association of rs1768208 in the MOBP gene (P = 3.29 × 10-13 ) and rs1411478 in STX6 (P = 3.45 × 10-10 ). The population-attributable risk from the MAPT, MOBP, and STX6 single-nucleotide polymorphisms was found to be 0.37, 0.26, and 0.08, respectively. In addition, we found 2 instances of copy number variants spanning the MAPT gene in patients with PSP. These copy number variants include tau but few other genes within the chromosome 17 haplotype region, providing additional support for the direct pathogenicity of MAPT in PSP. CONCLUSIONS Clinicians should also be aware of MAPT duplication as a possible genetic cause of PSP, especially in patients presenting with young age at onset. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Zhongbo Chen
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Jason A Chen
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Stephanie N Kravitz
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Lauren Lawrence
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts Universitat zu Kiel, Kiel, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and Molecular Determinants of Aging Diseases, Labex-Distalz, Lille, France
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Jean-François Dartigues
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, UMR-1219, CHU Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpétrière, Assistance Publique Hôpitaux de Paris, Paris; Pharmacologie, Universités Paris-Sorbonne, UPMC Paris 06, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Jeff M Bronstein
- Program in Movement Disorders, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Center for Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, UK
- Department of Human Genetics, University of California, Los Angeles, California, USA
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
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20
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Iacoangeli A, Al Khleifat A, Sproviero W, Shatunov A, Jones AR, Opie-Martin S, Naselli E, Topp SD, Fogh I, Hodges A, Dobson RJ, Newhouse SJ, Al-Chalabi A. ALSgeneScanner: a pipeline for the analysis and interpretation of DNA sequencing data of ALS patients. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:207-215. [PMID: 30835568 PMCID: PMC6567555 DOI: 10.1080/21678421.2018.1562553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/13/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS, MND) is a neurodegenerative disease of upper and lower motor neurons resulting in death from neuromuscular respiratory failure, typically within two years of first symptoms. Genetic factors are an important cause of ALS, with variants in more than 25 genes having strong evidence, and weaker evidence available for variants in more than 120 genes. With the increasing availability of next-generation sequencing data, non-specialists, including health care professionals and patients, are obtaining their genomic information without a corresponding ability to analyze and interpret it. Furthermore, the relevance of novel or existing variants in ALS genes is not always apparent. Here we present ALSgeneScanner, a tool that is easy to install and use, able to provide an automatic, detailed, annotated report, on a list of ALS genes from whole-genome sequencing (WGS) data in a few hours and whole exome sequence data in about 1 h on a readily available mid-range computer. This will be of value to non-specialists and aid in the interpretation of the relevance of novel and existing variants identified in DNA sequencing data.
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Affiliation(s)
- Alfredo Iacoangeli
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King’s College London, London, UK
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Ersilia Naselli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Simon D. Topp
- UK Dementia Research Institute, King’s College London, London, UK
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico, Milan, Italy
| | - Angela Hodges
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Richard J. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King’s College London, London, UK
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust, King’s College London, London, UK
| | - Stephen J. Newhouse
- Department of Biostatistics and Health Informatics, Institute of Psychiatry Psychology and Neuroscience, King’s College London, London, UK
- Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
- National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust, King’s College London, London, UK
| | - Ammar Al-Chalabi
- UK Dementia Research Institute, King’s College London, London, UK
- Department of Neurology, King’s College Hospital, London, UK
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21
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Iacoangeli A, Al Khleifat A, Sproviero W, Shatunov A, Jones AR, Morgan SL, Pittman A, Dobson RJ, Newhouse SJ, Al-Chalabi A. DNAscan: personal computer compatible NGS analysis, annotation and visualisation. BMC Bioinformatics 2019; 20:213. [PMID: 31029080 PMCID: PMC6487045 DOI: 10.1186/s12859-019-2791-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step. RESULTS We have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub. CONCLUSIONS DNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available.
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Affiliation(s)
- A Iacoangeli
- Department of Biostatistics and Health Informatics, King's College London, London, UK. .,Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.
| | - A Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - W Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - A Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - A R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - S L Morgan
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - A Pittman
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - R J Dobson
- Department of Biostatistics and Health Informatics, King's College London, London, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - S J Newhouse
- Department of Biostatistics and Health Informatics, King's College London, London, UK.,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK.,National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - A Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK.,King's College Hospital, Bessemer Road, London, SE5 9RS, UK
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22
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Gowland A, Opie-Martin S, Scott KM, Jones AR, Mehta PR, Batts CJ, Ellis CM, Leigh PN, Shaw CE, Sreedharan J, Al-Chalabi A. Predicting the future of ALS: the impact of demographic change and potential new treatments on the prevalence of ALS in the United Kingdom, 2020-2116. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:264-274. [PMID: 30961394 PMCID: PMC6567553 DOI: 10.1080/21678421.2019.1587629] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Objective: To model the effects of demographic change under various scenarios of possible future treatment developments in ALS. Methods: Patients diagnosed with ALS at the King’s College Hospital Motor Nerve Clinic between 2004 and 2017, and living within the London boroughs of Lambeth, Southwark, and Lewisham (LSL), were included as incident cases. We also ascertained incident cases from the Canterbury region over the same period. Future incidence of ALS was estimated by applying the calculated age- and sex-specific incidence rates to the UK population projections from 2020 to 2116. The number of prevalent cases for each future year was estimated based on an established method. Assuming constant incidence, we modelled four possible future prevalence scenarios by altering the median disease duration for varying subsets of the population, to represent the impact of new treatments. Results: The total number of people newly diagnosed with ALS per year in the UK is projected to rise from a baseline of 1415 UK cases in 2010 to 1701 in 2020 and 2635 in 2116. Overall prevalence of ALS was predicted to increase from 8.58 per 100,000 persons in 2020 to 9.67 per 100,000 persons in 2116. Halting disease progression in patients with C9orf72 mutations would yield the greatest impact of the modelled treatment scenarios, increasing prevalence in the year 2066 from a baseline of 9.50 per 100,000 persons to 15.68 per 100,000 persons. Conclusions: Future developments in treatment would combine with the effects of demographic change to result in more people living longer with ALS.
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Affiliation(s)
- Alison Gowland
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK
| | - Sarah Opie-Martin
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK
| | - Kirsten M Scott
- b Department of Clinical Neuroscience , University of Cambridge , Cambridge , UK
| | - Ashley R Jones
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK
| | - Puja R Mehta
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK.,c King's College Hospital , London , UK
| | - Christine J Batts
- d Kent and Canterbury Hospital , East Kent Hospital NHS University Foundation Trust , Canterbury , UK
| | | | - P Nigel Leigh
- e Department of Neuroscience, Brighton and Sussex Medical School , Trafford Centre for Biomedical Research, University of Sussex , Brighton , UK , and
| | - Christopher E Shaw
- f United Kingdom Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience , King's College London , London , UK
| | - Jemeen Sreedharan
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK
| | - Ammar Al-Chalabi
- a Department of Basic and Clinical Neuroscience , King's College London, Maurice Wohl Clinical Neuroscience Institute , London , UK.,c King's College Hospital , London , UK
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23
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Al Khleifat A, Iacoangeli A, Shatunov A, Fang T, Sproviero W, Jones AR, Opie-Martin S, Morrison KE, Shaw PJ, Shaw CE, Powell JF, Dobson R, Newhouse SJ, Al-Chalabi A. Telomere length is greater in ALS than in controls: a whole genome sequencing study. Amyotroph Lateral Scler Frontotemporal Degener 2019; 20:229-234. [PMID: 30931641 PMCID: PMC6567548 DOI: 10.1080/21678421.2019.1586951] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background: Amyotrophic lateral sclerosis is a neurodegenerative disease of motor neurons resulting in progressive paralysis and death, typically within 3-5 years. Although the heritability of ALS is about 60%, only about 11% is explained by common gene variants, suggesting that other forms of genetic variation are important. Telomeres maintain DNA integrity during cellular replication and shorten naturally with age. Gender and age are risk factors for ALS and also associated with telomere length. We therefore investigated telomere length in ALS. Methods: We estimated telomere length by applying a bioinformatics analysis to whole genome sequence data of leukocyte-derived DNA from people with ALS and age and gender-matched matched controls in a UK population. We tested the association of telomere length with ALS and ALS survival. Results: There were 1241 people with ALS and 335 controls. The median age for ALS was 62.5 years and for controls, 60.1 years, with a male-female ratio of 62:38. Accounting for age and sex, there was a 9% increase of telomere length in ALS compared to matched controls. Those with longer telomeres had a 16% increase in median survival. Of nine SNPs associated with telomere length, two were also associated with ALS: rs8105767 near the ZNF208 gene (p = 1.29 × 10-4) and rs6772228 (p = 0.001), which is in an intron for the PXK gene. Conclusions: Longer telomeres in leukocyte-derived DNA are associated with ALS, and with increased survival in those with ALS.
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Affiliation(s)
- Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK; ,Department of Biostatistics and Health Informatics, King’s College London, London, UK;
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Ton Fang
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Karen E. Morrison
- Faculty of Medicine, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK;
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK;
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK; ,King’s College Hospital, London, UK; ,Psychology and Neuroscience, United Kingdom Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, King’s College London, London, UK, and;
| | - John F. Powell
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK;
| | - Richard Dobson
- Department of Biostatistics and Health Informatics, King’s College London, London, UK; ,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Steven J. Newhouse
- Department of Biostatistics and Health Informatics, King’s College London, London, UK; ,Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London, UK; ,King’s College Hospital, London, UK; ,Correspondence: Ammar Al-Chalabi, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Road, LondonSE5 9RX, UK. Tel:+44 2078485192, +44 2078485190. E-mail:
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24
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Mehta PR, Jones AR, Opie-Martin S, Shatunov A, Iacoangeli A, Al Khleifat A, Smith BN, Topp S, Morrison KE, Shaw PJ, Shaw CE, Morgan S, Pittman A, Al-Chalabi A. Younger age of onset in familial amyotrophic lateral sclerosis is a result of pathogenic gene variants, rather than ascertainment bias. J Neurol Neurosurg Psychiatry 2019; 90:268-271. [PMID: 30270202 PMCID: PMC6518463 DOI: 10.1136/jnnp-2018-319089] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/31/2018] [Accepted: 08/18/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disease of motor neurons with a median survival of 2 years. Familial ALS has a younger age of onset than apparently sporadic ALS. We sought to determine whether this younger age of onset is a result of ascertainment bias or has a genetic basis. METHODS Samples from people with ALS were sequenced for 13 ALS genes. To determine the effect of genetic variation, age of onset was compared in people with sporadic ALS carrying a pathogenic gene variant and those who do not; to determine the effect of family history, we compared those with genetic sporadic ALS and familial ALS. RESULTS There were 941 people with a diagnosis of ALS, 100 with familial ALS. Of 841 with apparently sporadic ALS, 95 carried a pathogenic gene variant. The mean age of onset in familial ALS was 5.3 years younger than for apparently sporadic ALS (p=6.0×10-5, 95% CI 2.8 to 7.8 years). The mean age of onset of genetic sporadic ALS was 2.9 years younger than non-genetic sporadic ALS (p=0.011, 95% CI 0.7 to 5.2 years). There was no difference between the mean age of onset in genetic sporadic ALS and familial ALS (p=0.097). CONCLUSIONS People with familial ALS have an age of onset about 5 years younger than those with apparently sporadic ALS, and we have shown that this is a result of Mendelian gene variants lowering the age of onset, rather than ascertainment bias.
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Affiliation(s)
- Puja R Mehta
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Neurology, King's College Hospital, Denmark Hill, London, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sarah Opie-Martin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Karen E Morrison
- Faculty of Medicine, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Christopher E Shaw
- Department of Neurology, King's College Hospital, Denmark Hill, London, UK
- Institute of Psychiatry, Psychology and Neuroscience, UK Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Sarah Morgan
- Department of Molecular Neuroscience, Institute of Neurology, UCL, Queen Square, London, UK
| | - Alan Pittman
- Department of Molecular Neuroscience, Institute of Neurology, UCL, Queen Square, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
- Department of Neurology, King's College Hospital, Denmark Hill, London, UK
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25
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Chen JA, Chen Z, Won H, Huang AY, Lowe JK, Wojta K, Yokoyama JS, Bensimon G, Leigh PN, Payan C, Shatunov A, Jones AR, Lewis CM, Deloukas P, Amouyel P, Tzourio C, Dartigues JF, Ludolph A, Boxer AL, Bronstein JM, Al-Chalabi A, Geschwind DH, Coppola G. Joint genome-wide association study of progressive supranuclear palsy identifies novel susceptibility loci and genetic correlation to neurodegenerative diseases. Mol Neurodegener 2018; 13:41. [PMID: 30089514 PMCID: PMC6083608 DOI: 10.1186/s13024-018-0270-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/29/2018] [Indexed: 11/21/2022] Open
Abstract
Background Progressive supranuclear palsy (PSP) is a rare neurodegenerative disease for which the genetic contribution is incompletely understood. Methods We conducted a joint analysis of 5,523,934 imputed SNPs in two newly-genotyped progressive supranuclear palsy cohorts, primarily derived from two clinical trials (Allon davunetide and NNIPPS riluzole trials in PSP) and a previously published genome-wide association study (GWAS), in total comprising 1646 cases and 10,662 controls of European ancestry. Results We identified 5 associated loci at a genome-wide significance threshold P < 5 × 10− 8, including replication of 3 loci from previous studies and 2 novel loci at 6p21.1 and 12p12.1 (near RUNX2 and SLCO1A2, respectively). At the 17q21.31 locus, stepwise regression analysis confirmed the presence of multiple independent loci (localized near MAPT and KANSL1). An additional 4 loci were highly suggestive of association (P < 1 × 10− 6). We analyzed the genetic correlation with multiple neurodegenerative diseases, and found that PSP had shared polygenic heritability with Parkinson’s disease and amyotrophic lateral sclerosis. Conclusions In total, we identified 6 additional significant or suggestive SNP associations with PSP, and discovered genetic overlap with other neurodegenerative diseases. These findings clarify the pathogenesis and genetic architecture of PSP. Electronic supplementary material The online version of this article (10.1186/s13024-018-0270-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason A Chen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA
| | - Zhongbo Chen
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Hyejung Won
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Alden Y Huang
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA
| | - Jennifer K Lowe
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Kevin Wojta
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Gilbert Bensimon
- BESPIM, CHU-Nîmes, Nîmes, France.,Dept Pharmacologie Clinique, Pitié-Salpêtrière Hospital, AP-PH, Paris, France.,Pharmacology UPMC-Paris VI, Universite Paris-Sorbonne, Paris, France
| | - P Nigel Leigh
- Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton, UK
| | - Christine Payan
- BESPIM, CHU-Nîmes, Nîmes, France.,Dept Pharmacologie Clinique, Pitié-Salpêtrière Hospital, AP-PH, Paris, France
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Cathryn M Lewis
- Medical Research Council Social, Genetic and Developmental Psychiatry Centre, and Department of Medical and Molecular Genetics, King's College London, London, SE5 8AF, UK
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factor and molecular determinants of aging diseases, Labex-Distalz, F-59000, Lille, France
| | - Christophe Tzourio
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, F-33000 Bordeaux, France
| | - Jean-Francois Dartigues
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, CHU Bordeaux, F-33000 Bordeaux, France
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Oberer Eselsberg, Ulm, Germany
| | - Adam L Boxer
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Jeff M Bronstein
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, SE5 9RX, UK
| | - Daniel H Geschwind
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.,Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Giovanni Coppola
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA. .,Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA. .,Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA. .,Departments of Psychiatry and Neurology, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E Young Dr. South, Gonda Bldg, Rm 1524, Los Angeles, CA, 90095, USA.
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Jones AR, Aspinall MD, Joyce MJ. A remotely triggered fast neutron detection instrument based on a plastic organic scintillator. Rev Sci Instrum 2018; 89:023115. [PMID: 29495805 DOI: 10.1063/1.5012121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A detector system for the characterization of radiation fields of both fast neutrons and γ rays is described comprising of a gated photomultiplier tube (PMT), an EJ299-33 solid organic scintillator detector, and an external trigger circuit. The objective of this development was to conceive a means by which the PMT in such a system can be actuated remotely during the high-intensity bursts of pulsed γ-ray contamination that can arise during active interrogation procedures. The system is used to detect neutrons and γ rays using established pulse-shape discrimination (PSD) techniques. The gating circuit enables the PMT to be switched off remotely. This is compatible with use during intense radiation transients to avoid saturation and the disruption of the operation of the PMT during the burst. Data are presented in the form of pulse-height spectra and PSD scatter plots for the system triggered with a strobed light source. These confirm that the gain of the system and the throughput for both triggered and un-triggered scenarios are as expected, given the duty cycle of the stimulating radiation. This demonstrates that the triggering function does not perturb the system response of the detector.
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Affiliation(s)
- A R Jones
- Engineering Department, Lancaster University, Lancaster, United Kingdom
| | - M D Aspinall
- Engineering Department, Lancaster University, Lancaster, United Kingdom
| | - M J Joyce
- Engineering Department, Lancaster University, Lancaster, United Kingdom
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27
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Aspinall MD, Jones AR. Modeling Photo-multiplier Gain and Regenerating Pulse Height Data for Application Development. EPJ Web Conf 2018. [DOI: 10.1051/epjconf/201817007001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Systems that adopt organic scintillation detector arrays often require a calibration process prior to the intended measurement campaign to correct for significant performance variances between detectors within the array. These differences exist because of low tolerances associated with photo-multiplier tube technology and environmental influences. Differences in detector response can be corrected for by adjusting the supplied photo-multiplier tube voltage to control its gain and the effect that this has on the pulse height spectra from a gamma-only calibration source with a defined photo-peak. Automated methods that analyze these spectra and adjust the photo-multiplier tube bias accordingly are emerging for hardware that integrate acquisition electronics and high voltage control. However, development of such algorithms require access to the hardware, multiple detectors and calibration source for prolonged periods, all with associated constraints and risks. In this work, we report on a software function and related models developed to rescale and regenerate pulse height data acquired from a single scintillation detector. Such a function could be used to generate significant and varied pulse height data that can be used to integration-test algorithms that are capable of automatically response matching multiple detectors using pulse height spectra analysis. Furthermore, a function of this sort removes the dependence on multiple detectors, digital analyzers and calibration source. Results show a good match between the real and regenerated pulse height data. The function has also been used successfully to develop auto-calibration algorithms.
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28
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van Eijk RPA, Jones AR, Sproviero W, Shatunov A, Shaw PJ, Leigh PN, Young CA, Shaw CE, Mora G, Mandrioli J, Borghero G, Volanti P, Diekstra FP, van Rheenen W, Verstraete E, Eijkemans MJC, Veldink JH, Chio A, Al-Chalabi A, van den Berg LH, van Es MA. Meta-analysis of pharmacogenetic interactions in amyotrophic lateral sclerosis clinical trials. Neurology 2017; 89:1915-1922. [PMID: 28978660 PMCID: PMC5664299 DOI: 10.1212/wnl.0000000000004606] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE To assess whether genetic subgroups in recent amyotrophic lateral sclerosis (ALS) trials responded to treatment with lithium carbonate, but that the treatment effect was lost in a large cohort of nonresponders. METHODS Individual participant data were obtained from 3 randomized trials investigating the efficacy of lithium carbonate. We matched clinical data with data regarding the UNC13A and C9orf72 genotype. Our primary outcome was survival at 12 months. On an exploratory basis, we assessed whether the effect of lithium depended on the genotype. RESULTS Clinical data were available for 518 of the 606 participants. Overall, treatment with lithium carbonate did not improve 12-month survival (hazard ratio [HR] 1.0, 95% confidence interval [CI] 0.7-1.4; p = 0.96). Both the UNC13A and C9orf72 genotype were independent predictors of survival (HR 2.4, 95% CI 1.3-4.3; p = 0.006 and HR 2.5, 95% CI 1.1-5.2; p = 0.032, respectively). The effect of lithium was different for UNC13A carriers (p = 0.027), but not for C9orf72 carriers (p = 0.22). The 12-month survival probability for UNC13A carriers treated with lithium carbonate improved from 40.1% (95% CI 23.2-69.1) to 69.7% (95% CI 50.4-96.3). CONCLUSIONS This study incorporated genetic data into past ALS trials to determine treatment effects in a genetic post hoc analysis. Our results suggest that we should reorient our strategies toward finding treatments for ALS, start focusing on genotype-targeted treatments, and standardize genotyping in order to optimize randomization and analysis for future clinical trials.
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Affiliation(s)
- Ruben P A van Eijk
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Ashley R Jones
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - William Sproviero
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Aleksey Shatunov
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Pamela J Shaw
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - P Nigel Leigh
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Carolyn A Young
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Christopher E Shaw
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Gabriele Mora
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Jessica Mandrioli
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Giuseppe Borghero
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Paolo Volanti
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Frank P Diekstra
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Wouter van Rheenen
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Esther Verstraete
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Marinus J C Eijkemans
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Jan H Veldink
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Adriano Chio
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Ammar Al-Chalabi
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy.
| | - Leonard H van den Berg
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy
| | - Michael A van Es
- From the Department of Neurology, Brain Centre Rudolf Magnus (R.P.A.v.E., F.P.D., W.v.R., J.H.V., L.H.v.d.B., M.A.v.E.), and Department of Biostatistics and Research Support (M.J.C.E.), University Medical Centre Utrecht, the Netherlands; Maurice Wohl Clinical Neuroscience Institute and United Kingdom Dementia Research Institute Centre (A.R.J., W.S., A.S., C.E.S., A.A.-C.), Department of Basic and Clinical Neuroscience, King's College London; Sheffield Institute for Translational Neuroscience (SITraN) (P.J.S.), University of Sheffield, South Yorkshire; Department of Clinical Neuroscience (P.N.L.), Trafford Centre for Biomedical Research, Brighton and Sussex Medical School, Falmer, Brighton; The Walton Centre NHS Trust (C.A.Y.), Liverpool, UK; Istituti Clinici Scientifici Maugeri IRCSS (G.M.), Milan; Department of Neuroscience (J.M.), Sant'Agostino-Estense Hospital and University of Modena and Reggio Emilia, Modena; Department of Neurology (G.B.), Azienda Universitario Ospedaliera di Cagliari and University of Cagliari; Istituti Clinici Scientifici Maugeri IRCSS (P.V.), Mistretta, Italy; Rijnstate Ziekenhuis (E.V.), Arnhem, the Netherlands; Rita Levi Montalcini' Department of Neuroscience (A.C.), ALS Centre, University of Torino; and Azienda Ospedaliera Città della Salute e della Scienza (A.C.), Turin, Italy.
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Morgan S, Shatunov A, Sproviero W, Jones AR, Shoai M, Hughes D, Al Khleifat A, Malaspina A, Morrison KE, Shaw PJ, Shaw CE, Sidle K, Orrell RW, Fratta P, Hardy J, Pittman A, Al-Chalabi A. A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK. Brain 2017; 140:1611-1618. [PMID: 28430856 PMCID: PMC5445258 DOI: 10.1093/brain/awx082] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/18/2017] [Accepted: 02/05/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis is a progressive neurodegenerative disease of motor neurons. About 25 genes have been verified as relevant to the disease process, with rare and common variation implicated. We used next generation sequencing and repeat sizing to comprehensively assay genetic variation in a panel of known amyotrophic lateral sclerosis genes in 1126 patient samples and 613 controls. About 10% of patients were predicted to carry a pathological expansion of the C9orf72 gene. We found an increased burden of rare variants in patients within the untranslated regions of known disease-causing genes, driven by SOD1, TARDBP, FUS, VCP, OPTN and UBQLN2. We found 11 patients (1%) carried more than one pathogenic variant (P = 0.001) consistent with an oligogenic basis of amyotrophic lateral sclerosis. These findings show that the genetic architecture of amyotrophic lateral sclerosis is complex and that variation in the regulatory regions of associated genes may be important in disease pathogenesis.
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Affiliation(s)
- Sarah Morgan
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
| | - William Sproviero
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
| | - Maryam Shoai
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Deborah Hughes
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, North-East London and Essex Regional Motor Neuron Disease Care Centre, London, E1 2AT, UK
| | - Karen E. Morrison
- Faculty of Medicine, University of Southampton, MP801 University Hospital Southampton NHS Foundation Trust, SO16 6YD, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SiTraN), University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
| | - Katie Sidle
- Department of Clinical Neuroscience, UCL Institute of Neurology, Rowland Hill Street, London, NW3 2PF, UK
| | - Richard W. Orrell
- Department of Clinical Neuroscience, UCL Institute of Neurology, Rowland Hill Street, London, NW3 2PF, UK
| | - Pietro Fratta
- Department of Neurodegenerative Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Alan Pittman
- Department of Molecular Neuroscience, UCL, Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, SE5 9RX, UK
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30
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Parkinson KN, Reilly JJ, Basterfield L, Reilly JK, Janssen X, Jones AR, Cutler LR, Le Couteur A, Adamson AJ. Mothers' perceptions of child weight status and the subsequent weight gain of their children: a population-based longitudinal study. Int J Obes (Lond) 2017; 41:801-806. [PMID: 28119532 PMCID: PMC5418556 DOI: 10.1038/ijo.2017.20] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/14/2017] [Accepted: 01/11/2017] [Indexed: 11/09/2022]
Abstract
BACKGROUND There is a plethora of cross-sectional work on maternal perceptions of child weight status showing that mothers typically do not classify their overweight child as being overweight according to commonly used clinical criteria. Awareness of overweight in their child is regarded as an important prerequisite for mothers to initiate appropriate action. The gap in the literature is determining whether, if mothers do classify their overweight child's weight status correctly, this is associated with a positive outcome for the child's body mass index (BMI) at a later stage. OBJECTIVE To explore longitudinal perceptions of child weight status from mothers of a contemporary population-based birth cohort (Gateshead Millennium Study) and relationships of these perceptions with future child weight gain. METHODS Data collected in the same cohort at 7, 12 and 15 years of age: mothers' responses to two items concerning their child's body size; child's and mother's BMI; pubertal maturation; demographic information. RESULTS Mothers' perceptions of whether their child was overweight did not change markedly over time. Child BMI was the only significant predictor of mothers' classification of overweight status, and it was only at the extreme end of the overweight range and in the obese range that mothers reliably described their child as overweight. Even when mothers did appropriately classify their child as overweight at an earlier stage, this was not related to relatively lower child BMI a few years later. CONCLUSIONS Mothers tend to classify their child as overweight in only more extreme cases. It is an important finding that no beneficial impact was shown on later child BMI in overweight children whose mothers classified their child's weight status as overweight at an earlier stage.
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Affiliation(s)
- K N Parkinson
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - J J Reilly
- Physical Activity for Health Group, School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - L Basterfield
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - J K Reilly
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - X Janssen
- Physical Activity for Health Group, School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - A R Jones
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - L R Cutler
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - A Le Couteur
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Northumberland, Tyne and Wear NHS Foundation Trust, Newcastle upon Tyne, UK
| | - A J Adamson
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
- Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
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Sproviero W, Shatunov A, Stahl D, Shoai M, van Rheenen W, Jones AR, Al-Sarraj S, Andersen PM, Bonini NM, Conforti FL, Van Damme P, Daoud H, Del Mar Amador M, Fogh I, Forzan M, Gaastra B, Gellera C, Gitler AD, Hardy J, Fratta P, La Bella V, Le Ber I, Van Langenhove T, Lattante S, Lee YC, Malaspina A, Meininger V, Millecamps S, Orrell R, Rademakers R, Robberecht W, Rouleau G, Ross OA, Salachas F, Sidle K, Smith BN, Soong BW, Sorarù G, Stevanin G, Kabashi E, Troakes C, van Broeckhoven C, Veldink JH, van den Berg LH, Shaw CE, Powell JF, Al-Chalabi A. ATXN2 trinucleotide repeat length correlates with risk of ALS. Neurobiol Aging 2017; 51:178.e1-178.e9. [PMID: 28017481 PMCID: PMC5302215 DOI: 10.1016/j.neurobiolaging.2016.11.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/13/2022]
Abstract
We investigated a CAG trinucleotide repeat expansion in the ATXN2 gene in amyotrophic lateral sclerosis (ALS). Two new case-control studies, a British dataset of 1474 ALS cases and 567 controls, and a Dutch dataset of 1328 ALS cases and 691 controls were analyzed. In addition, to increase power, we systematically searched PubMed for case-control studies published after 1 August 2010 that investigated the association between ATXN2 intermediate repeats and ALS. We conducted a meta-analysis of the new and existing studies for the relative risks of ATXN2 intermediate repeat alleles of between 24 and 34 CAG trinucleotide repeats and ALS. There was an overall increased risk of ALS for those carrying intermediate sized trinucleotide repeat alleles (odds ratio 3.06 [95% confidence interval 2.37-3.94]; p = 6 × 10-18), with an exponential relationship between repeat length and ALS risk for alleles of 29-32 repeats (R2 = 0.91, p = 0.0002). No relationship was seen for repeat length and age of onset or survival. In contrast to trinucleotide repeat diseases, intermediate ATXN2 trinucleotide repeat expansion in ALS does not predict age of onset but does predict disease risk.
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Affiliation(s)
- William Sproviero
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Daniel Stahl
- Department of Biostatistics, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Maryam Shoai
- Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Safa Al-Sarraj
- Department of Clinical Neuropathology, King's College Hospital NHS Foundation Trust, London, UK
| | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Philip Van Damme
- Neurology Department, University Hospitals Leuven, Leuven, Belgium; Vesalius Research Center, VIB, Leuven, Belgium; Disease (LIND), KU Leuven - University of Leuven, Leuven, Belgium
| | - Hussein Daoud
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Maria Del Mar Amador
- Department of Nervous System Diseases, ALS Paris ALS Center for Rare Diseases, Groupe Hospitalier Pitié Salpêtrière, APHP, Paris, France
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Monica Forzan
- Clinical Genetics Unit, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Ben Gaastra
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Cinzia Gellera
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - John Hardy
- Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Pietro Fratta
- Sobell Department of Motor Neuroscience and Movement Disorders, University College London (UCL) Institute of Neurology, London, UK
| | - Vincenzo La Bella
- ALS Clinical Research Center, Bio. Ne. C., University of Palermo, Palermo, Italy
| | - Isabelle Le Ber
- Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France; AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Centre de Référence des Démences Rares, Departement de Neurologie, Paris, France
| | - Tim Van Langenhove
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Insititute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Edegem, Belgium
| | - Serena Lattante
- Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Andrea Malaspina
- North-East London and Essex MND Care Centre - Neuroscience and Trauma Centre, Blizard, Institute of Cell and Molecular Medicine, Barts & the London School of Medicine & Dentistry, Barts Health NHS Trust, London, UK
| | - Vincent Meininger
- Hôpital de la Pitié-Salpêtrière, institut de recherche translationnelle en neurosciences (A-ICM), Paris, France; Hôpital de la Pitié-Salpêtrière, réseau SLA IdF, Paris, France
| | - Stéphanie Millecamps
- Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France
| | - Richard Orrell
- Department of Clinical Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Wim Robberecht
- Vesalius Research Center, VIB, Leuven, Belgium; Disease (LIND), KU Leuven - University of Leuven, Leuven, Belgium
| | - Guy Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Francois Salachas
- Department of Nervous System Diseases, ALS Paris ALS Center for Rare Diseases, Groupe Hospitalier Pitié Salpêtrière, APHP, Paris, France; Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France
| | - Katie Sidle
- Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Bing-Wen Soong
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan; Department of Neurology, National Yang-Ming University School of Medicine, Taipei, Taiwan; Brain Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Giovanni Stevanin
- Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France; Neurogenetics team, Ecole Pratique des Hautes Etudes, Paris, France
| | - Edor Kabashi
- Institut du Cerveau et de la Moelle épinière (ICM), Inserm U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMRS1127, Paris, France
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Christine van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Insititute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - John F Powell
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
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Meakin AS, Saif Z, Jones AR, Aviles PFV, Clifton VL. Review: Placental adaptations to the presence of maternal asthma during pregnancy. Placenta 2017; 54:17-23. [PMID: 28131319 DOI: 10.1016/j.placenta.2017.01.123] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/10/2017] [Accepted: 01/20/2017] [Indexed: 12/19/2022]
Abstract
Asthma is a highly prevalent chronic medical condition affecting an estimated 12% of pregnant, women each year, with prevalence of asthma greatest (up to 16%) among the socially disadvantaged. Maternal asthma is associated with significant perinatal morbidity and mortality including preterm births, neonatal hospitalisations and low birthweight outcomes each year. We have identified that the placenta adapts to the presence of chronic, maternal asthma during pregnancy in a sex specific manner that may confer sex differences in fetal outcome. The male fetus was at greater risk of a poor outcome than a female fetus in the presence of maternal asthma and an acute inflammatory event such as an asthma exacerbation. This review will examine the role of sex specific differences in placental function on fetal growth and survival.
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Affiliation(s)
- A S Meakin
- Mater Medical Research Institute, University of Queensland, Brisbane, Australia
| | - Z Saif
- Mater Medical Research Institute, University of Queensland, Brisbane, Australia
| | - A R Jones
- Mater Medical Research Institute, University of Queensland, Brisbane, Australia
| | | | - V L Clifton
- Mater Medical Research Institute, University of Queensland, Brisbane, Australia.
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Gaastra B, Shatunov A, Pulit S, Jones AR, Sproviero W, Gillett A, Chen Z, Kirby J, Fogh I, Powell JF, Leigh PN, Morrison KE, Shaw PJ, Shaw CE, van den Berg LH, Veldink JH, Lewis CM, Al-Chalabi A. Rare genetic variation in UNC13A may modify survival in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2016; 17:593-599. [PMID: 27584932 PMCID: PMC5125285 DOI: 10.1080/21678421.2016.1213852] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 12/13/2022]
Abstract
Our objective was to identify whether rare genetic variation in amyotrophic lateral sclerosis (ALS) candidate survival genes modifies ALS survival. Candidate genes were selected based on evidence for modifying ALS survival. Each tail of the extreme 1.5% of survival was selected from the UK MND DNA Bank and all samples available underwent whole genome sequencing. A replication set from the Netherlands was used for validation. Sequences of candidate survival genes were extracted and variants passing quality control with a minor allele frequency ≤0.05 were selected for association testing. Analysis was by burden testing using SKAT. Candidate survival genes UNC13A, KIFAP3, and EPHA4 were tested for association in a UK sample comprising 25 short survivors and 25 long survivors. Results showed that only SNVs in UNC13A were associated with survival (p = 6.57 × 10-3). SNV rs10419420:G > A was found exclusively in long survivors (3/25) and rs4808092:G > A exclusively in short survivors (4/25). These findings were not replicated in a Dutch sample. In conclusion, population specific rare variants of UNC13A may modulate survival in ALS.
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Affiliation(s)
- Benjamin Gaastra
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - Sara Pulit
- University Medical Centre Utrecht,
Utrecht,
The Netherlands
| | - Ashley R. Jones
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - Alexandra Gillett
- Department of Statistical Genetics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London, UK
| | - Zhongbo Chen
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience,
Sheffield, UK
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | - John F. Powell
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | | | | | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience,
Sheffield, UK
| | - Christopher E. Shaw
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
| | | | - Jan H. Veldink
- University Medical Centre Utrecht,
Utrecht,
The Netherlands
| | - Cathryn M. Lewis
- Department of Statistical Genetics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience,
London,
UK
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Abstract
INTRODUCTION Transitional care is an NHS priority with newly published NICE guidance. Many paediatric surgical patients need quality care to continue into adulthood. We undertook an evaluation of our departmental activity to assess the magnitude of this issue. METHODS We identified all outpatients ≥ 15 years (potentially requiring imminent transition) seen over a 12 month period for all five general paediatric surgery consultants in our tertiary centre. Those patients requiring transition were highlighted and the appropriate adult team for referral recorded. RESULTS There were 2989 general paediatric surgery clinic appointments within the year; 289 (9.7%) were for young people aged 15 years or older; 62 patients (28% of those ≥ 15years) were deemed to require transition into adult care. Significantly more patients having colorectal surgery required follow-up (P = 0.0009 Chi-square test) compared with patients in other subspecialties. CONCLUSIONS More patients than expected required transition. This may be the case in other units. Current best practice includes time intensive preclinic planning, careful preparation of patient and family, followed by joint clinics. A joint clinic appointment takes 30 minutes, allowing for comprehensive handover and forging new relationships. In our department, we need at least ten transition clinics across 2 years. Coalition with adult colleagues is vital. These data enable us to plan services to provide quality care for our adolescent patients and highlights colorectal surgery as a priority.
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Affiliation(s)
- A R Jones
- Department of Paediatric Surgery, Nottingham Children's Hospital, Queen's Medical Centre , Nottingham , UK
| | - M John
- Department of Paediatric Surgery and Urology, Nottingham Children's Hospital, Queen's Medical Centre , Nottingham , UK
| | - S J Singh
- Department of Paediatric Surgery and Urology, Nottingham Children's Hospital, Queen's Medical Centre , Nottingham , UK
| | - A R Williams
- Department of Paediatric Surgery and Urology, Nottingham Children's Hospital, Queen's Medical Centre , Nottingham , UK
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35
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Kenna KP, van Doormaal PTC, Dekker AM, Ticozzi N, Kenna BJ, Diekstra FP, van Rheenen W, van Eijk KR, Jones AR, Keagle P, Shatunov A, Sproviero W, Smith BN, van Es MA, Topp SD, Kenna A, Miller JW, Fallini C, Tiloca C, McLaughlin RL, Vance C, Troakes C, Colombrita C, Mora G, Calvo A, Verde F, Al-Sarraj S, King A, Calini D, de Belleroche J, Baas F, van der Kooi AJ, de Visser M, Ten Asbroek ALMA, Sapp PC, McKenna-Yasek D, Polak M, Asress S, Muñoz-Blanco JL, Strom TM, Meitinger T, Morrison KE, Lauria G, Williams KL, Leigh PN, Nicholson GA, Blair IP, Leblond CS, Dion PA, Rouleau GA, Pall H, Shaw PJ, Turner MR, Talbot K, Taroni F, Boylan KB, Van Blitterswijk M, Rademakers R, Esteban-Pérez J, García-Redondo A, Van Damme P, Robberecht W, Chio A, Gellera C, Drepper C, Sendtner M, Ratti A, Glass JD, Mora JS, Basak NA, Hardiman O, Ludolph AC, Andersen PM, Weishaupt JH, Brown RH, Al-Chalabi A, Silani V, Shaw CE, van den Berg LH, Veldink JH, Landers JE. NEK1 variants confer susceptibility to amyotrophic lateral sclerosis. Nat Genet 2016; 48:1037-42. [PMID: 27455347 PMCID: PMC5560030 DOI: 10.1038/ng.3626] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/24/2016] [Indexed: 12/11/2022]
Abstract
To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology.
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Affiliation(s)
- Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Perry T C van Doormaal
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Annelot M Dekker
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nicola Ticozzi
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Brendan J Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Frank P Diekstra
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Wouter van Rheenen
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Pamela Keagle
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Michael A van Es
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Simon D Topp
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Aoife Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jack W Miller
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Cinzia Tiloca
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Doctoral School in Molecular Medicine, Department of Sciences and Biomedical Technologies, Università degli Studi di Milano, Milan, Italy
| | - Russell L McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Caroline Vance
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claire Troakes
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claudia Colombrita
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Mora
- Salvatore Maugeri Foundation, IRCSS, Scientific Institute of Milano, Milan, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Federico Verde
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Safa Al-Sarraj
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Andrew King
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Daniela Calini
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | | | - Frank Baas
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneke J van der Kooi
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Marianne de Visser
- Department of Neurogenetics and Neurology, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneloor L M A Ten Asbroek
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter C Sapp
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diane McKenna-Yasek
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Seneshaw Asress
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - José Luis Muñoz-Blanco
- Unidad de ELA, Instituto de Investigación Hospital Gregorio Marañón de Madrid, Madrid, Spain
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kelly L Williams
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - P Nigel Leigh
- Trafford Centre for Medical Research, Brighton and Sussex Medical School, Falmer, UK
| | - Garth A Nicholson
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- ANZAC Research Institute, Concord Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Ian P Blair
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Claire S Leblond
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Patrick A Dion
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Hardev Pall
- Institute of Clinical Studies, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Department of Neurology, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - Pamela J Shaw
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Franco Taroni
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Jesús Esteban-Pérez
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Alberto García-Redondo
- Unidad de ELA, Instituto de Investigación Hospital 12 de Octubre de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U-723, Madrid, Spain
| | - Phillip Van Damme
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Wim Robberecht
- Laboratory of Neurobiology, Department of Neurosciences, KU Leuven and Vesalius Research Centre, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals, Leuven, Belgium
| | - Adriano Chio
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Carsten Drepper
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
- Department of Child and Adolescent Psychiatry, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Antonia Ratti
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Jonathan D Glass
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Jesús S Mora
- ALS Unit/Neurology, Hospital San Rafael, Madrid, Spain
| | - Nazli A Basak
- NDAL, Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | | | - Peter M Andersen
- Department of Pharmacology and Clinical Neuroscience, Umeå University, Umeå, Sweden
| | | | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Vincenzo Silani
- Department of Neurology, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, King's College London, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Leonard H van den Berg
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology Brain Centre, Brain Centre Rudolf Magnus, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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36
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van Rheenen W, Shatunov A, Dekker AM, McLaughlin RL, Diekstra FP, Pulit SL, van der Spek RAA, Võsa U, de Jong S, Robinson MR, Yang J, Fogh I, van Doormaal PT, Tazelaar GHP, Koppers M, Blokhuis AM, Sproviero W, Jones AR, Kenna KP, van Eijk KR, Harschnitz O, Schellevis RD, Brands WJ, Medic J, Menelaou A, Vajda A, Ticozzi N, Lin K, Rogelj B, Vrabec K, Ravnik-Glavač M, Koritnik B, Zidar J, Leonardis L, Grošelj LD, Millecamps S, Salachas F, Meininger V, de Carvalho M, Pinto S, Mora JS, Rojas-García R, Polak M, Chandran S, Colville S, Swingler R, Morrison KE, Shaw PJ, Hardy J, Orrell RW, Pittman A, Sidle K, Fratta P, Malaspina A, Topp S, Petri S, Abdulla S, Drepper C, Sendtner M, Meyer T, Ophoff RA, Staats KA, Wiedau-Pazos M, Lomen-Hoerth C, Van Deerlin VM, Trojanowski JQ, Elman L, McCluskey L, Basak AN, Tunca C, Hamzeiy H, Parman Y, Meitinger T, Lichtner P, Radivojkov-Blagojevic M, Andres CR, Maurel C, Bensimon G, Landwehrmeyer B, Brice A, Payan CAM, Saker-Delye S, Dürr A, Wood NW, Tittmann L, Lieb W, Franke A, Rietschel M, Cichon S, Nöthen MM, Amouyel P, Tzourio C, Dartigues JF, Uitterlinden AG, Rivadeneira F, Estrada K, Hofman A, Curtis C, Blauw HM, van der Kooi AJ, de Visser M, Goris A, Weber M, Shaw CE, Smith BN, Pansarasa O, Cereda C, Del Bo R, Comi GP, D'Alfonso S, Bertolin C, Sorarù G, Mazzini L, Pensato V, Gellera C, Tiloca C, Ratti A, Calvo A, Moglia C, Brunetti M, Arcuti S, Capozzo R, Zecca C, Lunetta C, Penco S, Riva N, Padovani A, Filosto M, Muller B, Stuit RJ, Blair I, Zhang K, McCann EP, Fifita JA, Nicholson GA, Rowe DB, Pamphlett R, Kiernan MC, Grosskreutz J, Witte OW, Ringer T, Prell T, Stubendorff B, Kurth I, Hübner CA, Leigh PN, Casale F, Chio A, Beghi E, Pupillo E, Tortelli R, Logroscino G, Powell J, Ludolph AC, Weishaupt JH, Robberecht W, Van Damme P, Franke L, Pers TH, Brown RH, Glass JD, Landers JE, Hardiman O, Andersen PM, Corcia P, Vourc'h P, Silani V, Wray NR, Visscher PM, de Bakker PIW, van Es MA, Pasterkamp RJ, Lewis CM, Breen G, Al-Chalabi A, van den Berg LH, Veldink JH. Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis. Nat Genet 2016; 48:1043-8. [PMID: 27455348 PMCID: PMC5556360 DOI: 10.1038/ng.3622] [Citation(s) in RCA: 374] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/20/2016] [Indexed: 12/15/2022]
Abstract
To elucidate the genetic architecture of amyotrophic lateral sclerosis (ALS) and find associated loci, we assembled a custom imputation reference panel from whole-genome-sequenced patients with ALS and matched controls (n = 1,861). Through imputation and mixed-model association analysis in 12,577 cases and 23,475 controls, combined with 2,579 cases and 2,767 controls in an independent replication cohort, we fine-mapped a new risk locus on chromosome 21 and identified C21orf2 as a gene associated with ALS risk. In addition, we identified MOBP and SCFD1 as new associated risk loci. We established evidence of ALS being a complex genetic trait with a polygenic architecture. Furthermore, we estimated the SNP-based heritability at 8.5%, with a distinct and important role for low-frequency variants (frequency 1-10%). This study motivates the interrogation of larger samples with full genome coverage to identify rare causal variants that underpin ALS risk.
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Affiliation(s)
- Wouter van Rheenen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Annelot M Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Frank P Diekstra
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sara L Pulit
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rick A A van der Spek
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Simone de Jong
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Matthew R Robinson
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Jian Yang
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Perry Tc van Doormaal
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gijs H P Tazelaar
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Max Koppers
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anna M Blokhuis
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - William Sproviero
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Ashley R Jones
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Kevin P Kenna
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kristel R van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Oliver Harschnitz
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Raymond D Schellevis
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - William J Brands
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jelena Medic
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Androniki Menelaou
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alice Vajda
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Tranplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Kuang Lin
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
| | - Katarina Vrabec
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Koritnik
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Janez Zidar
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Lea Leonardis
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Leja Dolenc Grošelj
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Stéphanie Millecamps
- Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Université Paris 06, UMRS 1127, Paris, France
| | - François Salachas
- Institut du Cerveau et de la Moelle Epinière, INSERM U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Université Paris 06, UMRS 1127, Paris, France
- Centre de Référence Maladies Rares SLA Ile de France, Département de Neurologie, Hôpital de la Pitié-Salpêtrière, Paris, France
- GRC-UPMC SLA et Maladies du Motoneurone, Paris, France
| | - Vincent Meininger
- Ramsay Generale de Santé, Hôpital Peupliers, Paris, France
- Réseau SLA Ile de France, Paris, France
| | - Mamede de Carvalho
- Institute of Physiology, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- Department of Neurosciences, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Susana Pinto
- Institute of Physiology, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- Department of Neurosciences, Hospital de Santa Maria-CHLN, Lisbon, Portugal
| | - Jesus S Mora
- Department of Neurology, Hospital San Rafael, Madrid, Spain
| | - Ricardo Rojas-García
- Neurology Department, Hospital de la Santa Creu i Sant Pau de Barcelona, Autonomous University of Barcelona, Barcelona, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Meraida Polak
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory ALS Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Siddharthan Chandran
- Euan MacDonald Centre for Motor Neuron Disease Research, Edinburgh, UK
- Centre for Neuroregeneration and Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Shuna Colville
- Euan MacDonald Centre for Motor Neuron Disease Research, Edinburgh, UK
| | - Robert Swingler
- Euan MacDonald Centre for Motor Neuron Disease Research, Edinburgh, UK
| | | | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Richard W Orrell
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, UK
| | - Alan Pittman
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
- Reta Lila Weston Institute, Institute of Neurology, University College London, London, UK
| | - Katie Sidle
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, UK
| | - Pietro Fratta
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London, UK
| | - Andrea Malaspina
- Centre for Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, UK
- North-East London and Essex Regional Motor Neuron Disease Care Centre, London, UK
| | - Simon Topp
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Susanne Abdulla
- Department of Neurology, Otto von Güricke University Magdeburg, Magdeburg, Germany
| | - Carsten Drepper
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Thomas Meyer
- Department of Neurology, Charité University Hospital, Humboldt University, Berlin, Germany
| | - Roel A Ophoff
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California, USA
| | - Kim A Staats
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, California, USA
| | - Martina Wiedau-Pazos
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Catherine Lomen-Hoerth
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren Elman
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leo McCluskey
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A Nazli Basak
- Neurodegeneration Research Laboratory, Bo[gcaron]aziçi University, Istanbul, Turkey
| | - Ceren Tunca
- Neurodegeneration Research Laboratory, Bo[gcaron]aziçi University, Istanbul, Turkey
| | - Hamid Hamzeiy
- Neurodegeneration Research Laboratory, Bo[gcaron]aziçi University, Istanbul, Turkey
| | - Yesim Parman
- Neurology Department, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Cindy Maurel
- INSERM U930, Université François Rabelais, Tours, France
| | - Gilbert Bensimon
- AP-HP, Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, Paris, France
- UPMC, Pharmacologie, Paris VI, Paris, France
- BESPIM, CHU de Nîmes, Nîmes, France
| | | | - Alexis Brice
- INSERM U1127, Hôpital de la Pitié-Salpêtrière, Paris, France
- CNRS UMR 7225, Hôpital de la Pitié-Salpêtrière, Paris, France
- Sorbonne Universités, UPMC Paris 06, UMRS 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
- Institut du Cerveau et de la Moelle Epinière, Hôpital de la Pitié-Salpêtrière, Paris, France
- AP-HP, Département de Génétique, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Christine A M Payan
- AP-HP, Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, Paris, France
- BESPIM, CHU de Nîmes, Nîmes, France
| | | | - Alexandra Dürr
- Department of Medical Genetics, Institut du Cerveau et de la Moelle Epinière, Hôptial Pitié-Salpêtrière, Paris, France
| | - Nicholas W Wood
- Department of Neurogenetics, Institute of Neurology, University College London, London, UK
| | - Lukas Tittmann
- PopGen Biobank and Institute of Epidemiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Wolfgang Lieb
- PopGen Biobank and Institute of Epidemiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Faculty of Medicine Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
- Division of Medical Genetics, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Philippe Amouyel
- University of Lille, INSERM, CHU de Lille, Institut Pasteur de Lille, U1167-RID-AGE Risk Factor and Molecular Determinants of Aging Diseases, Lille, France
| | - Christophe Tzourio
- Bordeaux University, ISPED, Centre INSERM U1219-Epidemiologie Biostatistique et CIC-1401, CHU de Bordeaux, Pôle de Santé Publique, Bordeaux, France
| | - Jean-François Dartigues
- Bordeaux University, ISPED, Centre INSERM U1219-Epidemiologie Biostatistique et CIC-1401, CHU de Bordeaux, Pôle de Santé Publique, Bordeaux, France
| | - Andre G Uitterlinden
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Karol Estrada
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Charles Curtis
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Hylke M Blauw
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anneke J van der Kooi
- Department of Neurology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marianne de Visser
- Department of Neurology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - An Goris
- Department of Neurosciences, Experimental Neurology, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, Leuven, Belgium
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Orietta Pansarasa
- Laboratory of Experimental Neurobiology, IRCCS 'C. Mondino' National Institute of Neurology Foundation, Pavia, Italy
| | - Cristina Cereda
- Laboratory of Experimental Neurobiology, IRCCS 'C. Mondino' National Institute of Neurology Foundation, Pavia, Italy
| | - Roberto Del Bo
- Neurologic Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giacomo P Comi
- Neurologic Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases, Università del Piemonte Orientale, Novara, Italy
| | - Cinzia Bertolin
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Letizia Mazzini
- Department of Neurology, Università del Piemonte Orientale, Novara, Italy
| | - Viviana Pensato
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Cinzia Gellera
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Tranplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
| | - Cristina Moglia
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
| | - Maura Brunetti
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
| | - Simona Arcuti
- Department of Clinical Research in Neurology, University of Bari 'A. Moro' at Pia Fondazione 'Card. G. Panico', Tricase, Italy
| | - Rosa Capozzo
- Department of Clinical Research in Neurology, University of Bari 'A. Moro' at Pia Fondazione 'Card. G. Panico', Tricase, Italy
| | - Chiara Zecca
- Department of Clinical Research in Neurology, University of Bari 'A. Moro' at Pia Fondazione 'Card. G. Panico', Tricase, Italy
| | - Christian Lunetta
- NEMO Clinical Center, Serena Onlus Foundation, Niguarda Ca' Granda Hostipal, Milan, Italy
| | - Silvana Penco
- Medical Genetics Unit, Department of Laboratory Medicine, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Nilo Riva
- Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Massimiliano Filosto
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | | | | | - Ian Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Katharine Zhang
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jennifer A Fifita
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
- University of Sydney, ANZAC Research Institute, Concord Hospital, Sydney, New South Wales, Australia
| | - Dominic B Rowe
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Roger Pamphlett
- Stacey MND Laboratory, Department of Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Julian Grosskreutz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Thomas Ringer
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Tino Prell
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | | | - P Nigel Leigh
- Department of Neurology, Brighton and Sussex Medical School Trafford Centre for Biomedical Research, University of Sussex, Falmer, UK
| | - Federico Casale
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Adriano Chio
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Azienda Ospedaliera Città della Salute e della Scienza, Turin, Italy
| | - Ettore Beghi
- Laboratory of Neurological Diseases, Department of Neuroscience, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Elisabetta Pupillo
- Laboratory of Neurological Diseases, Department of Neuroscience, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Rosanna Tortelli
- Department of Clinical Research in Neurology, University of Bari 'A. Moro' at Pia Fondazione 'Card. G. Panico', Tricase, Italy
| | - Giancarlo Logroscino
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari 'Aldo Moro', Bari, Italy
- Unit of Neurodegenerative Diseases, Department of Clinical Research in Neurology, University of Bari 'Aldo Moro' at Pia Fondazione Cardinale G. Panico, Tricase, Italy
| | - John Powell
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | | | | | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, Leuven, Belgium
- Vesalius Research Center, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, Leuven, Belgium
- Vesalius Research Center, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Tune H Pers
- Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Genetics, Boston Children's Hospital, Boston, Massachusetts, USA
- Center for Basic Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jonathan D Glass
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory ALS Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Peter M Andersen
- Department of Neurology, Ulm University, Ulm, Germany
- Department of Pharmacology and Clinical Neurosience, Umeå University, Umeå, Sweden
| | - Philippe Corcia
- INSERM U930, Université François Rabelais, Tours, France
- Centre SLA, CHRU de Tours, Tours, France
- Federation des Centres SLA Tours and Limoges, LITORALS, Tours, France
| | | | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Tranplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Diamantina Institute, University of Queensland Translational Research Institute, Brisbane, Queensland, Australia
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Michael A van Es
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cathryn M Lewis
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, King's College London, London, UK
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
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Benigni M, Ricci C, Jones AR, Giannini F, Al-Chalabi A, Battistini S. Identification of miRNAs as Potential Biomarkers in Cerebrospinal Fluid from Amyotrophic Lateral Sclerosis Patients. Neuromolecular Med 2016; 18:551-560. [PMID: 27119371 DOI: 10.1007/s12017-016-8396-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/15/2016] [Indexed: 12/31/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disorder. Since no diagnostic laboratory test exists, the identification of specific biomarkers could be fundamental in clinical practice. microRNAs (miRNAs) are considered promising biomarkers for neurodegenerative diseases. The aim of the study was to identify a CSF miRNA set that could differentiate ALS from non-ALS condition. miRNA profiling in CSF from ALS patients (n = 24; eight with C9orf72 expansion) and unaffected control subjects (n = 24) by quantitative reverse transcription PCR identified fourteen deregulated miRNAs. Validation experiments confirmed eight miRNAs as significantly deregulated in ALS. No significant differences were observed between ALS patients with or without C9orf72 expansion. The receiver operator characteristic (ROC) curve analyses revealed the highest diagnostic accuracy for the upregulated miR181a-5p and the downregulated miR21-5p and miR15b-5p. The miR181a-5p/miR21-5p and miR181a-5p/miR15b-5p ratios detected ALS with 90 and 85 % sensitivity and 87 and 91 % specificity, respectively, confirming the application potential as disease biomarkers. These deregulated miRNAs are implicated in apoptotic way and provide insight into processes responsible for motor neuron degeneration.
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Affiliation(s)
- Michele Benigni
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy.
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Fabio Giannini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Stefania Battistini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
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Bedwell P, Mortimer K, Wellings J, Sherwood J, Leadbetter SJ, Haywood SM, Charnock T, Jones AR, Hort MC. An assessment of the doses received by members of the public in Japan following the nuclear accident at Fukushima Daiichi nuclear power plant. J Radiol Prot 2015; 35:869-890. [PMID: 26609838 DOI: 10.1088/0952-4746/35/4/869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The earthquake and tsunami on 11 March 2011, centred off the east coast of Japan, caused considerable destruction and substantial loss of life along large swathes of the Japanese coastline. The tsunami damaged the Fukushima Daiichi nuclear power plant (NPP), resulting in prolonged releases of radioactive material into the environment. This paper assesses the doses received by members of the public in Japan. The assessment is based on an estimated source term and atmospheric dispersion modelling rather than monitoring data. It is evident from this assessment that across the majority of Japan the estimates of dose are very low, for example they are estimated to be less than the annual average dose from natural background radiation in Japan. Even in the regions local to Fukushima Daiichi NPP (and not affected by any form of evacuation) the maximum lifetime effective dose is estimated to be well below the cumulative natural background dose over the same period. The impact of the urgent countermeasures on the estimates of dose was considered. And the relative contribution to dose from the range of exposure pathways and radionuclides were evaluated. Analysis of estimated doses focused on the geographic irregularity and the impact of the meteorological conditions. For example the dose to an infant's thyroid received over the first year was estimated to be greater in Hirono than in the non-evacuated region of Naraha, despite Hirono being further from the release location. A number of factors were identified and thought to contribute towards this outcome, including the local wind pattern which resulted in the recirculation of part of the release. The non-uniform nature of dose estimates strengthens the case for evaluations based on dispersion modelling.
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Affiliation(s)
- P Bedwell
- Centre for Radiation, Chemicals & Environmental Hazards, Public Health England, Chilton, Didcot, Oxon, OX11 0RQ, UK
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van der Kleij LA, Jones AR, Steen IN, Young CA, Shaw PJ, Shaw CE, Leigh PN, Turner MR, Al-Chalabi A. Regionality of disease progression predicts prognosis in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2015; 16:442-7. [DOI: 10.3109/21678421.2015.1051987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Lisa A. van der Kleij
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Ashley R. Jones
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - I Nick Steen
- Institute of Health and Society, University of Newcastle, UK
| | | | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Christopher E. Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - P. Nigel Leigh
- Brighton and Sussex Medical School, Trafford Centre for Biomedical Research, Falmer, Brighton, UK
| | - Martin R. Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
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40
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Jones AR, Troakes C, King A, Sahni V, De Jong S, Bossers K, Papouli E, Mirza M, Al-Sarraj S, Shaw CE, Shaw PJ, Kirby J, Veldink JH, Macklis JD, Powell JF, Al-Chalabi A. Stratified gene expression analysis identifies major amyotrophic lateral sclerosis genes. Neurobiol Aging 2015; 36:2006.e1-9. [PMID: 25801576 DOI: 10.1016/j.neurobiolaging.2015.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/15/2015] [Indexed: 01/10/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons resulting in progressive paralysis. Gene expression studies of ALS only rarely identify the same gene pathways as gene association studies. We hypothesized that analyzing tissues by matching on degree of disease severity would identify different patterns of gene expression from a traditional case-control comparison. We analyzed gene expression changes in 4 postmortem central nervous system regions, stratified by severity of motor neuron loss. An overall comparison of cases (n = 6) and controls (n = 3) identified known ALS gene, SOX5, as showing differential expression (log2 fold change = 0.09, p = 5.5 × 10(-5)). Analyses stratified by disease severity identified expression changes in C9orf72 (p = 2.77 × 10(-3)), MATR3 (p = 3.46 × 10(-3)), and VEGFA (p = 8.21 × 10(-4)), all implicated in ALS through genetic studies, and changes in other genes in pathways involving RNA processing and immune response. These findings suggest that analysis of gene expression stratified by disease severity can identify major ALS genes and may be more efficient than traditional case-control comparison.
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Affiliation(s)
- Ashley R Jones
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Claire Troakes
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Andrew King
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Vibhu Sahni
- Department of Stem Cell and Regenerative Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Simone De Jong
- MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Koen Bossers
- Synaptic Plasticity and Behavior Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Efterpi Papouli
- Biomedical Research Centre, King's College London, Guy's Hospital, London, UK; Cambridge Epigenetix Ltd, Babraham, UK
| | - Muddassar Mirza
- Biomedical Research Centre, King's College London, Guy's Hospital, London, UK
| | - Safa Al-Sarraj
- MRC London Neurodegenerative Diseases Brain Bank, King's College London, London, UK
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
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Jones AR, Wynn RB, Yésou P, Thébault L, Collins P, Suberg L, Lewis KM, Brereton TM. Using integrated land- and boat-based surveys to inform conservation of the Critically Endangered Balearic shearwater. ENDANGER SPECIES RES 2014. [DOI: 10.3354/esr00611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Guillozet-Bongaarts AL, Hyde TM, Dalley RA, Hawrylycz MJ, Henry A, Hof PR, Hohmann J, Jones AR, Kuan CL, Royall J, Shen E, Swanson B, Zeng H, Kleinman JE. Altered gene expression in the dorsolateral prefrontal cortex of individuals with schizophrenia. Mol Psychiatry 2014; 19:478-85. [PMID: 23528911 PMCID: PMC3965839 DOI: 10.1038/mp.2013.30] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/24/2013] [Accepted: 02/06/2013] [Indexed: 01/31/2023]
Abstract
The underlying pathology of schizophrenia (SZ) is likely as heterogeneous as its symptomatology. A variety of cortical and subcortical regions, including the prefrontal cortex, have been implicated in its pathology, and a number of genes have been identified as risk factors for disease development. We used in situ hybridization (ISH) to examine the expression of 58 genes in the dorsolateral prefrontal cortex (DLPFC, comprised of Brodmann areas 9 and 46) from 19 individuals with a premorbid diagnosis of SZ and 33 control individuals. Genes were selected based on: (1) previous identification as risk factors for SZ; (2) cell type markers or (3) laminar markers. Cell density and staining intensity were compared in the DLPFC, as well as separately in Brodmann areas 9 and 46. The expression patterns of a variety of genes, many of which are associated with the GABAergic system, were altered in SZ when compared with controls. Additional genes, including C8orf79 and NR4A2, showed alterations in cell density or staining intensity between the groups, highlighting the need for additional studies. Alterations were, with only a few exceptions, limited to Brodmann area 9, suggesting regional specificity of pathology in the DLPFC. Our results agree with previous studies on the GABAergic involvement in SZ, and suggest that areas 9 and 46 may be differentially affected in the disease. This study also highlights additional genes that may be altered in SZ, and indicates that these potentially interesting genes can be identified by ISH and high-throughput image analysis techniques.
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Affiliation(s)
- A L Guillozet-Bongaarts
- Allen Institute for Brain Science, Seattle, WA, USA,Data Annotations and Analysis, Allen Institute for Brain Science, 551North 34th Street, Seattle, WA 98103, USA. E-mail:
| | - T M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA,Clinical Brain Disorders Branch, Genes Cognition and Psychosis Program, Intramural Research Program, NIMH, NIH, Bethesda, MD, USA,Department of Psychiatry and Behavioral Sciences, and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - R A Dalley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - A Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - P R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - J Hohmann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - A R Jones
- Allen Institute for Brain Science, Seattle, WA, USA
| | - C L Kuan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - J Royall
- Allen Institute for Brain Science, Seattle, WA, USA
| | - E Shen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - B Swanson
- Allen Institute for Brain Science, Seattle, WA, USA
| | - H Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - J E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA,Clinical Brain Disorders Branch, Genes Cognition and Psychosis Program, Intramural Research Program, NIMH, NIH, Bethesda, MD, USA
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Jones AR, Jivraj N, Balendra R, Murphy C, Kelly J, Thornhill M, Young C, Shaw PJ, Leigh PN, Turner MR, Steen IN, McCrone P, Al-Chalabi A. Health utility decreases with increasing clinical stage in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:285-91. [PMID: 24641613 DOI: 10.3109/21678421.2013.872149] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease typically causing death within three years. Understanding the impact of disease on patients using health utility at different stages of ALS would allow meaningful cost-benefit analysis of new potential therapies. A common health-related quality of life measurement, developed and validated for the UK, is the EQ-5D. Using clinical trial data from the LiCALS study, we calculated health utility using the EQ-5D for each King's ALS clinical stage from 214 patients. We analysed whether health utility, and other health-related measures, significantly changed between each of the clinical stages. Results showed that mean health utility decreased by 0.487 (the scale runs from 1 to - 0.594) between clinical stages 2A and 4. Emotional states, measured using the Hospital Anxiety and Depression Scale (HADS), showed worsening depression and anxiety scores as ALS progressed. Age of onset, disease onset, gender and treatment group were not predictors of EQ-5D, depression or anxiety. In conclusion, increasing severity of King's ALS Clinical Stage is associated with a progressive decrease in EQ-5D health utility. This is useful for cost-benefit analysis of new therapies and validates this ALS clinical staging system.
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Affiliation(s)
- Ashley R Jones
- Department of Clinical Neuroscience, Institute of Psychiatry , King's College London, London
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Staats KA, Van Helleputte L, Jones AR, Bento-Abreu A, Van Hoecke A, Shatunov A, Simpson CL, Lemmens R, Jaspers T, Fukami K, Nakamura Y, Brown RH, Van Damme P, Liston A, Robberecht W, Al-Chalabi A, Van Den Bosch L. Genetic ablation of phospholipase C delta 1 increases survival in SOD1G93A mice. Neurobiol Dis 2013; 60:11-7. [DOI: 10.1016/j.nbd.2013.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/31/2013] [Accepted: 08/07/2013] [Indexed: 12/12/2022] Open
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Abel O, Shatunov A, Jones AR, Andersen PM, Powell JF, Al-Chalabi A. Development of a Smartphone App for a Genetics Website: The Amyotrophic Lateral Sclerosis Online Genetics Database (ALSoD). JMIR Mhealth Uhealth 2013; 1:e18. [PMID: 25098641 PMCID: PMC4114449 DOI: 10.2196/mhealth.2706] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/21/2013] [Accepted: 06/30/2013] [Indexed: 12/21/2022] Open
Abstract
Background The ALS Online Genetics Database (ALSoD) website holds mutation, geographical, and phenotype data on genes implicated in amyotrophic lateral sclerosis (ALS) and links to bioinformatics resources, publications, and tools for analysis. On average, there are 300 unique visits per day, suggesting a high demand from the research community. To enable wider access, we developed a mobile-friendly version of the website and a smartphone app. Objective We sought to compare data traffic before and after implementation of a mobile version of the website to assess utility. Methods We identified the most frequently viewed pages using Google Analytics and our in-house analytic monitoring. For these, we optimized the content layout of the screen, reduced image sizes, and summarized available information. We used the Microsoft .NET framework mobile detection property (HttpRequest.IsMobileDevice in the Request.Browser object in conjunction with HttpRequest.UserAgent), which returns a true value if the browser is a recognized mobile device. For app development, we used the Eclipse integrated development environment with Android plug-ins. We wrapped the mobile website version with the WebView object in Android. Simulators were downloaded to test and debug the applications. Results The website automatically detects access from a mobile phone and redirects pages to fit the smaller screen. Because the amount of data stored on ALSoD is very large, the available information for display using smartphone access is deliberately restricted to improve usability.
Visits to the website increased from 2231 to 2820, yielding a 26% increase from the pre-mobile to post-mobile period and an increase from 103 to 340 visits (230%) using mobile devices (including tablets). The smartphone app is currently available on BlackBerry and Android devices and will be available shortly on iOS as well. Conclusions Further development of the ALSoD website has allowed access through smartphones and tablets, either through the website or directly through a mobile app, making genetic data stored on the database readily accessible to researchers and patients across multiple devices.
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Affiliation(s)
- Olubunmi Abel
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, United Kingdom
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46
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Jones AR, Woollacott I, Shatunov A, Cooper-Knock J, Buchman V, Sproviero W, Smith B, Scott KM, Balendra R, Abel O, McGuffin P, Ellis CM, Shaw PJ, Morrison KE, Farmer A, Lewis CM, Leigh PN, Shaw CE, Powell JF, Al-Chalabi A. Residual association at C9orf72 suggests an alternative amyotrophic lateral sclerosis-causing hexanucleotide repeat. Neurobiol Aging 2013; 34:2234.e1-7. [PMID: 23587638 PMCID: PMC3753508 DOI: 10.1016/j.neurobiolaging.2013.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons. Single-nucleotide polymorphism rs3849942 is associated with ALS, tagging a hexanucleotide repeat mutation in the C9orf72 gene. It is possible that there is more than 1 disease-causing genetic variation at this locus, in which case association might remain after removal of cases carrying the mutation. DNA from patients with ALS was therefore tested for the mutation. Genome-wide association testing was performed first using all samples, and then restricting the analysis to samples not carrying the mutation. rs3849942 and rs903603 were strongly associated with ALS when all samples were included (rs3849942, p = [3 × 2] × 10(-6), rank 7/442,057; rs903603, p = [7 × 6] × 10(-8), rank 2/442,057). Removal of the mutation-carrying cases resulted in loss of association for rs3849942 (p = [2 × 6] × 10(-3), rank 1225/442,068), but had little effect on rs903603 (p = [1 × 9] × 10(-5), rank 8/442,068). Those with a risk allele of rs903603 had an excess of apparent homozygosity for wild type repeat alleles, consistent with polymerase chain reaction failure of 1 allele because of massive repeat expansion. These results indicate residual association at the C9orf72 locus suggesting a second disease-causing repeat mutation.
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Affiliation(s)
- Ashley R. Jones
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Ione Woollacott
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Aleksey Shatunov
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Johnathan Cooper-Knock
- Academic Unit of Neurology, Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, South Yorkshire, UK
| | - Vladimir Buchman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, UK
- Institute of Physiologically Active Compounds of RAS, Chernogolovka, Moscow Region, Russian Federation
| | - William Sproviero
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Bradley Smith
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Kirsten M. Scott
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Rubika Balendra
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Olubunmi Abel
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - Peter McGuffin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | | | - Pamela J. Shaw
- Academic Unit of Neurology, Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, South Yorkshire, UK
| | - Karen E. Morrison
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, and Neurosciences Division, University Hospitals Birmingham NHS Foundation Trust, Birmingham, West Midlands, UK
| | - Anne Farmer
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Cathryn M. Lewis
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - P. Nigel Leigh
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
- Brighton and Sussex Medical School, Trafford Centre for Biomedical Research, University of Sussex, Sussex, UK
| | - Christopher E. Shaw
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
| | - John F. Powell
- Department of Neuroscience, Institute of Psychiatry, King's College London, London, UK
| | - Ammar Al-Chalabi
- King's College London, Institute of Psychiatry, Department of Clinical Neuroscience, London, UK
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Parkinson KN, Drewett RF, Jones AR, Adamson AJ. Mothers' judgements about their child's weight: distinguishing facts from values. Child Care Health Dev 2013; 39:722-7. [PMID: 23039117 DOI: 10.1111/cch.12000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND Mothers' responses to questionnaire items assessing their child's weight status typically do not correspond to conventional clinical classifications based on body mass index (BMI). From this observation health professionals infer that mothers do not recognize overweight in their child. But the questions used have generally confounded factual judgements with values, so it is not clear whether the mothers are making factual errors, or differ from professionals in their values. METHODS Cross-sectional study of population-based birth cohort at 6-8 years and their mothers (n = 540). An objective BMI matching task was used to determine the accuracy of mothers' recognition of their child's weight. Mothers matched their child to sex- and age-specific images of children of known BMI ranging from very thin to obese, and chose a descriptor of their child's weight of the kind used in previous research. RESULTS Mothers tended to underestimate their child's BMI on the matching task. Matching errors significantly predicted mothers' description of their child's weight; those who overestimated their child's BMI on the matching task were more likely to say their child was overweight, while those who underestimated it were less likely to, independently of their child's actual BMI. CONCLUSIONS Educational programmes aimed at parents of young primary school children need to address separately the factual and the evaluative components of their assessment of child weight.
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Affiliation(s)
- K N Parkinson
- Institute of Health and Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK.
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Gonzalez-Galarza FF, Mack SJ, Hollenbach J, Fernandez-Vina M, Setterholm M, Kempenich J, Marsh SGE, Jones AR, Middleton D. 16(th) IHIW: extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles. Int J Immunogenet 2012. [PMID: 23198982 DOI: 10.1111/iji.12030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Continuing a project presented at the 15th International HLA and Immunogenetics Workshop (IHIWS) on the rarity of HLA alleles, we sought to expand the number of data sources and bioinformatics tools available in the Allele Frequencies Net Database website (AFND, www.allelefrequencies.net). In this 16th IHIWS Rare Alleles project, HLA alleles described in the latest IMGT/HLA Database (release 3.8.0) were queried against different sources including data from registries (stem cell) and from 74 different laboratories around the world. We demonstrated that approximately 40% of the alleles officially named in the IMGT/HLA Database have been reported only once across all different sources. To facilitate the large-scale analysis of rare alleles, we have produced an online tool called the Rare Allele Detector that simplifies the detection of alleles that are considered to be 'very rare', 'rare' or 'frequent'. Tools and associated data can be accessed via the www.allelefrequencies.net website.
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Abstract
OBJECTIVE To quantify how overweight children have to be for their mothers to classify them as overweight and to express concern about future overweight, and to investigate the adiposity cues in children that mothers respond to. DESIGN Cross-sectional. SUBJECTS A total of 531 children from the Gateshead Millennium Study cohort at 6-8 years and their mothers. MEASUREMENTS In the mother: responses to two questions concerning the child's adiposity; height; weight; educational qualifications; and economic status. In the child: height; weight; waist circumference; skinfold thicknesses; bioelectrical impedance; and bone frame measurements. RESULTS The body mass index (BMI) at which half the mothers classify their child as overweight was 21.3 (in the obese range for children of this age). The BMI at which half the mothers were concerned about their child becoming overweight in the future was 17.1 (below the overweight range). Waist circumference and skinfolds contributed most to mothers' responses. Although BMI and fat scores were important predictors individually, they did not contribute independently once waist circumference and skinfolds (their most visible manifestations) were included in the regression equations. Mothers were less likely to classify girls as overweight. Mothers with higher BMIs were less likely to classify their child as overweight, but were more likely to be concerned about future overweight. CONCLUSION Health promotion efforts directed at parents of young primary school children might better capitalise on their concern about future overweight in their child than on current weight status, and focus on mothers' response to more visible characteristics than the BMI.
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Affiliation(s)
- K N Parkinson
- Institute of Health and Society, Human Nutrition Research Centre, Framlington Place, Newcastle University, Newcastle upon Tyne, UK.
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