1
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Borbye-Lorenzen N, Zhu Z, Agerbo E, Albiñana C, Benros ME, Bian B, Børglum AD, Bulik CM, Debost JCPG, Grove J, Hougaard DM, McRae AF, Mors O, Mortensen PB, Musliner KL, Nordentoft M, Petersen LV, Privé F, Sidorenko J, Skogstrand K, Werge T, Wray NR, Vilhjálmsson BJ, McGrath JJ. The correlates of neonatal complement component 3 and 4 protein concentrations with a focus on psychiatric and autoimmune disorders. CELL GENOMICS 2023; 3:100457. [PMID: 38116117 PMCID: PMC10726496 DOI: 10.1016/j.xgen.2023.100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/03/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023]
Abstract
Complement components have been linked to schizophrenia and autoimmune disorders. We examined the association between neonatal circulating C3 and C4 protein concentrations in 68,768 neonates and the risk of six mental disorders. We completed genome-wide association studies (GWASs) for C3 and C4 and applied the summary statistics in Mendelian randomization and phenome-wide association studies related to mental and autoimmune disorders. The GWASs for C3 and C4 protein concentrations identified 15 and 36 independent loci, respectively. We found no associations between neonatal C3 and C4 concentrations and mental disorders in the total sample (both sexes combined); however, post-hoc analyses found that a higher C3 concentration was associated with a reduced risk of schizophrenia in females. Mendelian randomization based on C4 summary statistics found an altered risk of five types of autoimmune disorders. Our study adds to our understanding of the associations between C3 and C4 concentrations and subsequent mental and autoimmune disorders.
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Affiliation(s)
- Nis Borbye-Lorenzen
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Zhihong Zhu
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Esben Agerbo
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Integrated Register-based Research, Aarhus University, CIRRAU, 8210 Aarhus V, Denmark
| | - Clara Albiñana
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
| | - Michael E. Benros
- Copenhagen Research Center for Mental Health, Mental Health Center Copenhagen, Copenhagen University Hospital, Hellerup, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Beilei Bian
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department of Biomedicine and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus, Denmark
| | - Cynthia M. Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jean-Christophe Philippe Goldtsche Debost
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- Department of Psychosis, Aarhus University Hospital Skejby, Aarhus Nord, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus, Denmark
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- Bioinformatics Research Center, Aarhus University, 8000 Aarhus C, Denmark
| | - David M. Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department for Congenital Disorders, Statens Serum Institut, 2300 Copenhagen S, Denmark
| | - Allan F. McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Psychosis Research Unit, Aarhus University Hospital – Psychiatry, Aarhus, Denmark
| | - Preben Bo Mortensen
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Center for Integrated Register-based Research, Aarhus University, CIRRAU, 8210 Aarhus V, Denmark
| | - Katherine L. Musliner
- Department of Affective Disorders, Aarhus University and Aarhus University Hospital –Psychiatry, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Liselotte V. Petersen
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Florian Privé
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, University of Copenhagen, 2200 Copenhagen N, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | - Bjarni J. Vilhjálmsson
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus V, Denmark
- Bioinformatics Research Center, Aarhus University, 8000 Aarhus C, Denmark
| | - John J. McGrath
- National Center for Register-Based Research, Aarhus University, 8210 Aarhus V, Denmark
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD 4076, Australia
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2
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Albiñana C, Zhu Z, Borbye-Lorenzen N, Boelt SG, Cohen AS, Skogstrand K, Wray NR, Revez JA, Privé F, Petersen LV, Bulik CM, Plana-Ripoll O, Musliner KL, Agerbo E, Børglum AD, Hougaard DM, Nordentoft M, Werge T, Mortensen PB, Vilhjálmsson BJ, McGrath JJ. Genetic correlates of vitamin D-binding protein and 25-hydroxyvitamin D in neonatal dried blood spots. Nat Commun 2023; 14:852. [PMID: 36792583 PMCID: PMC9932173 DOI: 10.1038/s41467-023-36392-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
The vitamin D binding protein (DBP), encoded by the group-specific component (GC) gene, is a component of the vitamin D system. In a genome-wide association study of DBP concentration in 65,589 neonates we identify 26 independent loci, 17 of which are in or close to the GC gene, with fine-mapping identifying 2 missense variants on chromosomes 12 and 17 (within SH2B3 and GSDMA, respectively). When adjusted for GC haplotypes, we find 15 independent loci distributed over 10 chromosomes. Mendelian randomization analyses identify a unidirectional effect of higher DBP concentration and (a) higher 25-hydroxyvitamin D concentration, and (b) a reduced risk of multiple sclerosis and rheumatoid arthritis. A phenome-wide association study confirms that higher DBP concentration is associated with a reduced risk of vitamin D deficiency. Our findings provide valuable insights into the influence of DBP on vitamin D status and a range of health outcomes.
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Affiliation(s)
- Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Zhihong Zhu
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Nis Borbye-Lorenzen
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sanne Grundvad Boelt
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Clinical Mass Spectrometry, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Arieh S Cohen
- Testcenter Denmark, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark
| | - Kristin Skogstrand
- Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia
| | - Joana A Revez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Florian Privé
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
| | - Liselotte V Petersen
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Oleguer Plana-Ripoll
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- Department of Clinical Epidemiology, Aarhus University and Aarhus University Hospital, 8200, Aarhus N, Denmark
| | - Katherine L Musliner
- Department of Affective Disorders, Aarhus University and Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Esben Agerbo
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine and the iSEQ Center, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Department for Congenital Disorders, Statens Serum Institut, 2300, Copenhagen S, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, 2100, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen N, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- CIRRAU - Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210, Aarhus V, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus C, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, 8210, Aarhus V, Denmark.
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia.
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, 4076, Australia.
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3
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Ding Y, Owen M, Le J, Batalov S, Chau K, Kwon YH, Van Der Kraan L, Bezares-Orin Z, Zhu Z, Veeraraghavan N, Nahas S, Bainbridge M, Gleeson J, Baer RJ, Bandoli G, Chambers C, Kingsmore SF. Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots. NPJ Genom Med 2023; 8:5. [PMID: 36788231 PMCID: PMC9929090 DOI: 10.1038/s41525-023-00349-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Universal newborn screening (NBS) is a highly successful public health intervention. Archived dried bloodspots (DBS) collected for NBS represent a rich resource for population genomic studies. To fully harness this resource in such studies, DBS must yield high-quality genomic DNA (gDNA) for whole genome sequencing (WGS). In this pilot study, we hypothesized that gDNA of sufficient quality and quantity for WGS could be extracted from archived DBS up to 20 years old without PCR (Polymerase Chain Reaction) amplification. We describe simple methods for gDNA extraction and WGS library preparation from several types of DBS. We tested these methods in DBS from 25 individuals who had previously undergone diagnostic, clinical WGS and 29 randomly selected DBS cards collected for NBS from the California State Biobank. While gDNA from DBS had significantly less yield than from EDTA blood from the same individuals, it was of sufficient quality and quantity for WGS without PCR. All samples DBS yielded WGS that met quality control metrics for high-confidence variant calling. Twenty-eight variants of various types that had been reported clinically in 19 samples were recapitulated in WGS from DBS. There were no significant effects of age or paper type on WGS quality. Archived DBS appear to be a suitable sample type for WGS in population genomic studies.
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Affiliation(s)
- Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Mallory Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA.
| | - Jennie Le
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kevin Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong Hyun Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucita Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zaira Bezares-Orin
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shareef Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Matthew Bainbridge
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Joe Gleeson
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Rebecca J. Baer
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA ,grid.266102.10000 0001 2297 6811California Preterm Birth Initiative, University of California San Francisco, San Francisco, CA USA
| | - Gretchen Bandoli
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Christina Chambers
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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4
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Albiñana C, Boelt SG, Cohen AS, Zhu Z, Musliner KL, Vilhjálmsson BJ, McGrath JJ. Developmental exposure to vitamin D deficiency and subsequent risk of schizophrenia. Schizophr Res 2022; 247:26-32. [PMID: 34247885 DOI: 10.1016/j.schres.2021.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 01/22/2023]
Abstract
Over the last half century, a body of convergent evidence has accumulated linking disruption of early brain development with an increased risk of mental disorders, including schizophrenia. The orderly cascade of brain development may be disrupted by exposure to suboptimal concentrations of a range of biological substrates and micronutrients. We hypothesized that those exposed to vitamin D deficiency during early life, have an increased risk of neurodevelopmental disorders, including schizophrenia. The hypothesis was based on the link between an increased risk of schizophrenia in (a) those born in winter and spring, when vitamin D deficiency is more prevalent, and (b) the offspring of dark-skinned migrants living in cold climates, who have a markedly increased risk of vitamin D deficiency. In this review, we summarize evidence from analytic epidemiology related to this hypothesis. Two case-control studies based on Danish neonatal dried blood spots have found that neonatal vitamin deficiency is associated with an increased risk of schizophrenia. However, recent genetic analyses have also suggested that common variants linked to schizophrenia may lead to lower vitamin D concentrations (possibly mediated via reduced outdoor activity). We summarize limitations of the current evidence and outline suggestions that can guide future research. Based on currently available data, there is insufficient evidence to support public health recommendations related to this topic. However, we cannot reject the hypothesis that the provision of vitamin D supplementation to pregnant women and/or offspring in groups vulnerable to vitamin D deficiency may subsequently reduce the incidence of schizophrenia in the offspring.
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Affiliation(s)
- Clara Albiñana
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - the Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | | | - Arieh S Cohen
- Department of Inherited Diseases, Statens Serum Institut, Copenhagen, Denmark
| | - Zhihong Zhu
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Katherine L Musliner
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - the Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - the Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, Australia; Queensland Brain Institute, The University of Queensland, St Lucia, Australia.
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5
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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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6
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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: 86] [Impact Index Per Article: 21.5] [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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7
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Satterstrom FK, Walters RK, Singh T, Wigdor EM, Lescai F, Demontis D, Kosmicki JA, Grove J, Stevens C, Bybjerg-Grauholm J, Bækvad-Hansen M, Palmer DS, Maller JB, Nordentoft M, Mors O, Robinson EB, Hougaard DM, Werge TM, Bo Mortensen P, Neale BM, Børglum AD, Daly MJ. Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants. Nat Neurosci 2019; 22:1961-1965. [PMID: 31768057 PMCID: PMC6884695 DOI: 10.1038/s41593-019-0527-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
We analyze the exome sequences of approximately 8,000 children with autism spectrum disorder (ASD) and/or attention-deficit/hyperactivity disorder (ADHD) and 5,000 controls, and we find that ASD and ADHD have a similar burden of rare protein-truncating variants in evolutionarily constrained genes, both significantly higher than controls. This motivates a combined analysis across ASD and ADHD, which identifies microtubule-associated protein 1A (MAP1A) as a novel exome-wide significant gene conferring risk for childhood psychiatric disorders.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Raymond K Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emilie M Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Francesco Lescai
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre 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.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 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 Centre Copenhagen, 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
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, 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
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
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8
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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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9
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Thorup AAE, Jepsen JR, Ellersgaard DV, Burton BK, Christiani CJ, Hemager N, Skjærbæk M, Ranning A, Spang KS, Gantriis DL, Greve AN, Zahle KK, Mors O, Plessen KJ, Nordentoft M. The Danish High Risk and Resilience Study--VIA 7--a cohort study of 520 7-year-old children born of parents diagnosed with either schizophrenia, bipolar disorder or neither of these two mental disorders. BMC Psychiatry 2015; 15:233. [PMID: 26432691 PMCID: PMC4592560 DOI: 10.1186/s12888-015-0616-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 09/25/2015] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Severe mental illnesses like schizophrenia and bipolar disorder are known to be diseases that to some extent, but not entirely can be understood genetically. The dominating hypothesis is that these disorders should be understood in a neurodevelopmental perspective where genes and environment as well as gene-environment-interactions contribute to the risk of developing the disease. We aim to analyse the influences of genetic risk and environmental factors in a population of 520 7-year-old children with either 0, 1 or 2 parents diagnosed with schizophrenia spectrum psychosis or bipolar disorder on mental health and level of functioning. We hypothesize that a larger proportion of children growing up with an ill parent will display abnormal or delayed development, behavioural problems or psychiatric symptoms compared to the healthy controls. METHODS/DESIGN We are establishing a cohort of 5207 year old children and both their parents for a comprehensive investigation with main outcome measures being neurocognition, behaviour, psychopathology and neuromotor development of the child. Parents and children are examined with a comprehensive battery of instruments and are asked for genetic material (saliva or blood) for genetic analyses. The participants are recruited via Danish registers to ensure representativity. Data from registers concerning social status, birth complications, somatic illnesses and hospitalization are included in the database. Psychological and relational factors like emotional climate in the family, degree of stimulation and support in the home and attachment style are also investigated. DISCUSSION Data collection started January 1, 2013, and is successfully ongoing. By Aug 2015 424 families are included. About 20% of the invited families decline to participate, equal for all groups.
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Affiliation(s)
- Anne A. E. Thorup
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark ,Child and Adolescent Mental Health Center, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark ,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
| | - Jens Richardt Jepsen
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,Child and Adolescent Mental Health Center, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark. .,Center for Neuropsychiatric Schizophrenia Research, Psychiatric Center Glostrup, Mental Health Services Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Ditte Vestbjerg Ellersgaard
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Birgitte Klee Burton
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Camilla Jerlang Christiani
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Nicoline Hemager
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,Child and Adolescent Mental Health Center, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Mette Skjærbæk
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Anne Ranning
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Katrine Søborg Spang
- Child and Adolescent Mental Health Center, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Ditte Lou Gantriis
- Research Department P, Risskov, Aarhus University Hospital, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Aja Neergaard Greve
- Research Department P, Risskov, Aarhus University Hospital, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Kate Kold Zahle
- Research Department P, Risskov, Aarhus University Hospital, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Ole Mors
- Research Department P, Risskov, Aarhus University Hospital, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Kerstin Jessica Plessen
- Child and Adolescent Mental Health Center, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
| | - Merete Nordentoft
- Mental Health Center Copenhagen, Research Unit, Mental Health Services, Capital Region of Denmark, University of Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
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10
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Nordentoft M, Larsen JT, Pedersen CB, Sørensen HJ, Hollegaard MV, Hougaard DM, Mortensen PB, Petersen L. Delay in blood sampling for routine newborn screening is associated with increased risk of schizophrenia. Schizophr Res 2015; 162:90-6. [PMID: 25631455 DOI: 10.1016/j.schres.2015.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 12/29/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022]
Abstract
BACKGROUND The Danish Neonatal Screening Biobank, containing dried blood spot samples from all newborn in Denmark, is a unique source of data that can be utilized for analyses of genetic and environmental exposures related to schizophrenia and other mental disorders. In previous analyses, we have found that early and late blood sampling, compared to sampling at day 5, was associated with increased risk of schizophrenia. As delay in sampling of blood for neonatal screening cannot in itself influence the risk of schizophrenia, it must be seen as a proxy for unknown underlying causes responsible for this association. Therefore, we investigated whether the increased risk can be explained by other risk factors for schizophrenia. METHODS A case-control design was applied. A total of 846 cases with schizophrenia were selected from the Danish Psychiatric Case Register. One control was selected for each case, matched on sex and exact date of birth. RESULTS Both early and late blood sampling was associated with increased risk for schizophrenia. Compared to blood sampling at day 5, sampling at days 0 to 4 after birth was associated with an incidence rate ratio (IRR) of 1.46 (95% CI 1.15-1.87) for development of schizophrenia, and sampling at days 6 to 9 and at days 10 to 53 was associated with an IRR of 1.5 (95% CI 1.13-1.98) and 3.00 (95% CI 1.59-5.67), respectively. After adjusting the estimates for place of birth, both parents' psychiatric illness, maternal and paternal age, parents' country of origin, child admission, and parental education and income, the estimates were slightly different. Thus, blood collection at 0-4days was associated with an IRR of 1.27 (95% CI 0.94-1.71), 6-9days 1.31 (95% CI 0.94-1.84) and 10+days 3.52 (95% CI 1.50 to 8.24). DISCUSSION After adjusting risk estimates for well-known risk factors, delay in sampling of blood for neonatal screening was associated with unexplained increased risk of schizophrenia. Thus, a key finding is that age at test is a proxy for unobserved risk factors for schizophrenia due to unexplained reasons for late blood sampling. Date of sampling will be included in future analyses of genetic and environmental risk factors.
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Affiliation(s)
- Merete Nordentoft
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark.
| | - Janne Tidselbak Larsen
- iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark; National Centre for Register-based Research, Aarhus University, Denmark
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark; National Centre for Register-based Research, Aarhus University, Denmark
| | - Holger Jelling Sørensen
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark
| | | | | | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark; National Centre for Register-based Research, Aarhus University, Denmark
| | - Liselotte Petersen
- iPSYCH, The Lundbeck Foundation Initiative for Psychiatric Research, Denmark; National Centre for Register-based Research, Aarhus University, Denmark
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11
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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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12
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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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13
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Hollegaard MV, Skogstrand K, Thorsen P, Nørgaard-Pedersen B, Hougaard DM, Grove J. Joint Analysis of SNPs and Proteins Identifies RegulatoryIL18Gene Variations Decreasing the Chance of Spastic Cerebral Palsy. Hum Mutat 2012; 34:143-8. [DOI: 10.1002/humu.22173] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/16/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Mads Vilhelm Hollegaard
- Department of Clinical Biochemistry; Immunology, and Genetics, Section of Neonatal Screening and Hormones, Statens Serum Institut; Denmark
| | - Kristin Skogstrand
- Department of Clinical Biochemistry; Immunology, and Genetics, Section of Neonatal Screening and Hormones, Statens Serum Institut; Denmark
| | - Poul Thorsen
- Department of Obstetrics and Gynecology; Lillebaelt Hospital; Kolding; Denmark
| | - Bent Nørgaard-Pedersen
- Department of Clinical Biochemistry; Immunology, and Genetics, Section of Neonatal Screening and Hormones, Statens Serum Institut; Denmark
| | - David Michael Hougaard
- Department of Clinical Biochemistry; Immunology, and Genetics, Section of Neonatal Screening and Hormones, Statens Serum Institut; Denmark
| | - Jakob Grove
- Department of Biomedicine and Bioinformatics Research Centre (BiRC); Aarhus University; Aarhus; Denmark
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14
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Agerbo E, Mortensen PB, Wiuf C, Pedersen MS, McGrath J, Hollegaard MV, Nørgaard-Pedersen B, Hougaard DM, Mors O, Pedersen CB. Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: a Danish national birth cohort-based study. Schizophr Res 2012; 134:246-52. [PMID: 22108675 DOI: 10.1016/j.schres.2011.10.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/06/2011] [Accepted: 10/29/2011] [Indexed: 01/28/2023]
Abstract
BACKGROUND Epidemiological studies indicate that having any family member with schizophrenia increases the risk of schizophrenia in the probands. However, genome-wide association studies (GWAS) have accounted for little of this variation. The aim of this study was to use a population-based sample to explore the influence of single-nucleotide polymorphisms (SNPs) on the excess schizophrenia risk in offspring of parents with a psychotic, bipolar affective or other psychiatric disorder. METHOD A nested case-control study with 739 cases with schizophrenia and 800 controls. Their parents and siblings. Information from national health registers and GWAS data from the national neonatal biobank. RESULTS Offspring schizophrenia risk was elevated in those whose mother, father or siblings had been diagnosed with schizophrenia or related psychosis, bipolar affective disorder or any other psychiatric disorder. The rate ratio was 9.31 (3.85; 22.44) in offspring whose 1st degree relative was diagnosed with schizophrenia. This rate ranged between 8.31 and 11.34 when adjusted for each SNP individually and shrank to 8.23 (3.13; 21.64) when adjusted for 25% of the SNP-variation in candidate genes. The percentage of the excess risk associated with a family history of schizophrenia mediated through genome-wide SNP-variation ranged between -6.1%(-17.0%;2.6%) and 4.1%(-3.9%;15.2%). Analogous results were seen for each parent and for histories of bipolar affective and other psychiatric diagnoses. CONCLUSIONS The excess risk of schizophrenia in offspring of parents who have a psychotic, bipolar affective or other psychiatric disorder is not currently explained by the SNP variation included in this study in accordance with findings from published genetic studies.
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Affiliation(s)
- Esben Agerbo
- National Centre for Register-Based Research, Aarhus University, Denmark.
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15
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Hollegaard MV, Grove J, Grauholm J, Kreiner-Møller E, Bønnelykke K, Nørgaard M, Benfield TL, Nørgaard-Pedersen B, Mortensen PB, Mors O, Sørensen HT, Harboe ZB, Børglum AD, Demontis D, Ørntoft TF, Bisgaard H, Hougaard DM. Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source. BMC Genet 2011; 12:58. [PMID: 21726430 PMCID: PMC3142526 DOI: 10.1186/1471-2156-12-58] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 07/04/2011] [Indexed: 12/17/2022] Open
Abstract
Background The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix. Results This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P < 0.05) affected by the year of storage and storage conditions. Nine (0.2%) DBS samples failed whole-genome amplification. A total of 4,586 (98.8%) samples met our criterion of success of a genetic call-rate above 97%. The three studies used different arrays, with mean genotyping call-rates of 99.385% (Illumina Infinium Human610-Quad), 99.722% (Illumina Infinium HD HumanOmni1-Quad), and 99.206% (Affymetrix Axiom Genome-Wide CEU). We observed a concordance rate of 99.997% in the 38 methodological replications, and 99.999% in the 27 technical replications. Handling variables such as time of storage, storage conditions and type of filter paper were shown too significantly (P < 0.05) affect the genotype call-rates in some of the arrays, although the effect was minimal. Conclusion Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.
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Affiliation(s)
- Mads V Hollegaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Ørestads Boulevard, Copenhagen, DK-2300, Denmark.
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16
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Winkel BG, Hollegaard MV, Olesen MS, Svendsen JH, Haunsø S, Hougaard DM, Tfelt-Hansen J. Whole-genome amplified DNA from stored dried blood spots is reliable in high resolution melting curve and sequencing analysis. BMC MEDICAL GENETICS 2011; 12:22. [PMID: 21306642 PMCID: PMC3045282 DOI: 10.1186/1471-2350-12-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 02/09/2011] [Indexed: 11/10/2022]
Abstract
Background The use of dried blood spots (DBS) samples in genomic workup has been limited by the relative low amounts of genomic DNA (gDNA) they contain. It remains to be proven that whole genome amplified DNA (wgaDNA) from stored DBS samples, constitutes a reliable alternative to gDNA. We wanted to compare melting curves and sequencing results from wgaDNA derived from DBS samples with gDNA derived from whole blood. Methods gDNA was extracted from whole blood obtained from 10 patients with lone atrial fibrillation (mean age 22.3 years). From their newborn DBS samples, stored at -24°C, genomic DNA was extracted and whole-genome amplified in triplicates. Using high resolution melting curve analysis and direct sequencing in both wgaDNA and gDNA samples, all coding regions and adjacent intron regions of the genes SCN5A and KCNA5 were investigated. Results Altered melting curves was present in 85 of wgaDNA samples and 81 of gDNA samples. Sequence analysis identified a total of 31 variants in the 10 wgaDNA samples. The same 31 variants were found in the exact same pattern of samples in the gDNA group. There was no false positive or negative sequence variation in the wgaDNA group. Conclusions The use of DNA amplified in triplicates from DBS samples is reliable and can be used both for high resolution curve melting analysis as well as direct sequence analysis. DBS samples therefore can serve as an alternative to whole blood in sequence analysis.
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Affiliation(s)
- Bo G Winkel
- Dept. of Cardiology, Rigshospitalet and Danish National Research Foundation Centre for Cardiac Arrhythmia (DARC), Copenhagen, Denmark.
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17
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Hollegaard MV, Thorsen P, Norgaard-Pedersen B, Hougaard DM. Genotyping whole-genome-amplified DNA from 3- to 25-year-old neonatal dried blood spot samples with reference to fresh genomic DNA. Electrophoresis 2009; 30:2532-5. [DOI: 10.1002/elps.200800655] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM. Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics 2009; 10:297. [PMID: 19575812 PMCID: PMC2713266 DOI: 10.1186/1471-2164-10-297] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 07/04/2009] [Indexed: 12/01/2022] Open
Abstract
Background Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference. Results Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls. Conclusion Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.
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Affiliation(s)
- Mads V Hollegaard
- Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark.
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Hollegaard MV, Grove J, Thorsen P, Nørgaard-Pedersen B, Hougaard DM. High-Throughput Genotyping on Archived Dried Blood Spot Samples. Genet Test Mol Biomarkers 2009; 13:173-9. [DOI: 10.1089/gtmb.2008.0073] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Mads V. Hollegaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Grove
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
| | - Poul Thorsen
- NANEA, Department of Epidemiology, Institute of Public Health, University of Aarhus, Aarhus, Denmark
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Bent Nørgaard-Pedersen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - David M. Hougaard
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Copenhagen, Denmark
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A population-based association study of glutamate decarboxylase 1 as a candidate gene for autism. J Neural Transm (Vienna) 2009; 116:381-8. [PMID: 19139806 DOI: 10.1007/s00702-008-0142-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 10/06/2008] [Indexed: 10/21/2022]
Abstract
Linkage studies, genome-wide scans and screening of possible candidate genes suggest that chromosome 2q31 may harbour one or more susceptibility genes for autism. The glutamate decarboxylase gene 1 (GAD1) located within chromosome 2q31 encodes the enzyme, GAD67, catalyzing the production of gamma-aminobutyric acid (GABA) from glutamate. Numerous independent findings have suggested the GABAergic system to be involved in autism. The present study investigates a Danish population-based, case-control sample of 444 subjects with childhood autism and 444 controls. Nine single nucleotide polymorphisms (SNPs) comprising the GAD1 gene and the microsatellite marker D2S2381 were examined for association with autism. We found no association between childhood autism and any single marker or 2-5 marker haplotypes. However, a rare nine-marker haplotype was associated with childhood autism. We cannot exclude neither GAD1 as a susceptibility gene nor the possibility of another susceptibility gene for autism to be located on chromosome 2q31.
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Nørgaard-Pedersen B, Hougaard DM. Storage policies and use of the Danish Newborn Screening Biobank. J Inherit Metab Dis 2007; 30:530-6. [PMID: 17632694 DOI: 10.1007/s10545-007-0631-x] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 03/15/2007] [Accepted: 05/31/2007] [Indexed: 01/13/2023]
Abstract
After routine newborn screening, residual dried blood spot samples (DBSS) are stored at -20 degrees C in the Danish Newborn Screening Biobank (NBS-Biobank), which contains DBSS from virtually all newborns in Denmark since 1982--about 1.8 million samples. The purpose of the storage is: (1) diagnosis and treatment of congenital disorders including documentation, repeat testing, quality assurance, statistics and improvement of screening methods; (2) diagnostic use later in infancy after informed consent; (3) legal use after court order; (4) the possibility of research projects after approval by the Scientific Ethical Committee System in Denmark, The Danish Data Protection Agency and the NBS-Biobank Steering Committee. The operation and use of the NBS-Biobank has until recently been regulated by an executive order of 1993 from the Danish Ministry of Health. The Ethical Council, the Central Scientific Ethical Committee and the National Board of Health were also involved in the regulations. These regulations have now been replaced by detailed general operational guidelines for biobanks in Denmark according to Acts on Processing of Personal Data, Patient's Rights, Health 546/2005 and the Biomedical Research Ethics Committee System. No specific Act on biobanks per se has been made in Denmark, but the new regulations and guidelines make the operations of the Danish NBS-Biobank even more clear-cut and safe. The Danish NBS-Biobank has been used in several research projects for aetiological studies of a number of disorders, recently employing new sensitive multiplex technologies and genetic analyses utilizing whole-genome amplified DNA.
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Affiliation(s)
- B Nørgaard-Pedersen
- Department of Clinical Biochemistry, Statens Serum Institut, Copenhagen, Denmark.
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