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Egeskov-Cavling AM, van Wijhe M, Yakimov V, Johannesen CK, Pollard AJ, Trebbien R, Bybjerg-Grauholm J, Fischer TK. Genome-wide Association Study of Susceptibility to Respiratory Syncytial Virus Hospitalization in Young Children <5 Years of age. J Infect Dis 2024; 230:e333-e341. [PMID: 37666001 PMCID: PMC11326809 DOI: 10.1093/infdis/jiad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/22/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Worldwide, respiratory syncytial virus (RSV) infections are among the most common causes of infant hospitalization. Host genetic factors influencing the risk and severity of RSV infection are not well known. METHODS We conducted a genome-wide association study (GWAS) to investigate single-nucleotide polymorphisms (SNPs) associated with severe RSV infections using a nested case-control design based on 2 Danish cohorts. We compared SNPs from 1786 children hospitalized with RSV to 45 060 controls without an RSV-coded hospitalization. We performed gene-based testing, tissue enrichment, gene-set enrichment, and a meta-analysis of the 2 cohorts. Finally, an analysis of potential associations between the severity of RSV infection and genetic markers was performed. RESULTS We did not detect any significant genome-wide associations between SNPs and RSV infection or the severity of RSV. We did find potential loci associated with RSV infections on chromosome 5 in 1 cohort but failed to replicate any signals in both cohorts. CONCLUSIONS Despite being the largest GWAS of severe RSV infection, we did not detect any genome-wide significant loci. This may be an indication of a lack of power or an absence of signal. Future studies might include mild illness and need to be larger to detect any significant associations.
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Affiliation(s)
- Amanda Marie Egeskov-Cavling
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen
- Department of Clinical Research, Nordsjællands Hospital, Hilleroed
| | - Maarten van Wijhe
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen
- Department of Science and Environment, Roskilde University
| | - Victor Yakimov
- Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Caroline Klint Johannesen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen
- Department of Clinical Research, Nordsjællands Hospital, Hilleroed
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford and National Institute for Health and Care Research Oxford Biomedical Research Centre, United Kingdom
| | - Ramona Trebbien
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen
| | | | - Thea Kølsen Fischer
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen
- Department of Clinical Research, Nordsjællands Hospital, Hilleroed
- Department of Public Health, University of Copenhagen, Denmark
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Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R, Padmanabhan S, Pell JP. Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review. Crit Rev Clin Lab Sci 2024:1-24. [PMID: 38855982 DOI: 10.1080/10408363.2024.2360996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
This scoping review aimed to synthesize the analytical techniques used and methodological limitations encountered when undertaking secondary research using residual neonatal dried blood spot (DBS) samples. Studies that used residual neonatal DBS samples for secondary research (i.e. research not related to newborn screening for inherited genetic and metabolic disorders) were identified from six electronic databases: Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, Medline, PubMed and Scopus. Inclusion was restricted to studies published from 1973 and written in or translated into English that reported the storage, extraction and testing of neonatal DBS samples. Sixty-seven studies were eligible for inclusion. Included studies were predominantly methodological in nature and measured various analytes, including nucleic acids, proteins, metabolites, environmental pollutants, markers of prenatal substance use and medications. Neonatal DBS samples were stored over a range of temperatures (ambient temperature, cold storage or frozen) and durations (two weeks to 40.5 years), both of which impacted the recovery of some analytes, particularly amino acids, antibodies and environmental pollutants. The size of DBS sample used and potential contamination were also cited as methodological limitations. Residual neonatal DBS samples retained by newborn screening programs are a promising resource for secondary research purposes, with many studies reporting the successful measurement of analytes even from neonatal DBS samples stored for long periods of time in suboptimal temperatures and conditions.
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Affiliation(s)
- Jordan Canning
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
| | - Rona J Strawbridge
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
- Division of Cardiovascular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, UK
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Riccardo E Marioni
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mads Melbye
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - David J Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Naveed Sattar
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Cathie L M Sudlow
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Health Data Research UK, London, UK
| | - Rory Collins
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sandosh Padmanabhan
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Jill P Pell
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
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Johannsen BMW, Larsen JT, Liu X, Madsen KB, Mægbæk ML, Albiñana C, Bergink V, Laursen TM, Bech BH, Mortensen PB, Nordentoft M, Børglum AD, Werge T, Hougaard DM, Agerbo E, Petersen LV, Munk-Olsen T. Identification of women at high risk of postpartum psychiatric episodes: A population-based study quantifying relative and absolute risks following exposure to selected risk factors and genetic liability. Acta Psychiatr Scand 2023:10.1111/acps.13622. [PMID: 37871908 PMCID: PMC11035484 DOI: 10.1111/acps.13622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND We quantified relative and absolute risks of postpartum psychiatric episodes (PPE) following risk factors: Young age, past personal or family history of psychiatric disorders, and genetic liability. METHODS We conducted a register-based study using the iPSYCH2012 case-cohort sample. Exposures were personal history of psychiatric episodes prior to childbirth, being a young mother (giving birth before the age of 21.5 years), having a family history of psychiatric disorders, and a high (highest quartile) polygenic score (PGS) for major depression. PPE was defined within 12 months postpartum by prescription of psychotropic medication or in- and outpatient contact to a psychiatric facility. We included primiparous women born 1981-1999, giving birth before January 1st, 2016. We conducted Cox regression to calculate hazard ratios (HRs) of PPE, absolute risks were calculated using cumulative incidence functions. RESULTS We included 8174 primiparous women, and the estimated baseline PPE risk was 6.9% (95% CI 6.0%-7.8%, number of PPE cases: 2169). For young mothers with a personal and family history of psychiatric disorders, the absolute risk of PPE was 21.6% (95% CI 15.9%-27.8%). Adding information on high genetic liability to depression, the risk increased to 29.2% (95% CI 21.3%-38.4%) for PPE. CONCLUSIONS Information on prior personal and family psychiatric episodes as well as age may assist in estimating a personalized risk of PPE. Furthermore, additional information on genetic liability could add even further to this risk assessment.
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Affiliation(s)
| | | | - Xiaoqin Liu
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | | | - Merete Lund Mægbæk
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Clara Albiñana
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Veerle Bergink
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas M. Laursen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU, Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Bodil H. Bech
- Department of Public Health, Research Unit of Epidemiology, Aarhus University, Aarhus, Denmark
| | - Preben Bo Mortensen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CORE Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Mental Health Services in the Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders D. Børglum
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine—Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- LF Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - David M. Hougaard
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department for Congenital Disorders and Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Esben Agerbo
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU, Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Liselotte Vogdrup Petersen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU, Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Trine Munk-Olsen
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- Psychiatric Research Unit, Institute for Clinical Research, University of Southern Denmark, Odense, Denmark
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4
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Grob ST, Miller KR, Sanford B, Donson AM, Jones K, Griesinger AM, Amani V, Foreman NK, Liu A, Handler M, Hankinson TC, Milgrom S, Levy JMM. Genetic predictors of neurocognitive outcomes in survivors of pediatric brain tumors. J Neurooncol 2023; 165:161-169. [PMID: 37878192 PMCID: PMC10638163 DOI: 10.1007/s11060-023-04472-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Neurocognitive deficits are common in pediatric brain tumor survivors. The use of single nucleotide polymorphism (SNP) analysis in DNA repair genes may identify children treated with radiation therapy for brain tumors at increased risk for treatment toxicity and adverse neurocognitive outcomes. MATERIALS The Human 660W-Quad v1.0 DNA BeadChip analysis (Illumina) was used to evaluate 1048 SNPs from 59 DNA repair genes in 46 subjects. IQ testing was measured by the Wechsler Intelligence Scale for Children. Linear regression was used to identify the 10 SNPs with the strongest association with IQ scores while adjusting for radiation type. RESULTS The low vs high IQ patient cohorts were well matched for time from first treatment to most recent IQ, first treatment age, sex, and treatments received. 5 SNPs on 3 different genes (CYP29, XRCC1, and BRCA1) and on 3 different chromosomes (10, 19, and 17) had the strongest association with most recent IQ score that was not modified by radiation type. Furthermore, 5 SNPs on 4 different genes (WRN, NR3C1, ERCC4, RAD51L1) on 4 different chromosomes (8, 5, 16, 14) had the strongest association with change in IQ independent of radiation type, first IQ, and years between IQ measures. CONCLUSIONS SNPs offer the potential to predict adverse neurocognitive outcomes in pediatric brain tumor survivors. Our results require validation in a larger patient cohort. Improving the ability to identify children at risk of treatment related neurocognitive deficits could allow for better treatment stratification and early cognitive interventions.
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Affiliation(s)
- Sydney T Grob
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
| | - Kristen R Miller
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Bridget Sanford
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
| | - Kenneth Jones
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
- Department of Neurosurgery, Children's Hospital Colorado, Aurora, CO, USA
| | - Arthur Liu
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
- Department of Radiation Oncology, University of Colorado Anschutz, Aurora, CO, USA
| | - Michael Handler
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
- Department of Neurosurgery, Children's Hospital Colorado, Aurora, CO, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
- Department of Neurosurgery, Children's Hospital Colorado, Aurora, CO, USA
| | - Sarah Milgrom
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA
- Department of Radiation Oncology, University of Colorado Anschutz, Aurora, CO, USA
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Jean M Mulcahy Levy
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, USA.
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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5
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Morgunova A, Ibrahim P, Chen GG, Coury SM, Turecki G, Meaney MJ, Gifuni A, Gotlib IH, Nagy C, Ho TC, Flores C. Preparation and processing of dried blood spots for microRNA sequencing. Biol Methods Protoc 2023; 8:bpad020. [PMID: 37901452 PMCID: PMC10603595 DOI: 10.1093/biomethods/bpad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.
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Affiliation(s)
- Alice Morgunova
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Gary Gang Chen
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Saché M Coury
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Gustavo Turecki
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore City 138632, Singapore
| | - Anthony Gifuni
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
| | - Corina Nagy
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Tiffany C Ho
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Cecilia Flores
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
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6
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Foss-Skiftesvik J, Li S, Rosenbaum A, Hagen CM, Stoltze UK, Ljungqvist S, Hjalmars U, Schmiegelow K, Morimoto L, de Smith AJ, Mathiasen R, Metayer C, Hougaard D, Melin B, Walsh KM, Bybjerg-Grauholm J, Dahlin AM, Wiemels JL. Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus. Neuro Oncol 2023; 25:1709-1720. [PMID: 36810956 PMCID: PMC10484172 DOI: 10.1093/neuonc/noad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date. METHODS Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes. RESULTS Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8). CONCLUSIONS In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Adam Rosenbaum
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sally Ljungqvist
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Libby Morimoto
- Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - David Hougaard
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kyle M Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | | | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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7
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Musliner KL, Andersen KK, Agerbo E, Albiñana C, Vilhjalmsson BJ, Rajagopal VM, Bybjerg-Grauholm J, Bækved-Hansen M, Pedersen CB, Pedersen MG, Munk-Olsen T, Benros ME, Als TD, Grove J, Werge T, Børglum AD, Hougaard DM, Mors O, Nordentoft M, Mortensen PB, Suppli NP. Polygenic liability, stressful life events and risk for secondary-treated depression in early life: a nationwide register-based case-cohort study. Psychol Med 2023; 53:217-226. [PMID: 33949298 DOI: 10.1017/s0033291721001410] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND In this study, we examined the relationship between polygenic liability for depression and number of stressful life events (SLEs) as risk factors for early-onset depression treated in inpatient, outpatient or emergency room settings at psychiatric hospitals in Denmark. METHODS Data were drawn from the iPSYCH2012 case-cohort sample, a population-based sample of individuals born in Denmark between 1981 and 2005. The sample included 18 532 individuals who were diagnosed with depression by a psychiatrist by age 31 years, and a comparison group of 20 184 individuals. Information on SLEs was obtained from nationwide registers and operationalized as a time-varying count variable. Hazard ratios and cumulative incidence rates were estimated using Cox regressions. RESULTS Risk for depression increased by 35% with each standard deviation increase in polygenic liability (p < 0.0001), and 36% (p < 0.0001) with each additional SLE. There was a small interaction between polygenic liability and SLEs (β = -0.04, p = 0.0009). The probability of being diagnosed with depression in a hospital-based setting between ages 15 and 31 years ranged from 1.5% among males in the lowest quartile of polygenic liability with 0 events by age 15, to 18.8% among females in the highest quartile of polygenic liability with 4+ events by age 15. CONCLUSIONS These findings suggest that although there is minimal interaction between polygenic liability and SLEs as risk factors for hospital-treated depression, combining information on these two important risk factors could potentially be useful for identifying high-risk individuals.
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Affiliation(s)
- Katherine L Musliner
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Klaus K Andersen
- Unit for Statistics and Pharmacoepidemiology (SPE), Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Clara Albiñana
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Bjarni J Vilhjalmsson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Veera M Rajagopal
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genome Analysis and Personalized Medicine, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Marie Bækved-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Carsten B Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Marianne G Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Trine Munk-Olsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Michael E Benros
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Genome Analysis and Personalized Medicine, Aarhus, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Nis P Suppli
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
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8
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Boelt SG, Plana-Ripoll O, Albiñana C, Vilhjálmsson B, McGrath JJ, Cohen AS. A method to correct for the influence of bovine serum albumin-associated vitamin D metabolites in protein extracts from neonatal dried blood spots. BMC Res Notes 2022; 15:194. [PMID: 35659347 PMCID: PMC9166528 DOI: 10.1186/s13104-022-06077-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Objective We developed an assay to measure the concentration of 25 hydroxyvitamin D2 and D3 in protein extracts derived from stored neonatal dried blood spots. During this study, we postulated that these samples had been contaminated with exogenous vitamin D metabolites because of the addition of bovine serum albumin (BSA) as part of an extraction step undertaken 7 years earlier. The aim of the current study was to develop methods in order to adjust for this contamination. Results We identified between-plate variations in 25 hydroxyvitamin D2 and D3 concentrations which suggested the presence of three different BSA batches. Based on repeat extraction (without the addition of BSA) and testing of 395 samples, we developed models to correct for the exogenous 25 hydroxyvitamin D2 and D3. The regression models were Diff25OHD3 = − 8.2 + 1.8* Diff25OHD2 for low contamination, Diff25OHD3 = 23.8 + 1.7* Diff25OHD2 for middle contamination, and Diff25OHD3 = 14.3 + 3.0* Diff25OHD2 for high contamination. After these corrections, the three subsamples had comparable distributions within the expected range for both 25 hydroxyvitamin D2 and D3. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06077-1.
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Affiliation(s)
- Sanne Grundvad Boelt
- Center for Neonatal Screening, Department of Congenital Disorders-Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark.,Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, Olof Palmes Allé 43-45 Aarhus N, 8200, Aarhus, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark
| | - Bjarni Vilhjálmsson
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, Building 1110 Aarhus C, DK-8000, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640 Aarhus V, DK-8210, Aarhus, Denmark. .,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, University of Queensland, St. Lucia, QLD-4072, Australia. .,Queensland Brain Institute, University of Queensland, St. Lucia, QLD-4072, Australia.
| | - Arieh S Cohen
- Center for Neonatal Screening, Department of Congenital Disorders-Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
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9
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Boelt SG, Melgaard L, Thorbek MJ, MacSween NSJ, McGrath JJ, Cohen AS. Sensitive and Robust LC-MS/MS Assay to Quantify 25-Hydroxyvitamin D in Leftover Protein Extract from Dried Blood Spots. Int J Neonatal Screen 2021; 7:ijns7040082. [PMID: 34940052 PMCID: PMC8704356 DOI: 10.3390/ijns7040082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022] Open
Abstract
Neonatal dried blood spots (DBS) provide a remarkable resource for biobanks. These microsamples can provide information related to the genetic correlates of disease and can be used to quantify a range of analytes, such as proteins and small molecules. However, after routine neonatal screening, the amount of DBS sample available is limited. To optimize the use of these samples, there is a need for sensitive assays which are integrated across different analytic platforms. For example, after DNA extraction, protein extracts are available for additional analyses. We describe a sensitive and robust LC-MS/MS method for 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 optimized for leftover protein extracts from DBS, which has excellent recovery, precision, and accuracy.
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Affiliation(s)
- Sanne Grundvad Boelt
- Center for Neonatal Screening, Department of Congenital Disorders—Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (S.G.B.); (L.M.); (M.J.T.); (N.S.J.M.); (A.S.C.)
| | - Lars Melgaard
- Center for Neonatal Screening, Department of Congenital Disorders—Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (S.G.B.); (L.M.); (M.J.T.); (N.S.J.M.); (A.S.C.)
| | - Marta Jadwiga Thorbek
- Center for Neonatal Screening, Department of Congenital Disorders—Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (S.G.B.); (L.M.); (M.J.T.); (N.S.J.M.); (A.S.C.)
| | - Nadia Sara Jensen MacSween
- Center for Neonatal Screening, Department of Congenital Disorders—Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (S.G.B.); (L.M.); (M.J.T.); (N.S.J.M.); (A.S.C.)
| | - John J. McGrath
- National Centre for Register-Based Research, Department of Economics and Business Economics, Aarhus University, Fuglesangs Allé 26, Building 2640, DK-8210 Aarhus V, Denmark
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD 4076, Australia
- Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence:
| | - Arieh S. Cohen
- Center for Neonatal Screening, Department of Congenital Disorders—Clinical Mass Spectrometry Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (S.G.B.); (L.M.); (M.J.T.); (N.S.J.M.); (A.S.C.)
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10
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Bulik CM, Thornton LM, Parker R, Kennedy H, Baker JH, MacDermod C, Guintivano J, Cleland L, Miller AL, Harper L, Larsen JT, Yilmaz Z, Grove J, Sullivan PF, Petersen LV, Jordan J, Kennedy MA, Martin NG. The Eating Disorders Genetics Initiative (EDGI): study protocol. BMC Psychiatry 2021; 21:234. [PMID: 33947359 PMCID: PMC8097919 DOI: 10.1186/s12888-021-03212-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/13/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The Eating Disorders Genetics Initiative (EDGI) is an international investigation exploring the role of genes and environment in anorexia nervosa, bulimia nervosa, and binge-eating disorder. METHODS A total of 14,500 individuals with eating disorders and 1500 controls will be included from the United States (US), Australia (AU), New Zealand (NZ), and Denmark (DK). In the US, AU, and NZ, participants will complete comprehensive online phenotyping and will submit a saliva sample for genotyping. In DK, individuals with eating disorders will be identified by the National Patient Register, and genotyping will occur using bloodspots archived from birth. A genome-wide association study will be conducted within EDGI and via meta-analysis with other data from the Eating Disorders Working Group of the Psychiatric Genomics Consortium (PGC-ED). DISCUSSION EDGI represents the largest genetic study of eating disorders ever to be conducted and is designed to rapidly advance the study of the genetics of the three major eating disorders (anorexia nervosa, bulimia nervosa, and binge-eating disorder). We will explicate the genetic architecture of eating disorders relative to each other and to other psychiatric and metabolic disorders and traits. Our goal is for EDGI to deliver "actionable" findings that can be transformed into clinically meaningful insights. TRIAL REGISTRATION EDGI is a registered clinical trial: clinicaltrials.gov NCT04378101 .
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Affiliation(s)
- Cynthia M. Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Laura M. Thornton
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
| | - Richard Parker
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital, Herston, QLD 4029 Australia
| | - Hannah Kennedy
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Jessica H. Baker
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
| | - Casey MacDermod
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
| | - Jerry Guintivano
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
| | - Lana Cleland
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Allison L. Miller
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Lauren Harper
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
| | - Janne T. Larsen
- National Centre for Register-based Research, Aarhus BSS, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Zeynep Yilmaz
- National Centre for Register-based Research, Aarhus BSS, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Patrick F. Sullivan
- Department of Psychiatry, University of North Carolina at Chapel Hill, CB #7160, 101 Manning Drive, Chapel Hill, NC 27599-7160 USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Liselotte V. Petersen
- National Centre for Register-based Research, Aarhus BSS, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Jennifer Jordan
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nicholas G. Martin
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital, Herston, QLD 4029 Australia
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11
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Foss-Skiftesvik J, Hagen CM, Mathiasen R, Adamsen D, Bækvad-Hansen M, Børglum AD, Nordentoft M, Werge T, Christiansen M, Schmiegelow K, Juhler M, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J. Genome-wide association study across pediatric central nervous system tumors implicates shared predisposition and points to 1q25.2 (PAPPA2) and 11p12 (LRRC4C) as novel candidate susceptibility loci. Childs Nerv Syst 2021; 37:819-830. [PMID: 33226468 DOI: 10.1007/s00381-020-04946-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Central nervous system (CNS) tumors constitute the most common form of solid neoplasms in children, but knowledge on genetic predisposition is sparse. In particular, whether susceptibility attributable to common variants is shared across CNS tumor types in children has not been investigated. The purpose of this study was to explore potential common genetic risk variants exhibiting pleiotropic effects across pediatric CNS tumors. We also investigated whether such susceptibility differs between early and late onset of disease. METHOD A Danish nationwide genome-wide association study (GWAS) of 1,097 consecutive patients (< 15 years of age) with CNS tumors and a cohort of 4,745 population-based controls. RESULTS For both the overall cohort and patients diagnosed after the age of four, the strongest association was rs12064625 which maps to PAPPA2 at 1q25.2 (p = 3.400 × 10-7 and 9.668 × 10-8, respectively). PAPPA2 regulates local bioavailability of insulin-like growth factor I (IGF-I). IGF-I is fundamental to CNS development and is involved in tumorigenesis across a wide range of different cancers. For the younger children, the strongest association was provided by rs11036373 mapping to LRRC4C at 11p12 (p = 7.620 × 10-7), which encoded protein acts as an axon guidance molecule during CNS development and has not formerly been associated with brain tumors. DISCUSSION This GWAS indicates shared susceptibility attributable to common variants across pediatric CNS tumor types. Variations in genetic loci with roles in CNS development appear to be involved, possibly via altered IGF-I related pathways.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark.
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark.
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.
| | - Christian Munch Hagen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Dea Adamsen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Department of Biomedicine, Aarhus University and Centre for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Aarhus Genome Center, Aarhus, Denmark
| | - Merete Nordentoft
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Michael Christiansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Juhler
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurosurgery, Aarhus University Hospital, Aarhus, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - David Michael Hougaard
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
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12
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Dahlin AM, Wibom C, Andersson U, Bybjerg-Grauholm J, Deltour I, Hougaard DM, Scheurer ME, Lau CC, McKean-Cowdin R, Kennedy RJ, Hung LT, Yee J, Margol AS, Barrington-Trimis J, Gauderman WJ, Feychting M, Schüz J, Röösli M, Kjaerheim K, Januszkiewicz-Lewandowska D, Fichna M, Nowak J, Searles Nielsen S, Asgharzadeh S, Mirabello L, Hjalmars U, Melin B. A genome-wide association study on medulloblastoma. J Neurooncol 2020; 147:309-315. [PMID: 32056145 PMCID: PMC7136185 DOI: 10.1007/s11060-020-03424-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Medulloblastoma is a malignant embryonal tumor of the cerebellum that occurs predominantly in children. To find germline genetic variants associated with medulloblastoma risk, we conducted a genome-wide association study (GWAS) including 244 medulloblastoma cases and 247 control subjects from Sweden and Denmark. METHODS Genotyping was performed using Illumina BeadChips, and untyped variants were imputed using IMPUTE2. RESULTS Fifty-nine variants in 11 loci were associated with increased medulloblastoma risk (p < 1 × 10-5), but none were statistically significant after adjusting for multiple testing (p < 5 × 10-8). Thirteen of these variants were genotyped, whereas 46 were imputed. Genotyped variants were further investigated in a validation study comprising 249 medulloblastoma cases and 629 control subjects. In the validation study, rs78021424 (18p11.23, PTPRM) was associated with medulloblastoma risk with OR in the same direction as in the discovery cohort (ORT = 1.59, pvalidation = 0.02). We also selected seven medulloblastoma predisposition genes for investigation using a candidate gene approach: APC, BRCA2, PALB2, PTCH1, SUFU, TP53, and GPR161. The strongest evidence for association was found for rs201458864 (PALB2, ORT = 3.76, p = 3.2 × 10-4) and rs79036813 (PTCH1, ORA = 0.42, p = 2.6 × 10-3). CONCLUSION The results of this study, including a novel potential medulloblastoma risk loci at 18p11.23, are suggestive but need further validation in independent cohorts.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - David M Hougaard
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Ching C Lau
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rebekah J Kennedy
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Long T Hung
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Janis Yee
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Ashley S Margol
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jessica Barrington-Trimis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maria Feychting
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Martin Röösli
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Danuta Januszkiewicz-Lewandowska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Jerzy Nowak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Susan Searles Nielsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Shahab Asgharzadeh
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Saban Research Institute at Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
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13
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Sok P, Lupo PJ, Richard MA, Rabin KR, Ehli EA, Kallsen NA, Davies GE, Scheurer ME, Brown AL. Utilization of archived neonatal dried blood spots for genome-wide genotyping. PLoS One 2020; 15:e0229352. [PMID: 32084225 PMCID: PMC7034898 DOI: 10.1371/journal.pone.0229352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/04/2020] [Indexed: 01/14/2023] Open
Abstract
Introduction Heel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment may vary across biobanks and across time within biobanks. With increased applications of DNA extracted from spots for genetic studies, identifying factors associated with genotyping success is critical to maximize DNA quality for future studies. Method We evaluated 399 blood spots, which were part of a genome-wide association study of childhood leukemia risk in children with Down syndrome, archived at the Michigan Neonatal Biobank between 1992 and 2008. High quality DNA was defined as having post-quality control call rate ≥ 99.0% based on the Illumina GenomeStudio 2.0 GenCall algorithm after processing the samples on the Illumina Infinium Global Screening Array. Bivariate analyses and multivariable logistic regression models were applied to evaluate effects of storage environment and storage duration on DNA genotyping quality. Results Both storage environment and duration were associated with sample genotyping call rates (p-values < 0.001). Sample call rates were associated with storage duration independent of storage environment (p-trend = 0.006 for DBS archived in an uncontrolled environment and p-trend = 0.002 in a controlled environment). However, 95% of the total sample had high genotyping quality with a call rate ≥ 95.0%, a standard threshold for acceptable sample quality in many genetic studies. Conclusion Blood spot DNA quality was lower in samples archived in uncontrolled storage environments and for samples archived for longer durations. Still, regardless of storage environment or duration, neonatal biobanks including the Michigan Neonatal Biobanks can provide access to large collections of spots with DNA quality acceptable for most genotyping studies.
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Affiliation(s)
- Pagna Sok
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip J. Lupo
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Melissa A. Richard
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Karen R. Rabin
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Michael E. Scheurer
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Austin L. Brown
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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14
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Erlangsen A, Appadurai V, Wang Y, Turecki G, Mors O, Werge T, Mortensen PB, Starnawska A, Børglum AD, Schork A, Nudel R, Bækvad-Hansen M, Bybjerg-Grauholm J, Hougaard DM, Thompson WK, Nordentoft M, Agerbo E. Genetics of suicide attempts in individuals with and without mental disorders: a population-based genome-wide association study. Mol Psychiatry 2020; 25:2410-2421. [PMID: 30116032 PMCID: PMC7515833 DOI: 10.1038/s41380-018-0218-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/14/2018] [Accepted: 06/04/2018] [Indexed: 01/30/2023]
Abstract
Family studies have shown an aggregation of suicidal behavior in families. Yet, molecular studies are needed to identify loci accounting for genetic heritability. We conducted a genome-wide association study and estimated single nucleotide polymorphisms (SNP) heritability for a suicide attempt. In a case-cohort study, national data on all individuals born in Denmark after 1981 and diagnosed with severe mental disorders prior to 2013 (n = 57,377) and individuals from the general population (n = 30,000) were obtained. After quality control, the sample consisted of 6024 cases with an incidence of suicide attempt and 44,240 controls with no record of a suicide attempt. Suggestive associations between SNPs, rs6880062 (p-value: 5.4 × 10-8) and rs6880461 (p-value: 9.5 × 10-8), and suicide attempt were identified when adjusting for socio-demographics. Adjusting for mental disorders, three significant associations, all on chromosome 20, were identified: rs4809706 (p-value: 2.8 × 10-8), rs4810824 (p-value: 3.5 × 10-8), and rs6019297 (p-value: 4.7 × 108). Sub-group analysis of cases with affective disorders revealed SNPs associated with suicide attempts when compared to the general population for gene PDE4B. All SNPs explained 4.6% [CI-95: 2.9-6.3%] of the variation in suicide attempt. Controlling for mental disorders reduced the heritability to 1.9% [CI-95: 0.3-3.5%]. Affective and autism spectrum disorders exhibited a SNP heritability of 5.6% [CI-95: 1.9-9.3%] and 9.6% [CI-95: 1.1-18.1%], respectively. Using the largest sample to date, we identified significant SNP associations with suicide attempts and support for a genetic transmission of suicide attempt, which might not solely be explained by mental disorders.
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Affiliation(s)
- Annette Erlangsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,Danish Research Institute for Suicide Prevention, Mental Health Centre Copenhagen, Copenhagen, Denmark. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. .,Center of Mental Health Research, Australian National University, Canberra, Australia.
| | - Vivek Appadurai
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Yunpeng Wang
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.5510.10000 0004 1936 8921Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,grid.5510.10000 0004 1936 8921Division of Mental Health and Addiction, University of Oslo, Oslo, Norway
| | - Gustavo Turecki
- grid.14709.3b0000 0004 1936 8649McGill Group for Suicide Studies, Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Montreal, Canada
| | - Ole Mors
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Thomas Werge
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Roskilde, Denmark ,grid.5254.60000 0001 0674 042XInstitute of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Preben B. Mortensen
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722National Centre for Register-based Research (NCRR) and Centre for Integrated Register-based Research (CIRRAU), Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Anders D. Børglum
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark ,grid.154185.c0000 0004 0512 597XCentre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Andrew Schork
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Ron Nudel
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Marie Bækvad-Hansen
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.6203.70000 0004 0417 4147Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.6203.70000 0004 0417 4147Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - David M. Hougaard
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.6203.70000 0004 0417 4147Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Wesley K. Thompson
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.5510.10000 0004 1936 8921Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,grid.5510.10000 0004 1936 8921Division of Mental Health and Addiction, University of Oslo, Oslo, Norway ,grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital, Risskov, Denmark ,grid.266100.30000 0001 2107 4242Division of Biostatistics, Department of Family Medicine and Public Health, University of California, San Diego, CA USA
| | - Merete Nordentoft
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.466916.a0000 0004 0631 4836Danish Research Institute for Suicide Prevention, Mental Health Centre Copenhagen, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XInstitute of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XResearch Unit, Mental Health Centre Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- grid.452548.a0000 0000 9817 5300The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722National Centre for Register-based Research (NCRR) and Centre for Integrated Register-based Research (CIRRAU), Aarhus University, Aarhus, Denmark
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15
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [PMID: 31815249 DOI: 10.12688/gatesopenres.12855.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods: The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result: Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 - 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can't be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples. Conclusion: The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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Affiliation(s)
- Abhinendra Kumar
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sharayu Mhatre
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sheela Godbole
- Department of Biostatistics and Epidemiology, National AIDS Research Institute, Pune, Maharashtra, 411026, India
| | - Prabhat Jha
- Li Ka Shing Knowledge Institiute, St Michael's Hospital, Center for Global Health Research, Toronto, ON, Canada
| | - Rajesh Dikshit
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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16
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [PMID: 31815249 PMCID: PMC6883222 DOI: 10.12688/gatesopenres.12855.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 11/20/2022] Open
Abstract
Background: Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods: The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result: Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 – 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can’t be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples. Conclusion: The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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Affiliation(s)
- Abhinendra Kumar
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sharayu Mhatre
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Sheela Godbole
- Department of Biostatistics and Epidemiology, National AIDS Research Institute, Pune, Maharashtra, 411026, India
| | - Prabhat Jha
- Li Ka Shing Knowledge Institiute, St Michael's Hospital, Center for Global Health Research, Toronto, ON, Canada
| | - Rajesh Dikshit
- Centre for Cancer Epidemiology, Tata Memorial Centre, Mumbai, Maharashtra, 410210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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17
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Bauer AE, Liu X, Byrne EM, Sullivan PF, Wray NR, Agerbo E, Nyegaard M, Grove J, Musliner KL, Ingstrup KG, Johannsen BMW, Mægbæk ML, Wang Y, Nordentoft M, Mors O, Børglum AD, Werge T, Hougaard DM, Mortensen PB, Munk-Olsen T, Meltzer-Brody S. Genetic risk scores for major psychiatric disorders and the risk of postpartum psychiatric disorders. Transl Psychiatry 2019; 9:288. [PMID: 31712652 PMCID: PMC6848186 DOI: 10.1038/s41398-019-0629-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/18/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022] Open
Abstract
Postpartum psychiatric disorders are heritable, but how genetic liability varies by other significant risk factors is unknown. We aimed to (1) estimate associations of genetic risk scores (GRS) for major depression (MD), bipolar disorder (BD), and schizophrenia (SCZ) with postpartum psychiatric disorders, (2) examine differences by prior psychiatric history, and (3) compare genetic and familial risk of postpartum psychiatric disorders. We conducted a nested case-control study based on Danish population-based registers of all women in the iPSYCH2012 cohort who had given birth before December 31, 2015 (n = 8850). Cases were women with a diagnosed psychiatric disorder or a filled psychotropic prescription within one year after delivery (n = 5829 cases, 3021 controls). Association analyses were conducted between GRS calculated from Psychiatric Genomics Consortium discovery meta-analyses for MD, BD, and SCZ and case-control status of a postpartum psychiatric disorder. Parental psychiatric history was associated with postpartum psychiatric disorders among women with previous psychiatric history (OR, 1.14; 95% CI 1.02-1.28) but not without psychiatric history (OR, 1.08; 95% CI: 0.81-1.43). GRS for MD was associated with an increased risk of postpartum psychiatric disorders in both women with (OR, 1.44; 95% CI: 1.19-1.74) and without (OR, 1.88; 95% CI: 1.26-2.81) personal psychiatric history. SCZ GRS was only minimally associated with postpartum disorders and BD GRS was not. Results suggest GRS of lifetime psychiatric illness can be applied to the postpartum period, which may provide clues about distinct environmental or genetic elements of postpartum psychiatric disorders and ultimately help identify vulnerable groups.
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Affiliation(s)
- Anna E Bauer
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Xiaoqin Liu
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Enda M Byrne
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Patrick F Sullivan
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Esben Agerbo
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU - Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing and, Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing and, Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Katherine L Musliner
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Katja G Ingstrup
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Benedicte M W Johannsen
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Merete L Mægbæk
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Yunpeng Wang
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway
| | - Merete Nordentoft
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Centre Copenhagen, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing and, Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
| | - David M Hougaard
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU - Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing and, Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Trine Munk-Olsen
- NCRR - National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Samantha Meltzer-Brody
- Department of Psychiatry, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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18
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Gasse C, Wimberley T, Wang Y, Mors O, Børglum A, Als TD, Werge T, Nordentoft M, Hougaard DM, Horsdal HT. Schizophrenia polygenic risk scores, urbanicity and treatment-resistant schizophrenia. Schizophr Res 2019; 212:79-85. [PMID: 31447354 DOI: 10.1016/j.schres.2019.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/10/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
INTRODUCTION To investigate the impact of a polygenic risk score for schizophrenia (PRS-SZ) and urbanicity on the risk of treatment-resistant schizophrenia (TRS) in people diagnosed with schizophrenia and to evaluate the association between PRS-SZ and TRS across levels of urbanicity. METHODS Cohort study of people born after 1981 with a first registered diagnosis of schizophrenia between 1996 and 2012 using Danish population registry data. Through linkage to genome-wide data, we calculated PRS-SZ based on a Psychiatric Genomics Consortium meta-analysis. We assessed urbanicity at birth (capital, provincial and rural areas). TRS was defined using prescription and hospital data. Performing Cox regression analysis, we calculated hazard rate ratios (HRs) and 95% confidence intervals (CI). RESULTS Among 4475 people with schizophrenia, we identified 593 (13.3%) with TRS during 17,558 person years of follow-up. The adjusted HR for TRS associated with one standard deviation (SD) increase in the PRS-SZ was 1.11 (95% CI: 1.00-1.24). The adjusted HRs for TRS across levels of urbanicity were 1.20 (95% CI: 0.98-1.47) for provincial areas and 1.19 (95% CI 0.96-1.47) for rural areas compared with the capital area. Within strata of urbanicity, the adjusted HR for TRS was 1.39 (95% CI: 1.14-1.70) in the capital area with 1 SD increase in the PRS-SZ, 0.99 (95% CI 0.84-1.17) in provincial areas, and 1.03 (95% CI: 0.86-1.25) in rural areas. CONCLUSION The effect of genetic liability (i.e. PRS) on risk of TRS varied across urbanicity levels and was highest for people with schizophrenia born in the capital areas.
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Affiliation(s)
- Christiane Gasse
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; CIRRAU - Centre for Integrated Register-Based Research at Aarhus University, Aarhus, Denmark; Department for Depression and Anxiety, Aarhus University Hospital - Psychiatry, Aarhus, Denmark.
| | - Theresa Wimberley
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Yungpeng Wang
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States of America; Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, United States of America
| | - Ole Mors
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Psychosis Research Unit, Aarhus University Hospital - Psychiatry, Aarhus, Denmark
| | - Anders Børglum
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Thomas Damm Als
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Merete Nordentoft
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Copenhagen University Hospital, Mental Health Center Copenhagen, Mental Health Services in the Capital Region of Denmark, Denmark
| | - David M Hougaard
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, Denmark
| | - Henriette Thisted Horsdal
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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19
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Kumar A, Mhatre S, Godbole S, Jha P, Dikshit R. Optimization of extraction of genomic DNA from archived dried blood spot (DBS): potential application in epidemiological research & bio banking. Gates Open Res 2019; 2:57. [DOI: 10.12688/gatesopenres.12855.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
Background:Limited infrastructure is available to collect, store and transport venous blood in field epidemiological studies. Dried blood spot (DBS) is a robust potential alternative sample source for epidemiological studies & bio banking. A stable source of genomic DNA (gDNA) is required for long term storage in bio bank for its downstream applications. Our objective is to optimize the methods of gDNA extraction from stored DBS and with the aim of revealing its utility in large scale epidemiological studies. Methods:The purpose of this study was to extract the maximum amount of gDNA from DBS on Whatman 903 protein saver card. gDNA was extracted through column (Qiagen) & magnetic bead based (Invitrogen) methods. Quantification of extracted gDNA was performed with a spectrophotometer, fluorometer, and integrity analyzed by agarose gel electrophoresis. Result:Large variation was observed in quantity & purity (260/280 ratio, 1.8-2.9) of the extracted gDNA. The intact gDNA bands on the electrophoresis gel reflect the robustness of DBS for gDNA even after prolonged storage time. The extracted gDNA amount 2.16 – 24 ng/µl is sufficient for its PCR based downstream application, but unfortunately it can’t be used for whole genome sequencing or genotyping from extracted gDNA. Sequencing or genotyping can be achieved by after increasing template copy number through whole genome amplification of extracted gDNA. The obtained results create a base for future research to develop high-throughput research and extraction methods from blood samples.Conclusion:The above results reveal, DBS can be utilized as a potential and robust sample source for bio banking in field epidemiological studies.
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20
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Dahlin AM, Wibom C, Andersson U, Hougaard DM, Bybjerg-Grauholm J, Deltour I, Hultman CM, Kähler AK, Karlsson R, Hjalmars U, Melin B. Genetic Variants in the 9p21.3 Locus Associated with Glioma Risk in Children, Adolescents, and Young Adults: A Case-Control Study. Cancer Epidemiol Biomarkers Prev 2019; 28:1252-1258. [PMID: 31040135 DOI: 10.1158/1055-9965.epi-18-1026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 04/26/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified germline genetic variants in 25 genetic loci that increase the risk of developing glioma in adulthood. It is not known if these variants increase the risk of developing glioma in children and adolescents and young adults (AYA). To date, no studies have performed genome-wide analyses to find novel genetic variants associated with glioma risk in children and AYA. METHODS We investigated the association between 8,831,628 genetic variants and risk of glioma in 854 patients diagnosed up to the age of 29 years and 3,689 controls from Sweden and Denmark. Recruitment of patients and controls was population based. Genotyping was performed using Illumina BeadChips, and untyped variants were imputed with IMPUTE2. We selected 41 established adult glioma risk variants for detailed investigation. RESULTS Three adult glioma risk variants, rs634537, rs2157719, and rs145929329, all mapping to the 9p21.3 (CDKN2B-AS1) locus, were associated with glioma risk in children and AYA. The strongest association was seen for rs634537 (odds ratioG = 1.21; 95% confidence interval = 1.09-1.35; P = 5.8 × 10-4). In genome-wide analysis, an association with risk was suggested for 129 genetic variants (P <1 × 10-5). CONCLUSIONS Carriers of risk alleles in the 9p21.3 locus have an increased risk of glioma throughout life. The results from genome-wide association analyses require validation in independent cohorts. IMPACT Our findings line up with existing evidence that some, although not all, established adult glioma risk variants are associated with risk of glioma in children and AYA. Validation of results from genome-wide analyses may reveal novel susceptibility loci for glioma in children and AYA.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - David M Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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21
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Wang Y, Karstoft KI, Nievergelt CM, Maihofer AX, Stein MB, Ursano RJ, Bybjerg-Grauholm J, Bækvad-Hansen M, Hougaard DM, Andreassen OA, Werge T, Thompson WK, Andersen SB. Post-traumatic stress following military deployment: Genetic associations and cross-disorder genetic correlations. J Affect Disord 2019; 252:350-357. [PMID: 30999091 DOI: 10.1016/j.jad.2019.04.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/22/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Post-traumatic stress disorder (PTSD) is a complex psychiatric disorder that occurs with relatively high frequency after deployment to warzones (∼10%). While twin studies have estimated the heritability to be up to 40%, thus indicating a considerable genetic component in the etiology, the biological mechanisms underlying risk and development of PTSD remain unknown. METHODS Here, we conduct a genome-wide association study (GWAS; N = 2,481) to identify genome regions that associate with PTSD in a highly homogenous, trauma-exposed sample of Danish soldiers deployed to war and conflict zones. We perform integrated analyses of our results with gene-expression and chromatin-contact datasets to prioritized genes. We also leverage on other large GWAS (N>300,000) to investigate genetic correlations between PTSD and other psychiatric disorders and traits. RESULTS We discover, but do not replicate, one region, 4q31, close to the IL15 gene, which is genome-wide significantly associated with PTSD. We demonstrate that gene-set enrichment, polygenic risk score and genetic correlation analyses show consistent and significant genetic correlations between PTSD and depression, insomnia and schizophrenia. LIMITATIONS The limited sample size, the lack of replication, and the PTSD case definition by questionnaire are limitations to the study. CONCLUSIONS Our results suggest that genetic perturbations of inflammatory response may contribute to the risk of PTSD. In addition, shared genetic components contribute to observed correlations between PTSD and depression, insomnia and schizophrenia.
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Affiliation(s)
- Yunpeng Wang
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway; Department of Psychology, University of Oslo, Harald Schelderups Hus Forskningsveien 3A 0373 Oslo
| | - Karen-Inge Karstoft
- Research and Knowledge Center, The Danish Veteran Center, Garnisonen 1, 4100 Ringsted, Denmark; Department of Psychology, University of Copenhagen, Øster Farimagsgade 2A, 1353 Copenhagen, Denmark.
| | - Caroline M Nievergelt
- VA Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla Village Drive 3350, 92161 La Jolla, CA, USA; Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Adam X Maihofer
- VA Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla Village Drive 3350, 92161 La Jolla, CA, USA; Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Murray B Stein
- Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA; Department of Family Medicine and Public Health, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Jones Bridge Road 4301, 20814 Bethesda, MD, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Wesley K Thompson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway; Division of Biostatistics, Department of Family Medicine and Public Health, University of California, San Diego
| | - Søren B Andersen
- Research and Knowledge Center, The Danish Veteran Center, Garnisonen 1, 4100 Ringsted, Denmark
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22
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Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Bækvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Churchhouse C, Dellenvall K, Demontis D, De Rubeis S, Devlin B, Djurovic S, Dumont AL, Goldstein JI, Hansen CS, Hauberg ME, Hollegaard MV, Hope S, Howrigan DP, Huang H, Hultman CM, Klei L, Maller J, Martin J, Martin AR, Moran JL, Nyegaard M, Nærland T, Palmer DS, Palotie A, Pedersen CB, Pedersen MG, dPoterba T, Poulsen JB, Pourcain BS, Qvist P, Rehnström K, Reichenberg A, Reichert J, Robinson EB, Roeder K, Roussos P, Saemundsen E, Sandin S, Satterstrom FK, Davey Smith G, Stefansson H, Steinberg S, Stevens CR, Sullivan PF, Turley P, Walters GB, Xu X, Stefansson K, Geschwind DH, Nordentoft M, Hougaard DM, Werge T, Mors O, Mortensen PB, Neale BM, Daly MJ, Børglum AD. Identification of common genetic risk variants for autism spectrum disorder. Nat Genet 2019; 51:431-444. [PMID: 30804558 PMCID: PMC6454898 DOI: 10.1038/s41588-019-0344-8] [Citation(s) in RCA: 1228] [Impact Index Per Article: 245.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/12/2018] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD.
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Affiliation(s)
- Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Manuel Mattheisen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonatan Pallesen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Richard Anney
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Swapnil Awashti
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Rich Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Francesco Bettella
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Felecia Cerrato
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jane H Christensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karin Dellenvall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Srdjan Djurovic
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ashley L Dumont
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christine S Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark
| | - Mads Engel Hauberg
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Mads V Hollegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sigrun Hope
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- Department of Neurohabilitation, Oslo University Hospital, Oslo, Norway
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Julian Maller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Genomics plc, Oxford, UK
- Vertex Pharmaceuticals, Abingdon, UK
| | - Joanna Martin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mette Nyegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Terje Nærland
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway
- NevSom, Department of Rare Disorders and Disabilities, , Oslo University Hospital, Oslo, Norway
| | - Duncan S Palmer
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Carsten Bøcker Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Marianne Giørtz Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Timothy dPoterba
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jesper Buchhave Poulsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Per Qvist
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | | | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer Reichert
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elise B Robinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kathryn Roeder
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | | | - Christine R Stevens
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick Turley
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - G Bragi Walters
- deCODE genetics/Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment and Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
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23
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Thornton LM, Munn-Chernoff MA, Baker JH, Juréus A, Parker R, Henders AK, Larsen JT, Petersen L, Watson HJ, Yilmaz Z, Kirk KM, Gordon S, Leppä VM, Martin FC, Whiteman DC, Olsen CM, Werge TM, Pedersen NL, Kaye W, Bergen AW, Halmi KA, Strober M, Kaplan AS, Woodside DB, Mitchell J, Johnson CL, Brandt H, Crawford S, Horwood LJ, Boden JM, Pearson JF, Duncan LE, Grove J, Mattheisen M, Jordan J, Kennedy MA, Birgegård A, Lichtenstein P, Norring C, Wade TD, Montgomery GW, Martin NG, Landén M, Mortensen PB, Sullivan PF, Bulik CM. The Anorexia Nervosa Genetics Initiative (ANGI): Overview and methods. Contemp Clin Trials 2018; 74:61-69. [PMID: 30287268 DOI: 10.1016/j.cct.2018.09.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/17/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Genetic factors contribute to anorexia nervosa (AN); and the first genome-wide significant locus has been identified. We describe methods and procedures for the Anorexia Nervosa Genetics Initiative (ANGI), an international collaboration designed to rapidly recruit 13,000 individuals with AN and ancestrally matched controls. We present sample characteristics and the utility of an online eating disorder diagnostic questionnaire suitable for large-scale genetic and population research. METHODS ANGI recruited from the United States (US), Australia/New Zealand (ANZ), Sweden (SE), and Denmark (DK). Recruitment was via national registers (SE, DK); treatment centers (US, ANZ, SE, DK); and social and traditional media (US, ANZ, SE). All cases had a lifetime AN diagnosis based on DSM-IV or ICD-10 criteria (excluding amenorrhea). Recruited controls had no lifetime history of disordered eating behaviors. To assess the positive and negative predictive validity of the online eating disorder questionnaire (ED100K-v1), 109 women also completed the Structured Clinical Interview for DSM-IV (SCID), Module H. RESULTS Blood samples and clinical information were collected from 13,363 individuals with lifetime AN and from controls. Online diagnostic phenotyping was effective and efficient; the validity of the questionnaire was acceptable. CONCLUSIONS Our multi-pronged recruitment approach was highly effective for rapid recruitment and can be used as a model for efforts by other groups. High online presence of individuals with AN rendered the Internet/social media a remarkably effective recruitment tool in some countries. ANGI has substantially augmented Psychiatric Genomics Consortium AN sample collection. ANGI is a registered clinical trial: clinicaltrials.govNCT01916538; https://clinicaltrials.gov/ct2/show/NCT01916538?cond=Anorexia+Nervosa&draw=1&rank=3.
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Affiliation(s)
- Laura M Thornton
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Jessica H Baker
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
| | - Richard Parker
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | | | - Janne T Larsen
- Aarhus University, Norde Ringgade 1, 8000 Aarhus, Denmark
| | | | - Hunna J Watson
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Zeynep Yilmaz
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine M Kirk
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - Scott Gordon
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - Virpi M Leppä
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
| | - Felicity C Martin
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - Catherine M Olsen
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - Thomas M Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Bartholin Alle 6, 8000 Aarhus, Denmark; Mental Health Services, Institute for Biological Psychiatry, MHC Sct. Hans, Kristineberg 3, 2100 Copenhagen, Denmark; University of Copenhagen, Nørregade 10, DK-1165 Copenhagen, Denmark
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
| | - Walter Kaye
- University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Andrew W Bergen
- Biorealm Research, 6101 W Centinela Ave # 270, Culver City, CA 90230, USA; Oregon Research Institute, Eugene, OR 97403, USA
| | - Katherine A Halmi
- Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Michael Strober
- University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Allan S Kaplan
- University of Toronto, 27 King's College Circle, Toronto, ON M5S 1A1, Canada
| | - D Blake Woodside
- University of Toronto, 27 King's College Circle, Toronto, ON M5S 1A1, Canada; Toronto General Hospital, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada
| | - James Mitchell
- Neuropsychiatric Research Institute, 120 8th Street South, Fargo, ND 58103, USA
| | - Craig L Johnson
- Eating Recovery Center, 7351 E. Lowry Blvd., Suite 200, Denver, CO 80230, USA
| | - Harry Brandt
- The Center for Eating Disorders at Sheppard Pratt, 6501 N. Charles Street, Baltimore, MD 21204, USA
| | - Steven Crawford
- The Center for Eating Disorders at Sheppard Pratt, 6501 N. Charles Street, Baltimore, MD 21204, USA
| | - L John Horwood
- Christchurch School of Medicine & Health Sciences, University of Otago, 2 Riccarton Avenue, PO Box 4345, Christchurch 8140, New Zealand
| | - Joseph M Boden
- Christchurch School of Medicine & Health Sciences, University of Otago, 2 Riccarton Avenue, PO Box 4345, Christchurch 8140, New Zealand
| | - John F Pearson
- Christchurch School of Medicine & Health Sciences, University of Otago, 2 Riccarton Avenue, PO Box 4345, Christchurch 8140, New Zealand
| | - Laramie E Duncan
- Stanford University, 450 Serra Mall, Stanford, CA 94305-2004, USA
| | - Jakob Grove
- Aarhus University, Norde Ringgade 1, 8000 Aarhus, Denmark
| | - Manuel Mattheisen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden; Aarhus University, Norde Ringgade 1, 8000 Aarhus, Denmark; Stockholm Health Care Services, Stockholm County Council, Box 45436, 104 31 Stockholm, Sweden; University of Würzburg, Sanderring 2, 97070 Würzburg, Germany
| | - Jennifer Jordan
- Christchurch School of Medicine & Health Sciences, University of Otago, 2 Riccarton Avenue, PO Box 4345, Christchurch 8140, New Zealand
| | - Martin A Kennedy
- Christchurch School of Medicine & Health Sciences, University of Otago, 2 Riccarton Avenue, PO Box 4345, Christchurch 8140, New Zealand
| | - Andreas Birgegård
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden; Stockholm Health Care Services, Stockholm County Council, Box 45436, 104 31 Stockholm, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
| | - Claes Norring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden; Stockholm Health Care Services, Stockholm County Council, Box 45436, 104 31 Stockholm, Sweden
| | - Tracey D Wade
- Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | | | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital QLD 4029, Australia
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden; Gothenburg University, Box 100, SE-405 30 Gothenburg, Sweden
| | - Preben Bo Mortensen
- Aarhus University, Norde Ringgade 1, 8000 Aarhus, Denmark; Mental Health Services, Institute for Biological Psychiatry, MHC Sct. Hans, Kristineberg 3, 2100 Copenhagen, Denmark; University of Copenhagen, Nørregade 10, DK-1165 Copenhagen, Denmark
| | - Patrick F Sullivan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden
| | - Cynthia M Bulik
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden.
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24
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Murphy MSQ, Hawken S, Cheng W, Wilson LA, Lamoureux M, Henderson M, Potter B, Little J, Chakraborty P, Wilson K. Metabolic profiles derived from residual blood spot samples: A longitudinal analysis. Gates Open Res 2018; 2:28. [PMID: 30234195 PMCID: PMC6139383 DOI: 10.12688/gatesopenres.12822.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
Background: Secondary use of newborn screening dried blood spot samples include use for biomedical or epidemiological research. However, the effects of storage conditions on archival samples requires further examination. The objective of this study was to determine the utility of residual newborn samples for deriving reliable metabolic gestational age estimates. Methods: Residual newborn dried blood spot samples that had been stored for 2-, 4-, 6-, or 12-months in temperature controlled (21°C) conditions were re-analyzed for the full panel of newborn screening analytes offered by a provincial newborn screening lab in Ottawa, Canada. Data from re-analyzed samples were compared to corresponding baseline newborn screening values for absolute agreement, and Pearson and intraclass correlation. Performance of a gestational age estimation algorithm originally developed from baseline newborn screening values was then validated on data derived from stored samples. Results: A total of 307 samples were used for this study. 17-hydroxyprogesterone and newborn hemoglobin profiles measured by immunoassay and high-performance liquid chromatography, respectively, were among the most stable markers across all time points of analysis. Acylcarnitines exhibited the greatest degree of variation in stability upon repeat measurement. The largest shifts in newborn analyte profiles and the poorest performance of metabolic gestational age algorithms were observed when samples were analyzed 12-months after sample collection. Conclusions: Duration of sample storage, independent of temperature and humidity, affects newborn screening profiles and gestational age estimates derived from metabolic gestational dating algorithms. When considering use of dried blood spot samples either for clinical or research purposes, care should be taken when interpreting data stemming from secondary use.
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Affiliation(s)
- Malia S Q Murphy
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Steven Hawken
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Wei Cheng
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Lindsay A Wilson
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
| | - Monica Lamoureux
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Matthew Henderson
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Beth Potter
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, K1G 5Z3, Canada
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, K1G 5Z3, Canada
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, K1H 5B2, Canada
| | - Kumanan Wilson
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, K1Y 4E9, Canada
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25
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Fadista J, Lund M, Skotte L, Geller F, Nandakumar P, Chatterjee S, Matsson H, Granström AL, Wester T, Salo P, Virtanen V, Carstensen L, Bybjerg-Grauholm J, Hougaard DM, Pakarinen M, Perola M, Nordenskjöld A, Chakravarti A, Melbye M, Feenstra B. Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus. Eur J Hum Genet 2018; 26:561-569. [PMID: 29379196 DOI: 10.1038/s41431-017-0053-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/03/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Hirschsprung disease (HSCR) is a congenital disorder with a population incidence of ~1/5000 live births, defined by an absence of enteric ganglia along variable lengths of the colon. HSCR genome-wide association studies (GWAS) have found common associated variants at RET, SEMA3, and NRG1, but they still fail to explain all of its heritability. To enhance gene discovery, we performed a GWAS of 170 cases identified from the Danish nationwide pathology registry with 4717 controls, based on 6.2 million variants imputed from the haplotype reference consortium panel. We found a novel low-frequency variant (rs144432435), which, when conditioning on the lead RET single-nucleotide polymorphism (SNP), was of genome-wide significance in the discovery analysis. This conditional association signal was replicated in a Swedish HSCR cohort with discovery plus replication meta-analysis conditional odds ratio of 6.6 (P = 7.7 × 10-10; 322 cases and 4893 controls). The conditional signal was, however, not replicated in two HSCR cohorts from USA and Finland, leading to the hypothesis that rs144432435 tags a rare haplotype present in Denmark and Sweden. Using the genome-wide complex trait analysis method, we estimated the SNP heritability of HSCR to be 88%, close to estimates based on classical family studies. Moreover, by using Lasso (least absolute shrinkage and selection operator) regression we were able to construct a genetic HSCR predictor with a area under the receiver operator characteristics curve of 76% in an independent validation set. In conclusion, we combined the largest collection of sporadic Hirschsprung cases to date (586 cases) to further elucidate HSCR's genetic architecture.
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Affiliation(s)
- João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
| | - Marie Lund
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Priyanka Nandakumar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sumantra Chatterjee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans Matsson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anna Löf Granström
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Wester
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Perttu Salo
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Valtter Virtanen
- Pediatric Surgery, Children's Hospital, University of Helsinki, Helsinki, Finland
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Mikko Pakarinen
- Pediatric Surgery, Children's Hospital, University of Helsinki, Helsinki, Finland
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden.,Center of Molecular Medicine, Karolinska institutet, Stockholm, Sweden
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
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26
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Pedersen CB, Bybjerg-Grauholm J, Pedersen MG, Grove J, Agerbo E, Bækvad-Hansen M, Poulsen JB, Hansen CS, McGrath JJ, Als TD, Goldstein JI, Neale BM, Daly MJ, Hougaard DM, Mors O, Nordentoft M, Børglum AD, Werge T, Mortensen PB. The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders. Mol Psychiatry 2018; 23:6-14. [PMID: 28924187 PMCID: PMC5754466 DOI: 10.1038/mp.2017.196] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 12/16/2022]
Abstract
The Integrative Psychiatric Research (iPSYCH) consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005, including 1 472 762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3540), autism (N=16 146), attention-deficit/hyperactivity disorder (N=18 726) and affective disorder (N=26 380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30 000). Within the sample of 86 189 individuals, a total of 57 377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information, and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.
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Affiliation(s)
- C B Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Fuglesangs Allé 4, Aarhus 8210, Denmark. E-mail:
| | - J Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - M G Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - J Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark,BiRC-Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - E Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - M Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J B Poulsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - C S Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J J McGrath
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - T D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - J I Goldstein
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - B M Neale
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - M J Daly
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - D M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - O Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - M Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - A D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - T Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - P B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
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27
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Debost JC, Debost M, Grove J, Mors O, Hougaard DM, Børglum AD, Mortensen PB, Petersen L. COMT Val158Met and MTHFR C677T moderate risk of schizophrenia in response to childhood adversity. Acta Psychiatr Scand 2017; 136:85-95. [PMID: 28556887 DOI: 10.1111/acps.12761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/08/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Mesolimbic dopamine sensitization has been hypothesized to be a mediating factor of childhood adversity (CA) on schizophrenia risk. Activity of catechol-O-methyltransferase (COMT) Val158Met increases mesolimbic dopamine signaling and may be further regulated by methylenetetrahydrofolate reductase (MTHFR) C677T. This study investigates the three-way interaction between CA, COMT, and MTHFR. METHODS We conducted a nested case-control study on individuals born after 1981, linking population-based registers to study the three-way interaction. We included 1699 schizophrenia cases and 1681 controls, and used conditional logistic regression to report incidence rate ratios (IRRs). RESULTS Childhood adversity was robustly associated with schizophrenia. No main genetic effects were observed. MTHFR C677T increased schizophrenia risk in a dose-dependent manner per MTHFR T allele (P = 0.005) consequent upon CA exposure. After inclusion of the significant (P = 0.03) COMT × MTHFR × CA interaction, the risk was further increased per high-activity COMT Val allele. Hence, exposed COMT Val/Val and MTHFR T/T carriers had an IRR of 2.76 (95% CI, 1.66-4.61). Additional adjustments for ancestry and parental history of mental illness attenuated the results with the interaction being only marginally significant. CONCLUSION MTHFR C677T and COMT Val158Met interact with CA to increase risk of schizophrenia.
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Affiliation(s)
- J-C Debost
- Department of Economics and Business Economics, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - M Debost
- Department of Internal Medicine, Randers Regional Hospital, Randers NØ, Denmark
| | - J Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - O Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Centre for Psychiatric Research, Aarhus University Hospital Risskov, Aarhus, Denmark
| | - D M Hougaard
- Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - A D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - P B Mortensen
- Department of Economics and Business Economics, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrated Register-based Research (CIRRAU), Aarhus University, Aarhus, Denmark
| | - L Petersen
- Department of Economics and Business Economics, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
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Bækvad-Hansen M, Bybjerg-Grauholm J, Poulsen JB, Hansen CS, Hougaard DM, Hollegaard MV. Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality. Mol Genet Metab Rep 2017; 11:36-45. [PMID: 28487825 PMCID: PMC5408502 DOI: 10.1016/j.ymgmr.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 02/04/2023] Open
Abstract
Aim The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. Methods This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. Results The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Discussion Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.
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Affiliation(s)
- Marie Bækvad-Hansen
- Corresponding author at: Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.Danish Center for Neonatal ScreeningDepartment of Congenital DiseasesStatens Serum InstitutArtillerivej 5Copenhagen SDK-2300Denmark
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29
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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30
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Zakaria R, Allen KJ, Koplin JJ, Roche P, Greaves RF. Advantages and Challenges of Dried Blood Spot Analysis by Mass Spectrometry Across the Total Testing Process. EJIFCC 2016; 27:288-317. [PMID: 28149263 PMCID: PMC5282914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
INTRODUCTION Through the introduction of advanced analytical techniques and improved throughput, the scope of dried blood spot testing utilising mass spectrometric methods, has broadly expanded. Clinicians and researchers have become very enthusiastic about the potential applications of dried blood spot based mass spectrometric applications. Analysts on the other hand face challenges of sensitivity, reproducibility and overall accuracy of dried blood spot quantification. In this review, we aim to bring together these two facets to discuss the advantages and current challenges of non-newborn screening applications of dried blood spot quantification by mass spectrometry. METHODS To address these aims we performed a key word search of the PubMed and MEDLINE online databases in conjunction with individual manual searches to gather information. Keywords for the initial search included; "blood spot" and "mass spectrometry"; while excluding "newborn"; and "neonate". In addition, databases were restricted to English language and human specific. There was no time period limit applied. RESULTS As a result of these selection criteria, 194 references were identified for review. For presentation, this information is divided into: 1) clinical applications; and 2) analytical considerations across the total testing process; being pre-analytical, analytical and post-analytical considerations. CONCLUSIONS DBS analysis using MS applications is now broadly applied, with drug monitoring for both therapeutic and toxicological analysis being the most extensively reported. Several parameters can affect the accuracy of DBS measurement and further bridge experiments are required to develop adjustment rules for comparability between dried blood spot measures and the equivalent serum/plasma values. Likewise, the establishment of independent reference intervals for dried blood spot sample matrix is required.
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Affiliation(s)
- Rosita Zakaria
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia,Clinical Biochemistry, Austin Pathology, Heidelberg, Victoria, Australia,Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Katrina J. Allen
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia, Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia, Department of Allergy and Clinical Immunology, Royal Children’s Hospital, Parkville, Victoria, Australia
| | | | - Peter Roche
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Ronda F. Greaves
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia,Murdoch Children’s Research Institute, Parkville, Victoria, Australia,School of Health and Biomedical Sciences RMIT University PO Box 71, Bundoora, Victoria, 3083 Australia +61 (0)399257080
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31
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Poulsen JB, Lescai F, Grove J, Bækvad-Hansen M, Christiansen M, Hagen CM, Maller J, Stevens C, Li S, Li Q, Sun J, Wang J, Nordentoft M, Werge TM, Mortensen PB, Børglum AD, Daly M, Hougaard DM, Bybjerg-Grauholm J, Hollegaard MV. High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA. PLoS One 2016; 11:e0153253. [PMID: 27089011 PMCID: PMC4835089 DOI: 10.1371/journal.pone.0153253] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/26/2016] [Indexed: 12/16/2022] Open
Abstract
Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB_ref and a WB_ref replica sharing DNA extract with the WB_ref sample. Pilot 3: DBS_2x3.2, WB_ref, wgaDNA of 2x1.6 mm neonatal DBSs and wgaDNA of the WB reference sample. Following sequencing and data analysis, we compared pairwise variant calls to obtain a measure of similarity—the concordance rate. Concordance rates were slightly lower when comparing DBS vs WB sample types than for any two WB sample types of the same subject before filtering of the variant calls. The overall concordance rates were dependent on the variant type, with SNPs performing best. Post-filtering, the comparisons of DBS vs WB and WB vs WB sample types yielded similar concordance rates, with values close to 100%. WgaDNA of neonatal DBS samples performs with great accuracy and efficiency in exome sequencing. The wgaDNA performed similarly to matched high-quality reference—whole-blood DNA—based on concordance rates calculated from variant calls. No differences were observed substituting 2x3.2 with 2x1.6 mm discs, allowing for additional reduction of sample material in future projects.
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Affiliation(s)
- Jesper Buchhave Poulsen
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Francesco Lescai
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Molecular Medicine, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Munch Hagen
- Department for Congenital Disorders, Molecular Medicine, Statens Serum Institut, Copenhagen, Denmark
| | - Julian Maller
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - Christine Stevens
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - Shenting Li
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | | | | | - Jun Wang
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- BGI-Shenzhen, Shenzhen, China
| | - Merete Nordentoft
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- Mental Health Centre Copenhagen, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Mears Werge
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Institute for Biological Psychiatry, Capital Region of Denmark, Roskilde, Denmark
| | - Preben Bo Mortensen
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-based Research, School of Business and Social Sciences, Aarhus University, Aarhus, Denmark
| | - Anders Dupont Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH - Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark
- iSEQ - Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Mark Daly
- Broad Institute, Stanley Center, Cambridge, Massachusetts, United States of America
| | - David Michael Hougaard
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, The Danish Neonatal Screening Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Mads Vilhelm Hollegaard
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, Section of Neonatal Genetics, Statens Serum Institut, Copenhagen, Denmark
- Department for Congenital Disorders, Danish Centre for Neonatal Screening, The Danish Neonatal Screening Biobank, Statens Serum Institut, Copenhagen, Denmark
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32
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Shaik M, Shivanna DK, Kamate M, Ab V, Tp KV. Single Lysis-Salting Out Method of Genomic DNA Extraction From Dried Blood Spots. J Clin Lab Anal 2016; 30:1009-1012. [PMID: 27074880 DOI: 10.1002/jcla.21972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 01/16/2016] [Accepted: 03/01/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Dried blood spots (DBS) are an important form of bio-sampling and valuable approach for storing blood samples for genetic studies. This has necessitated in developing an effective protocol to isolate genomic DNA (gDNA) from DBS samples.In this study, we have elucidated a dependable and non-hazardous "single lysis-salting out" (SLSO) protocol of gDNA extraction from DBS and compared against the available commercial kits. METHODS For the purpose of this study, blood spots were collected on S&S 903 filter cards from 10 healthy volunteers and 30 patients with glutaric aciduria type I (GA-I). The gDNA was extracted from theseDBS samples by SLSO, QIAamp® gDNA Micro kit and innuPREP forensic kit methods. The quantity and quality of gDNA obtained from these methods were determined by measuring the absorbance using a Nanodrop spectrophotometer. RESULTS The SLSO method showed four-fold and eight-fold increased yield of gDNA in healthy volunteers and patient samples, respectively, compared to commercial kits (p<0.0001). The protocol was also found to be cost efficient, reducing the per sample cost to almost half. The suitability of this method for genetic studies was confirmed by performing R402W genotyping by RFLP in GA-I patients. The genotyping results showed the presence of R402W mutation in 20% (6/30) of patients. CONCLUSION The SLSO method was found to be inexpensive, non-hazardous and a suitable technique for isolating gDNA from DBS samples for genetic studies.
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Affiliation(s)
- Muntaj Shaik
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | | | - Mahesh Kamate
- Department of Pediatrics, Jawaharlal Nehru Medical College, KLE University, Belgaum, Karnataka, India
| | - Vedamurthy Ab
- Department of Biotechnology & Microbiology, Karnatak University Dharwad, Dharwad, Karnataka, India
| | - Kruthika-Vinod Tp
- Department of Neurochemistry, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India. ,
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DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards. Forensic Sci Int 2016; 261:148-53. [DOI: 10.1016/j.forsciint.2016.02.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
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Nissen JB, Hansen CS, Starnawska A, Mattheisen M, Børglum AD, Buttenschøn HN, Hollegaard M. DNA Methylation at the Neonatal State and at the Time of Diagnosis: Preliminary Support for an Association with the Estrogen Receptor 1, Gamma-Aminobutyric Acid B Receptor 1, and Myelin Oligodendrocyte Glycoprotein in Female Adolescent Patients with OCD. Front Psychiatry 2016; 7:35. [PMID: 27047397 PMCID: PMC4796012 DOI: 10.3389/fpsyt.2016.00035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/26/2016] [Indexed: 12/26/2022] Open
Abstract
Obsessive-compulsive disorder (OCD) is a neuropsychiatric disorder. Non-genetic factors and their interaction with genes have attracted increasing attention. Epigenetics is regarded an important interface between environmental signals and activation/repression of genomic responses. Epigenetic mechanisms have not previously been examined in OCD in children and adolescents. The aim of the present study was to examine the DNA methylation profile of selected genes in blood spots from neonates later diagnosed with OCD and in the same children/adolescents at the time of diagnosis compared with age- and sex-matched controls. Furthermore, we wanted to characterize the association of the differential methylation profiles with the severity of OCD and treatment outcome. Dried and new blood spot samples were obtained from 21 female children/adolescents with verified OCD and 12 female controls. The differential methylation was analyzed using a linear model and the correlation with the severity of OCD and treatment outcome was analyzed using the Pearson correlation. We evaluated selected Illumina Infinium HumanMethylation450 BeadChip probes within and up to 100,000 bp up- and downstream of 14 genes previously associated with OCD (SLC1A1, SLC25A12, GABBR1, GAD1, DLGAP1, MOG, BDNF, OLIG2, NTRK2 and 3, ESR1, SL6A4, TPH2, and COMT). The study found no significantly differential methylation. However, preliminary support for a difference was found for the gamma-aminobutyric acid (GABA) B receptor 1 (cg10234998, cg17099072) in blood samples at birth and for the estrogen receptor 1 (ESR1) (cg10939667), the myelin oligodendrocyte glycoprotein (MOG) (cg16650906), and the brain-derived neurotrophic factor (BDNF) (cg14080521) in blood samples at the time of diagnosis. Preliminary support for an association was observed between the methylation profiles of GABBR1 and MOG and baseline severity, treatment effect, and responder status; and between the methylation profile of ESR1 and baseline severity. To our knowledge, this is the first study to examine the DNA methylation profiles in OCD. The study points towards possible differences in the methylation profiles and suggests a correlation with the severity of OCD. However, the results warrant further studies in larger sample sets.
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Affiliation(s)
- Judith Becker Nissen
- Center of Child and Adolescent Psychiatry (BUC), Aarhus University Hospital , Risskov , Denmark
| | - Christine Søholm Hansen
- Department of Congenital Diseases, Neonatal Genetics, Statens Serum Institut , Copenhagen , Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | - Anders Dupont Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | | | - Mads Hollegaard
- Department of Congenital Diseases, Neonatal Genetics, Statens Serum Institut , Copenhagen , Denmark
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35
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Grauholm J, Khoo SK, Nickolov RZ, Poulsen JB, Bækvad-Hansen M, Hansen CS, Hougaard DM, Hollegaard MV. Gene expression profiling of archived dried blood spot samples from the Danish Neonatal Screening Biobank. Mol Genet Metab 2015. [PMID: 26212339 DOI: 10.1016/j.ymgme.2015.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A large part of the human genome is transcribed into various forms of RNA, and the global gene expression profile (GEP) has been studied for several years using technology such as RNA-microarrays. In this study, we evaluate whether neonatal dried blood spot (DBS) samples stored in the Danish Neonatal Screening Biobank (DNSB) can be used for GEP. This paper is divided into sub-studies examining the effects of: 1) different whole transcriptome amplification kits (WTA); 2) years of storage and storage in room temperature (RT) versus freezers (-20°C) on DNSB DBS samples; 3) effects of RT storage vs freezer storage on DBS samples from the USA and DNSB, and 4) using smaller disc sizes, thereby decreasing DBS use. We present evidence that reliable and reproducible GEPs can be obtained using neonatal DBS samples. The main source of variation is the storage condition. When samples are stored at -20°C, the dynamic range is increased, and Pearson correlations are higher. Differential analysis reveals no statistically significant differences between samples collected a decade apart and stored at -20°C. However, samples stored at RT show differential expression for a third of the gene-specific probes. Our data also suggests that using alternate WTA kits significantly changes the GEP. Finally, the amount of input material, i.e., the size and number of DBS discs used, can be reduced to preserve this valuable and limited material. We conclude that DNSB DBS samples provide a reproducible resource for GEP. Results are improved if the cards are stored at -20°C. Furthermore, it is important to use a single type of kit for analysis because using alternate kits introduces differential expression.
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Affiliation(s)
- Jonas Grauholm
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA.
| | - Radoslav Z Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA.
| | - Jesper B Poulsen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Marie Bækvad-Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Christine S Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Mads V Hollegaard
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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Luo XJ, Mattheisen M, Li M, Huang L, Rietschel M, Børglum AD, Als TD, van den Oord EJ, Aberg KA, Mors O, Mortensen PB, Luo Z, Degenhardt F, Cichon S, Schulze TG, Nöthen MM, Su B, Zhao Z, Gan L, Yao YG. Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function. Schizophr Bull 2015; 41:1294-308. [PMID: 25759474 PMCID: PMC4601704 DOI: 10.1093/schbul/sbv017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies have identified multiple risk variants and loci that show robust association with schizophrenia. Nevertheless, it remains unclear how these variants confer risk to schizophrenia. In addition, the driving force that maintains the schizophrenia risk variants in human gene pool is poorly understood. To investigate whether expression-associated genetic variants contribute to schizophrenia susceptibility, we systematically integrated brain expression quantitative trait loci and genome-wide association data of schizophrenia using Sherlock, a Bayesian statistical framework. Our analyses identified ZNF323 as a schizophrenia risk gene (P = 2.22×10(-6)). Subsequent analyses confirmed the association of the ZNF323 and its expression-associated single nucleotide polymorphism rs1150711 in independent samples (gene-expression: P = 1.40×10(-6); single-marker meta-analysis in the combined discovery and replication sample comprising 44123 individuals: P = 6.85×10(-10)). We found that the ZNF323 was significantly downregulated in hippocampus and frontal cortex of schizophrenia patients (P = .0038 and P = .0233, respectively). Evidence for pleiotropic effects was detected (association of rs1150711 with lung function and gene expression of ZNF323 in lung: P = 6.62×10(-5) and P = 9.00×10(-5), respectively) with the risk allele (T allele) for schizophrenia acting as protective allele for lung function. Subsequent population genetics analyses suggest that the risk allele (T) of rs1150711 might have undergone recent positive selection in human population. Our findings suggest that the ZNF323 is a schizophrenia susceptibility gene whose expression may influence schizophrenia risk. Our study also illustrates a possible mechanism for maintaining schizophrenia risk variants in the human gene pool.
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Affiliation(s)
- Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; These authors contributed equally to this work.
| | - Manuel Mattheisen
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany;,These authors contributed equally to this work
| | - Ming Li
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Liang Huang
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Anders D. Børglum
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Research Department, Psychiatric Hospital, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas D. Als
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - Edwin J. van den Oord
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University
| | - Karolina A. Aberg
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Zhenwu Luo
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Franziska Degenhardt
- Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sven Cichon
- Division of Medical Genetics, Department of Biomedicine, University Basel, Basel, Switzerland;,Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - Thomas G. Schulze
- Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-Universität, 37075 Goettingen, Germany;,Institute of Psychiatric Phenomics and Genomics (IPPG), Ludwig-Maximilians-University Munich
| | - Markus M. Nöthen
- Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | | | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhongming Zhao
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lin Gan
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China;,CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai, 200031, China
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Debost JC, Petersen L, Grove J, Hedemand A, Khashan A, Henriksen T, Mors O, Hollegaard M, Hougaard D, Nyegaard M, Børglum A, Mortensen PB. Investigating interactions between early life stress and two single nucleotide polymorphisms in HSD11B2 on the risk of schizophrenia. Psychoneuroendocrinology 2015; 60:18-27. [PMID: 26115144 DOI: 10.1016/j.psyneuen.2015.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 01/22/2023]
Abstract
BACKGROUND To examine the risk of schizophrenia in a Danish population after exposure to early life stress, and whether this risk is modified by DNA sequence variation, specifically two single nucleotide polymorphisms (SNPs) (rs5479 and rs56303414) from the gene HSD11B2. This gene encodes the enzyme 11-β hydroxysteroid dehydrogenase type 2 which converts active cortisol into inactive cortisone. METHODS A two-stage analysis involving (1) a population-based cohort study, and (2) a nested case-control study using genotype information. Stage 1 included 1,141,447 people; here, we calculated incidence rate ratios (IRR) for the risk of schizophrenia among children of mothers who experienced loss or serious illness of close relatives before, during, and after pregnancy. In stage 2, we genotyped rs5479 and rs56303414 among 1275 schizophrenia cases and 1367 controls, and investigated interactions between genotypes and early life stress on the risk of schizophrenia. RESULTS In stage 1, no increased risk of schizophrenia was found in offspring after exposure during pregnancy, but offspring exposed to early life stress at age 0-2 years had a significantly increased risk of schizophrenia (adjusted IRR 1.18, 95% confidence interval 1.07-1.31). For rs5479, the minor allele was nucleotide A, and the major allele was nucleotide C. No interaction was found between rs5479 and exposure during pregnancy. Individuals with the minor A allele of rs5479, however, had a significantly increased risk of schizophrenia after exposure to early life stress at age 3-9 years (adjusted IRR 2.06, 1.04-4.06). No interaction was found between rs56303414 and exposure in any of the time periods. CONCLUSION No association was found between exposure to early life stress during pregnancy and schizophrenia in the offspring investigated, whereas individuals exposed to early life stress within the first two years of life had an increased risk. No interaction was found between HSD11B2 and exposure during pregnancy, but individuals with the A allele of rs5479 had an increased risk of schizophrenia after exposure at age 3-9 years.
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Affiliation(s)
- Jean-Christophe Debost
- National Center for Register-based Research, Department of Economics and Business, Aarhus University, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark.
| | - Liselotte Petersen
- National Center for Register-based Research, Department of Economics and Business, Aarhus University, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department of Biomedicine, Aarhus University, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark; iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anne Hedemand
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department of Biomedicine, Aarhus University, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Ali Khashan
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland; Department of Epidemiology and Public Health, University College Cork, Cork, Ireland
| | - Tine Henriksen
- Perinatal Epidemiology Research Unit, Department of Pediatrics, Aarhus University Hospital, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark; Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Mads Hollegaard
- Danish Centre for Neonatal Screening, Statens Serum Institut, Denmark
| | - David Hougaard
- Danish Centre for Neonatal Screening, Statens Serum Institut, Denmark
| | - Mette Nyegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department of Biomedicine, Aarhus University, Denmark; iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anders Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Department of Biomedicine, Aarhus University, Denmark; iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Preben Bo Mortensen
- National Center for Register-based Research, Department of Economics and Business, Aarhus University, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
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38
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Dahlin AM, Hollegaard MV, Wibom C, Andersson U, Hougaard DM, Deltour I, Hjalmars U, Melin B. CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 gene variants and risk of childhood medulloblastoma. J Neurooncol 2015; 125:75-8. [PMID: 26290144 PMCID: PMC4592490 DOI: 10.1007/s11060-015-1891-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/08/2015] [Indexed: 12/30/2022]
Abstract
Recent studies have described a number of genes that are frequently altered in medulloblastoma tumors and that have putative key roles in the development of the disease. We hypothesized that common germline genetic variations in these genes may be associated with medulloblastoma development. Based on recent publications, we selected 10 genes that were frequently altered in medulloblastoma: CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 (now renamed as KMT2D). Common genetic variants (single nucleotide polymorphisms) annotating these genes (n = 221) were genotyped in germline DNA (neonatal dried blood spot samples) from 243 childhood medulloblastoma cases and 247 control subjects from Sweden and Denmark. Eight genetic variants annotating three genes in the sonic hedgehog signaling pathway; CCND2, PTCH1, and GLI2, were found to be associated with the risk of medulloblastoma (P(combined) < 0.05). The findings were however not statistically significant following correction for multiple testing by the very stringent Bonferroni method. The results do not support our hypothesis that common germline genetic variants in the ten studied genes are associated with the risk of developing medulloblastoma.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Mads V Hollegaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - David M Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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39
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Sørensen KM. Whole Genome Amplification from Blood Spot Samples. Methods Mol Biol 2015; 1347:163-178. [PMID: 26374317 DOI: 10.1007/978-1-4939-2990-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole genome amplification is an invaluable technique when working with DNA extracted from blood spots, as the DNA obtained from this source often is too limited for extensive genetic analysis. Two techniques that amplify the entire genome are common. Here, both are described with focus on the benefits and drawbacks of each system. However, in order to obtain the best possible WGA result the quality of input DNA extracted from the blood spot is essential, but also time consumption, flexibility in format and elution volume and price of the technology are factors influencing system choice. Here, three DNA extraction techniques are described and the above aspects are compared between the systems.
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Affiliation(s)
- Karina Meden Sørensen
- The Danish National Biobank, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Danmark.
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40
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UGT1A1*28 polymorphism and acute lymphoblastic leukemia in children: a Danish case-control study. Pediatr Res 2014; 76:459-63. [PMID: 25105254 DOI: 10.1038/pr.2014.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/04/2014] [Indexed: 11/09/2022]
Abstract
BACKGROUND Oxidative stress is a possible risk factor in the development of acute lymphoblastic leukemia (ALL) in children. Bilirubin is a potent endogenous antioxidant, and the UGT1A1*28 polymorphism is the main genetic cause of variation in plasma bilirubin in Western Europe. METHODS In a case-control study of 665 incident cases of ALL in childhood in Denmark 1982-2010 and 1,379 controls, associations between UGT1A1*28 genotypes and ALL in childhood were estimated as odds ratios by logistic regression with adjustment for sex and birth decade. Subgroup analyses were carried out by age at onset in three groups, and on the ALL subtypes precursor B-cell, T-cell, and t(12;21) positive status. Cases were identified in The Danish Registry of Childhood Cancer, and genotypes were estimated from dried blood spots stored in The Danish Neonatal Screening Biobank. Controls were newborns with blood spots taken right before and after a case. RESULTS We found no association between ALL in childhood and UGT1A1*28 genotypes. The odds ratio was 1.01 (0.88-1.17) for heterozygotes and 1.03 (0.78-1.36) for homozygotes. Also, no associations were found in the subgroup analyses. CONCLUSION We found no association between the UGT1A1*28 genotypes and ALL in children.
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41
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Feenstra B, Pasternak B, Geller F, Carstensen L, Wang T, Huang F, Eitson JL, Hollegaard MV, Svanström H, Vestergaard M, Hougaard DM, Schoggins JW, Jan LY, Melbye M, Hviid A. Common variants associated with general and MMR vaccine-related febrile seizures. Nat Genet 2014; 46:1274-82. [PMID: 25344690 PMCID: PMC4244308 DOI: 10.1038/ng.3129] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/03/2014] [Indexed: 12/28/2022]
Abstract
Febrile seizures represent a recognized serious adverse event following measles, mumps, and rubella (MMR) vaccination. We conducted a series of genome-wide association scans comparing children with MMR-related febrile seizures, children with febrile seizures unrelated to vaccination, and controls with no history of febrile seizures. Two loci were distinctly associated with MMR-related febrile seizures, harboring the interferon-stimulated gene IFI44L (rs273259; P = 5.9×10−12 vs. controls; P =1.2×10−9 vs. MMR-unrelated febrile seizures) and the measles virus receptor CD46 (rs1318653; P = 9.6×10−11 vs. controls; P = 1.6×10−9 vs. MMR-unrelated febrile seizures). Furthermore, four loci were associated with febrile seizures in general implicating the sodium channel genes SCN1A (rs6432860; P = 2.2×10−16) and SCN2A (rs3769955; P = 3.1×10−10), a TMEM16 family gene (TMEM16C; rs114444506; P = 3.7×10−20), and a region associated with magnesium levels (12q21.33; rs11105468; P = 3.4×10−11). Finally, functional relevance of TMEM16C was demonstrated with electrophysiological experiments in wild-type and knockout rats.
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Affiliation(s)
- Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Björn Pasternak
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Tongfei Wang
- 1] Department of Physiology, University of California, San Francisco, San Francisco, California, USA. [2] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [3] Howard Hughes Medical Institute, San Francisco, California, USA
| | - Fen Huang
- 1] Department of Physiology, University of California, San Francisco, San Francisco, California, USA. [2] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [3] Howard Hughes Medical Institute, San Francisco, California, USA
| | - Jennifer L Eitson
- Department of Microbiology, University of Texas Southwestern Medical School, Dallas, Texas, USA
| | - Mads V Hollegaard
- Danish Centre for Neonatal Screening, Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Svanström
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mogens Vestergaard
- Research Unit and Section for General Practice, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical School, Dallas, Texas, USA
| | - Lily Yeh Jan
- 1] Department of Physiology, University of California, San Francisco, San Francisco, California, USA. [2] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [3] Howard Hughes Medical Institute, San Francisco, California, USA
| | - Mads Melbye
- 1] Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark. [2] Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. [3] Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Anders Hviid
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
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42
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Petersen JP, Henriksen TB, Hollegaard MV, Vandborg PK, Hougaard DM, Thorlacius-Ussing O, Ebbesen F. Extreme neonatal hyperbilirubinemia and a specific genotype: a population-based case-control study. Pediatrics 2014; 134:510-5. [PMID: 25092941 DOI: 10.1542/peds.2014-0035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Extreme hyperbilirubinemia (plasma bilirubin ≥ 24.5 mg/dL) is an important risk factor for severe bilirubin encephalopathy. Several risk factors for hyperbilirubinemia are known, but in a large number of patients, a causal factor is never established. UGT1A1 is the rate-limiting enzyme in bilirubin's metabolism. The genotype of Gilbert syndrome, the UGT1A1*28 allele, causes markedly reduced activity of this enzyme, but its association with neonatal hyperbilirubinemia is uncertain and its relationship with extreme hyperbilirubinemia has not been studied. We examined whether the UGT1A1*28 allele is associated with extreme hyperbilirubinemia. METHODS The UGT1A1*28 allele was assessed in a case-control study of 231 white infants who had extreme hyperbilirubinemia in Denmark from 2000 to 2007 and 432 white controls. Cases were identified in the Danish Extreme Hyperbilirubinemia Database that covers the entire population. Genotypes were obtained through the Danish Neonatal Screening Biobank. Subgroup analysis was done for AB0 incompatible cases. RESULTS No association was found between the UGT1A1*28 allele and extreme hyperbilirubinemia. With the common genotype as reference, the odds ratio of extreme hyperbilirubinemia was 0.87 (range, 0.68-1.13) for UGT1A1*28 heterozygotes and 0.77 (range, 0.46-1.27) for homozygotes. Also, no association was found for AB0 incompatible cases. CONCLUSIONS The UGT1A1*28 allele was not associated with risk for extreme hyperbilirubinemia in this study.
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Affiliation(s)
- Jesper Padkær Petersen
- Pediatric Department, and Pediatric Department, Aarhus University Hospital, Aarhus, Denmark; and
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43
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Langhoff-Roos J, Krebs L, Klungsøyr K, Bjarnadottir RI, Källén K, Tapper AM, Jakobsson M, Børdahl PE, Lindqvist PG, Gottvall K, Colmorn LB, Gissler M. The Nordic medical birth registers--a potential goldmine for clinical research. Acta Obstet Gynecol Scand 2014; 93:132-7. [PMID: 24237585 DOI: 10.1111/aogs.12302] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/11/2013] [Indexed: 11/29/2022]
Abstract
The Nordic medical birth registers have long been used for valuable clinical research. Their collection of data for more than four decades offers unusual possibilities for research across generations. At the same time, serum and blotting paper blood samples have been stored from most neonates. Two large cohorts (approximately 100 000 births) in Denmark and Norway have been described by questionnaires, interviews and collection of biological samples (blood, urine and milk teeth), as well as a systematic prospective follow-up of the offspring. National patient registers provide information on preceding, underlying and present health problems of the parents and their offspring. Researchers may, with permission from the national authorities, obtain access to individualized or anonymized data from the registers and tissue-banks. These data allow for multivariate analyses but their usefulness depends on knowledge of the specific registers and biological sample banks and on proper validation of the registers.
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Affiliation(s)
- Jens Langhoff-Roos
- Department of Obstetrics and Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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44
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Lehmann S, Delaby C, Vialaret J, Ducos J, Hirtz C. Current and future use of "dried blood spot" analyses in clinical chemistry. Clin Chem Lab Med 2014; 51:1897-909. [PMID: 23740687 DOI: 10.1515/cclm-2013-0228] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/19/2013] [Indexed: 11/15/2022]
Abstract
The analysis of blood spotted and dried on a matrix (i.e., "dried blood spot" or DBS) has been used since the 1960s in clinical chemistry; mostly for neonatal screening. Since then, many clinical analytes, including nucleic acids, small molecules and lipids, have been successfully measured using DBS. Although this pre-analytical approach represents an interesting alternative to classical venous blood sampling, its routine use is limited. Here, we review the application of DBS technology in clinical chemistry, and evaluate its future role supported by new analytical methods such as mass spectrometry.
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45
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Molteni CG, Terranova L, Zampiero A, Galeone C, Principi N, Esposito S. Comparison of manual methods of extracting genomic DNA from dried blood spots collected on different cards: implications for clinical practice. Int J Immunopathol Pharmacol 2014; 26:779-83. [PMID: 24067477 DOI: 10.1177/039463201302600324] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Isolating genomic DNA from blood samples is essential when studying the associations between genetic variants and susceptibility to a given clinical condition, or its severity. This study of three extraction techniques and two types of commercially available cards involved 219 children attending our outpatient pediatric clinic for follow-up laboratory tests after they had been hospitalised. An aliquot of venous blood was drawn into plastic tubes without additives and, after several inversions, 80 microL were put on circles of common paper cards and Whatman FTA-treated cards. Three extraction methods were compared: the Qiagen Investigator, Gensolve, and Masterpure. The best method in terms of final DNA yield was Masterpure, which led to a significantly higher yield regardless of the type of card (p less than 0.001), followed by Qiagen Investigator and Gensolve. Masterpure was also the best in terms of price, seemed to be simple and reliable, and required less hands-on time than other techniques. These conclusions support the use of Masterpure in studies that evaluate the associations between genetic variants and the severity or prevalence of infectious diseases.
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Affiliation(s)
- C G Molteni
- Pediatric Clinic 1, Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico, Milan, Italy
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46
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Børglum AD, Demontis D, Grove J, Pallesen J, Hollegaard MV, Pedersen CB, Hedemand A, Mattheisen M, Uitterlinden A, Nyegaard M, Ørntoft T, Wiuf C, Didriksen M, Nordentoft M, Nöthen MM, Rietschel M, Ophoff RA, Cichon S, Yolken RH, Hougaard DM, Mortensen PB, Mors O. Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Mol Psychiatry 2014; 19:325-33. [PMID: 23358160 PMCID: PMC3932405 DOI: 10.1038/mp.2013.2] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 11/22/2012] [Accepted: 12/14/2012] [Indexed: 12/13/2022]
Abstract
Genetic and environmental components as well as their interaction contribute to the risk of schizophrenia, making it highly relevant to include environmental factors in genetic studies of schizophrenia. This study comprises genome-wide association (GWA) and follow-up analyses of all individuals born in Denmark since 1981 and diagnosed with schizophrenia as well as controls from the same birth cohort. Furthermore, we present the first genome-wide interaction survey of single nucleotide polymorphisms (SNPs) and maternal cytomegalovirus (CMV) infection. The GWA analysis included 888 cases and 882 controls, and the follow-up investigation of the top GWA results was performed in independent Danish (1396 cases and 1803 controls) and German-Dutch (1169 cases, 3714 controls) samples. The SNPs most strongly associated in the single-marker analysis of the combined Danish samples were rs4757144 in ARNTL (P=3.78 × 10(-6)) and rs8057927 in CDH13 (P=1.39 × 10(-5)). Both genes have previously been linked to schizophrenia or other psychiatric disorders. The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A (P=9.04 × 10(-7)). A region-based analysis summarizing independent signals in segments of 100 kb identified a new region-based genome-wide significant locus overlapping the gene ZEB1 (P=7.0 × 10(-7)). This signal was replicated in the follow-up analysis (P=2.3 × 10(-2)). Significant interaction with maternal CMV infection was found for rs7902091 (P(SNP × CMV)=7.3 × 10(-7)) in CTNNA3, a gene not previously implicated in schizophrenia, stressing the importance of including environmental factors in genetic studies.
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Affiliation(s)
- A D Børglum
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - D Demontis
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - J Grove
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - J Pallesen
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - M V Hollegaard
- Section of Neonatal Screening and Hormones, Statens Serum Institute, Copenhagen, Denmark
| | - C B Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - A Hedemand
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - M Mattheisen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
- Institute for Genomic Mathematics, University of Bonn, Bonn, Germany
| | - GROUP investigators
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section of Neonatal Screening and Hormones, Statens Serum Institute, Copenhagen, Denmark
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
- Institute for Genomic Mathematics, University of Bonn, Bonn, Germany
- For a full list of members, see Appendix
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
- Department of Mathematical Science, University of Copenhagen, Copenhagen, Denmark
- Synaptic transmission, H. Lundbeck A/S, Valby, Denmark
- Psychiatric Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Disorders (DZNE), Bonn, Germany
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Heidelberg, Manheim, Germany
- Department of Medical Genetics and Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Nyegaard
- Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - T Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Denmark
| | - C Wiuf
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Department of Mathematical Science, University of Copenhagen, Copenhagen, Denmark
| | - M Didriksen
- Synaptic transmission, H. Lundbeck A/S, Valby, Denmark
| | - M Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- Psychiatric Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - M M Nöthen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Disorders (DZNE), Bonn, Germany
| | - M Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Heidelberg, Manheim, Germany
| | - R A Ophoff
- Department of Medical Genetics and Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - S Cichon
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - R H Yolken
- Stanley Division of Developmental Neurovirology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - D M Hougaard
- Section of Neonatal Screening and Hormones, Statens Serum Institute, Copenhagen, Denmark
| | - P B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - O Mors
- Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
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Bønnelykke K, Sleiman P, Nielsen K, Kreiner-Møller E, Mercader JM, Belgrave D, den Dekker HT, Husby A, Sevelsted A, Faura-Tellez G, Mortensen LJ, Paternoster L, Flaaten R, Mølgaard A, Smart DE, Thomsen PF, Rasmussen MA, Bonàs-Guarch S, Holst C, Nohr EA, Yadav R, March ME, Blicher T, Lackie PM, Jaddoe VWV, Simpson A, Holloway JW, Duijts L, Custovic A, Davies DE, Torrents D, Gupta R, Hollegaard MV, Hougaard DM, Hakonarson H, Bisgaard H. A genome-wide association study identifies CDHR3 as a susceptibility locus for early childhood asthma with severe exacerbations. Nat Genet 2014; 46:51-5. [PMID: 24241537 DOI: 10.1038/ng.2830] [Citation(s) in RCA: 410] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/28/2013] [Indexed: 12/14/2022]
Abstract
Asthma exacerbations are among the most frequent causes of hospitalization during childhood, but the underlying mechanisms are poorly understood. We performed a genome-wide association study of a specific asthma phenotype characterized by recurrent, severe exacerbations occurring between 2 and 6 years of age in a total of 1,173 cases and 2,522 controls. Cases were identified from national health registries of hospitalization, and DNA was obtained from the Danish Neonatal Screening Biobank. We identified five loci with genome-wide significant association. Four of these, GSDMB, IL33, RAD50 and IL1RL1, were previously reported as asthma susceptibility loci, but the effect sizes for these loci in our cohort were considerably larger than in the previous genome-wide association studies of asthma. We also obtained strong evidence for a new susceptibility gene, CDHR3 (encoding cadherin-related family member 3), which is highly expressed in airway epithelium. These results demonstrate the strength of applying specific phenotyping in the search for asthma susceptibility genes.
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Affiliation(s)
- Klaus Bønnelykke
- 1] Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark. [2] [3]
| | - Patrick Sleiman
- 1] Center for Applied Genomics, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania, USA. [2]
| | - Kasper Nielsen
- 1] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. [2]
| | - Eskil Kreiner-Møller
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Josep M Mercader
- Joint Institute for Research in Biomedicine and Barcelona Supercomputing Center (IRB-BSC) Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Danielle Belgrave
- 1] Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester, UK. [2] Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | - Herman T den Dekker
- 1] Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands. [2] Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands. [3] Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Anders Husby
- 1] Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark. [2] Brooke Laboratory, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Astrid Sevelsted
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Grissel Faura-Tellez
- 1] Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK. [2] Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Li Juel Mortensen
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Lavinia Paternoster
- Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Richard Flaaten
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - Anne Mølgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark
| | - David E Smart
- Brooke Laboratory, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Philip F Thomsen
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten A Rasmussen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Silvia Bonàs-Guarch
- Joint Institute for Research in Biomedicine and Barcelona Supercomputing Center (IRB-BSC) Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Claus Holst
- Institute of Preventive Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ellen A Nohr
- 1] Institute of Clinical Research, University of Southern Denmark, Aarhus, Denmark. [2] Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus, Denmark
| | - Rachita Yadav
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania, USA
| | - Thomas Blicher
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter M Lackie
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Vincent W V Jaddoe
- 1] Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands. [2] Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands. [3] Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Angela Simpson
- Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester, UK
| | - John W Holloway
- Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Liesbeth Duijts
- 1] Department of Pediatrics, Division of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands. [2] Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands. [3] Department of Pediatrics, Division of Neonatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adnan Custovic
- Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester and University Hospital of South Manchester, Manchester, UK
| | - Donna E Davies
- Brooke Laboratory, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - David Torrents
- 1] Joint Institute for Research in Biomedicine and Barcelona Supercomputing Center (IRB-BSC) Program on Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain. [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ramneek Gupta
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mads V Hollegaard
- Danish Centre for Neonatal Screening, Department of Clinical Biochemistry and Immunology, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department of Clinical Biochemistry and Immunology, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Hakon Hakonarson
- 1] Center for Applied Genomics, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania, USA. [2]
| | - Hans Bisgaard
- 1] Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen & Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Denmark. [2]
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48
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Hollegaard MV, Grauholm J, Nielsen R, Grove J, Mandrup S, Hougaard DM. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing. Mol Genet Metab 2013; 110:65-72. [PMID: 23830478 DOI: 10.1016/j.ymgme.2013.06.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 11/23/2022]
Abstract
Dried blood spot samples (DBSS) have been collected and stored for decades as part of newborn screening programmes worldwide. Representing almost an entire population under a certain age and collected with virtually no bias, the Newborn Screening Biobanks are of immense value in medical studies, for example, to examine the genetics of various disorders. We have previously demonstrated that DNA extracted from a fraction (2×3.2mm discs) of an archived DBSS can be whole genome amplified (wgaDNA) and used for accurate array genotyping. However, until now, it has been uncertain whether wgaDNA from DBSS can be used for accurate whole genome sequencing (WGS) and exome sequencing (WES). This study examined two individuals represented by three different types of samples each: whole-blood (reference samples), 3-year-old DBSS spotted with reference material (refDBSS), and 27- to 29-year-old archived neonatal DBSS (neoDBSS) stored at -20°C in the Danish Newborn Screening Biobank. The reference samples were genotyped using an Illumina Omni2.5M array, and all samples were sequenced on a HighSeq2000 Paired-End flow cell. First, we compared the array single nucleotide polymorphism (SNP) genotype data to the single nucleotide variation (SNV) calls from the WGS and WES SNV calls. We also compared the WGS and WES reference sample SNV calls to the DBSS SNV calls. The overall performance of the archived DBSS was similar to the whole blood reference sample. Plotting the error rates relative to coverage revealed that the error rates of DBSS were similar to that of their reference samples. SNVs called with a coverage<×8 had error rates between 1.5 and 35%, whereas the error rates of SNVs called with a coverage≥8 were <1.5%. In conclusion, the wgaDNA amplified from both new and old neonatal DBSS perform as well as their whole-blood reference samples with regards to error rates, strongly indicating that neonatal DBSS collected shortly after birth and stored for decades comprise an excellent resource for NGS studies of disease.
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Affiliation(s)
- Mads Vilhelm Hollegaard
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej, Copenhagen, Denmark.
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49
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Preslan ED, Mathews DJH. A comparative analysis of the governance and use of residual dried blood spots from state newborn screening programs and neonatal biobanks. J Empir Res Hum Res Ethics 2013; 8:22-33. [PMID: 23933773 DOI: 10.1525/jer.2013.8.3.22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In contrast to prior research, which has focused mainly on legislative content, this study aimed to characterize the current governance structures and procedures used by state newborn screening programs in the United States regarding the research use of residual dried blood spots. Content analysis was performed on newborn screening laws, program policies, survey responses, and online material, and was compared to information from two neonatal biobanks. Important differences between newborn screening programs and neonatal biobanks included the types of permissible research with blood spots, the evaluation criteria used for research requests, and characteristics of the research proposal reviewers. These findings can inform ongoing policy conversations with respect to the governance and use of residual dried blood spots.
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50
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St. Julien KR, Jelliffe-Pawlowski LL, Shaw GM, Stevenson DK, O’Brodovich HM, Krasnow MA. High quality genome-wide genotyping from archived dried blood spots without DNA amplification. PLoS One 2013; 8:e64710. [PMID: 23737996 PMCID: PMC3667813 DOI: 10.1371/journal.pone.0064710] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/17/2013] [Indexed: 11/19/2022] Open
Abstract
Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.
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Affiliation(s)
- Krystal R. St. Julien
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Laura L. Jelliffe-Pawlowski
- California Genetic Disease Screening Program of the California Department of Public Health, Richmond, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugh M. O’Brodovich
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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