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Mullin BH, Zhu K, Xu J, Brown SJ, Mullin S, Tickner J, Pavlos NJ, Dudbridge F, Walsh JP, Wilson SG. Expression Quantitative Trait Locus Study of Bone Mineral Density GWAS Variants in Human Osteoclasts. J Bone Miner Res 2018; 33:1044-1051. [PMID: 29473973 DOI: 10.1002/jbmr.3412] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 12/23/2022]
Abstract
Osteoporosis is a complex disease with a strong genetic component. Genomewide association studies (GWAS) have been very successful at identifying common genetic variants associated with bone parameters. A recently published study documented the results of the largest GWAS for bone mineral density (BMD) performed to date (n = 142,487), identifying 307 conditionally independent single-nucleotide polymorphisms (SNPs) as associated with estimated BMD (eBMD) at the genomewide significance level. The vast majority of these variants are non-coding SNPs. Expression quantitative trait locus (eQTL) studies using disease-specific cell types have increasingly been integrated with the results from GWAS to identify genes through which the observed GWAS associations are likely mediated. We generated a unique human osteoclast-specific eQTL data set using cells differentiated in vitro from 158 participants. We then used this resource to characterize the 307 recently identified BMD GWAS SNPs for association with nearby genes (±500 kb). After correction for multiple testing, 24 variants were found to be significantly associated with the expression of 32 genes in the osteoclast-like cells. Bioinformatics analysis suggested that these variants and those in strong linkage disequilibrium with them are enriched in regulatory regions. Several of the eQTL associations identified are relevant to genes that present strongly as having a role in bone, particularly IQGAP1, CYP19A1, CTNNB1, and COL6A3. Supporting evidence for many of the associations was obtained from publicly available eQTL data sets. We have also generated strong evidence for the presence of a regulatory region on chromosome 15q21.2 relevant to both the GLDN and CYP19A1 genes. In conclusion, we have generated a unique osteoclast-specific eQTL resource and have used this to identify 32 eQTL associations for recently identified BMD GWAS loci, which should inform functional studies of osteoclast biology. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia.,School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia.,School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Suzanne J Brown
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Shelby Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia.,School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Jennifer Tickner
- School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, Australia
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia.,Medical School, University of Western Australia, Crawley, Australia
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia.,School of Biomedical Sciences, University of Western Australia, Crawley, Australia.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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4
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Alonso N, Estrada K, Albagha OME, Herrera L, Reppe S, Olstad OK, Gautvik KM, Ryan NM, Evans KL, Nielson CM, Hsu YH, Kiel DP, Markozannes G, Ntzani EE, Evangelou E, Feenstra B, Liu X, Melbye M, Masi L, Brandi ML, Riches P, Daroszewska A, Olmos JM, Valero C, Castillo J, Riancho JA, Husted LB, Langdahl BL, Brown MA, Duncan EL, Kaptoge S, Khaw KT, Usategui-Martín R, Del Pino-Montes J, González-Sarmiento R, Lewis JR, Prince RL, D’Amelio P, García-Giralt N, NoguéS X, Mencej-Bedrac S, Marc J, Wolstein O, Eisman JA, Oei L, Medina-Gómez C, Schraut KE, Navarro P, Wilson JF, Davies G, Starr J, Deary I, Tanaka T, Ferrucci L, Gianfrancesco F, Gennari L, Lucas G, Elosua R, Uitterlinden AG, Rivadeneira F, Ralston SH. Identification of a novel locus on chromosome 2q13, which predisposes to clinical vertebral fractures independently of bone density. Ann Rheum Dis 2018; 77:378-385. [PMID: 29170203 PMCID: PMC5912156 DOI: 10.1136/annrheumdis-2017-212469] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/01/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To identify genetic determinants of susceptibility to clinical vertebral fractures, which is an important complication of osteoporosis. METHODS Here we conduct a genome-wide association study in 1553 postmenopausal women with clinical vertebral fractures and 4340 controls, with a two-stage replication involving 1028 cases and 3762 controls. Potentially causal variants were identified using expression quantitative trait loci (eQTL) data from transiliac bone biopsies and bioinformatic studies. RESULTS A locus tagged by rs10190845 was identified on chromosome 2q13, which was significantly associated with clinical vertebral fracture (P=1.04×10-9) with a large effect size (OR 1.74, 95% CI 1.06 to 2.6). Bioinformatic analysis of this locus identified several potentially functional SNPs that are associated with expression of the positional candidate genes TTL (tubulin tyrosine ligase) and SLC20A1 (solute carrier family 20 member 1). Three other suggestive loci were identified on chromosomes 1p31, 11q12 and 15q11. All these loci were novel and had not previously been associated with bone mineral density or clinical fractures. CONCLUSION We have identified a novel genetic variant that is associated with clinical vertebral fractures by mechanisms that are independent of BMD. Further studies are now in progress to validate this association and evaluate the underlying mechanism.
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Affiliation(s)
- Nerea Alonso
- Rheumatology and Bone disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Karol Estrada
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Omar M E Albagha
- Rheumatology and Bone disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lizbeth Herrera
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Sjur Reppe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Clinical Biochemistry, Lovisenberg Diakonale Hospital, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ole K Olstad
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kaare M Gautvik
- Department of Clinical Biochemistry, Lovisenberg Diakonale Hospital, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Niamh M Ryan
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Carrie M Nielson
- Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Yi-Hsiang Hsu
- Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- BROAD Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Musculoskeletal Research Center, Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, USA
| | - Douglas P Kiel
- BROAD Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Musculoskeletal Research Center, Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - George Markozannes
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Evangelia E Ntzani
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Centre for Evidence Synthesis in Health, Department of Health Services, Policy and Practice, School of Public Health, Brown University, Rhode Island, USA
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Xueping Liu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Stanford School of Medicine, Stanford, California, USA
| | - Laura Masi
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Maria Luisa Brandi
- Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Philip Riches
- Rheumatology and Bone disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Anna Daroszewska
- Rheumatology and Bone disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Institute of Ageing and Chronic Disease, The MRC-Arthritis Research UK Centre for Integrated Research into Musculoskeletal Ageing, University of Liverpool, Liverpool, UK
| | - José Manuel Olmos
- Department of Internal Medicine, Hospital UM Valdecilla, University of Cantabria, IDIVAL, RETICEF, Santander, Spain
| | - Carmen Valero
- Department of Internal Medicine, Hospital UM Valdecilla, University of Cantabria, IDIVAL, RETICEF, Santander, Spain
| | - Jesús Castillo
- Department of Internal Medicine, Hospital UM Valdecilla, University of Cantabria, IDIVAL, RETICEF, Santander, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital UM Valdecilla, University of Cantabria, IDIVAL, RETICEF, Santander, Spain
| | - Lise B Husted
- Department of Endocrinology and Internal Medicine THG, Aarhus University Hospital, Aarhus, Denmark
| | - Bente L Langdahl
- Department of Endocrinology and Internal Medicine THG, Aarhus University Hospital, Aarhus, Denmark
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Emma L Duncan
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Endocrinology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
| | - Stephen Kaptoge
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, School of Medicine, University of Cambridge, Cambridge, UK
| | - Ricardo Usategui-Martín
- Molecular Medicine Unit, Department of Medicine and Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca – CSIC, Salamanca, Spain
| | - Javier Del Pino-Montes
- Molecular Medicine Unit, Department of Medicine and Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca – CSIC, Salamanca, Spain
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit, Department of Medicine and Biomedical Research Institute of Salamanca (IBSAL), University Hospital of Salamanca, University of Salamanca – CSIC, Salamanca, Spain
| | - Joshua R Lewis
- School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia
- Centre for Kidney Research, School of Public Health, University of Sydney, Sydney, New South Wales, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Richard L Prince
- School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Patrizia D’Amelio
- Gerontology and Bone Metabolic Diseases Unit, Department of Medical Science, University of Torino, Torino, Italy
| | - Natalia García-Giralt
- Department of Internal Medicine, Hospital del Mar-IMIM, RETICEF, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Xavier NoguéS
- Department of Internal Medicine, Hospital del Mar-IMIM, RETICEF, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Simona Mencej-Bedrac
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Orit Wolstein
- Osteoporosis and Bone Biology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - John A Eisman
- Osteoporosis and Bone Biology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ling Oei
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Carolina Medina-Gómez
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Edinburgh/British Heart Foundation Centre for Cardiovascular Science, QMRI, University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- MRC Human Genetics Unit, MRC, IGMM, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, MRC, IGMM, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - John Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ian Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Fernando Gianfrancesco
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council of Italy, Naples, Italy
| | - Luigi Gennari
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Gavin Lucas
- Grup de Recerca en Genètica i Epidemiologia Cardiovascular, IMIM, Barcelona, Spain
| | - Roberto Elosua
- Grup de Recerca en Genètica i Epidemiologia Cardiovascular, IMIM, Barcelona, Spain
| | - André G Uitterlinden
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Departments of Internal Medicine and Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Stuart H Ralston
- Rheumatology and Bone disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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5
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Han JH, Cai XJ, Sun HJ, Dong GH, He B, Zhang HX, Zhou X, Yan JQ. Identifying dysregulated pathways in postmenopausal osteoporosis through investigation of crosstalk between pathways. Mol Med Rep 2017; 16:9029-9034. [PMID: 28990094 DOI: 10.3892/mmr.2017.7703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/09/2017] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to identify potential dysregulated pathways to further reveal the molecular mechanisms of postmenopausal osteoporosis (PMOP) based on pathway‑interaction network (PIN) analysis, which considers crosstalk between pathways. Protein‑protein interaction (PPI) data and pathway information were derived from STRING and Reactome Pathway databases, respectively. According to the gene expression profiles, pathway data and PPI information, a PIN was constructed with each node representing a biological pathway. Principal component analysis was used to compute the pathway activity for each pathway, and the seed pathway was selected. Subsequently, dysregulated pathways were extracted from the PIN based on the seed pathway and the increased classification accuracy, which was measured using the area under the curve (AUC) index according to 5‑fold cross validation. A PIN comprising 2,725 interactions was constructed, which was used to detect dysregulated pathways. Notably, the 'mitotic prometaphase' pathway was selected and defined as a seed pathway. Starting with the seed pathway, network‑based analysis successfully identified one pathway set for PMOP comprising eight dysregulated pathways (such as mitotic prometaphase, resolution of sister chromatid cohesion, mRNA splicing and mRNA splicing‑major) with an AUC score of 0.85, which may provide potential biomarkers for targeted therapy for PMOP.
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Affiliation(s)
- Jian-Hua Han
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Xiao-Jun Cai
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Hou-Jie Sun
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Ge-Hui Dong
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Bin He
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Han-Xiang Zhang
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Xin Zhou
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
| | - Jia-Qiang Yan
- Department of Orthopedics, Zunyi First People's Hospital, Zunyi, Guizhou 563002, P.R. China
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7
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Reppe S, Lien TG, Hsu YH, Gautvik VT, Olstad OK, Yu R, Bakke HG, Lyle R, Kringen MK, Glad IK, Gautvik KM. Distinct DNA methylation profiles in bone and blood of osteoporotic and healthy postmenopausal women. Epigenetics 2017. [PMID: 28650214 DOI: 10.1080/15592294.2017.1345832] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation affects expression of associated genes and may contribute to the missing genetic effects from genome-wide association studies of osteoporosis. To improve insight into the mechanisms of postmenopausal osteoporosis, we combined transcript profiling with DNA methylation analyses in bone. RNA and DNA were isolated from 84 bone biopsies of postmenopausal donors varying markedly in bone mineral density (BMD). In all, 2529 CpGs in the top 100 genes most significantly associated with BMD were analyzed. The methylation levels at 63 CpGs differed significantly between healthy and osteoporotic women at 10% false discovery rate (FDR). Five of these CpGs at 5% FDR could explain 14% of BMD variation. To test whether blood DNA methylation reflect the situation in bone (as shown for other tissues), an independent cohort was selected and BMD association was demonstrated in blood for 13 of the 63 CpGs. Four transcripts representing inhibitors of bone metabolism-MEPE, SOST, WIF1, and DKK1-showed correlation to a high number of methylated CpGs, at 5% FDR. Our results link DNA methylation to the genetic influence modifying the skeleton, and the data suggest a complex interaction between CpG methylation and gene regulation. This is the first study in the hitherto largest number of postmenopausal women to demonstrate a strong association among bone CpG methylation, transcript levels, and BMD/fracture. This new insight may have implications for evaluation of osteoporosis stage and susceptibility.
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Affiliation(s)
- Sjur Reppe
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway.,b Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute , Oslo , Norway.,c University of Oslo, Institute of Basic Medical Sciences , Oslo , Norway
| | - Tonje G Lien
- d Department of Mathematics , University of Oslo , Oslo , Norway
| | - Yi-Hsiang Hsu
- e Hebrew SeniorLife Institute for Aging Research and Harvard Medical School , Boston , MA , USA.,f Broad Institute of MIT and Harvard , Cambridge , MA , USA.,g Molecular and Physiological Sciences Program, Harvard School of Public Health , Boston , MA , USA.,h Gerontology Division , Department of Medicine , Beth Israel Deaconess Medical Center , Boston , MA , USA
| | - Vigdis T Gautvik
- c University of Oslo, Institute of Basic Medical Sciences , Oslo , Norway
| | - Ole K Olstad
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Rona Yu
- e Hebrew SeniorLife Institute for Aging Research and Harvard Medical School , Boston , MA , USA
| | - Hege G Bakke
- i Center for Psychopharmacology, Diakonhjemmet Hospital , Oslo , Norway
| | - Robert Lyle
- j Department of Medical Genetics , Oslo University Hospital , Oslo , Norway.,k Department of Medical Genetics , University of Oslo , Oslo , Norway
| | | | - Ingrid K Glad
- d Department of Mathematics , University of Oslo , Oslo , Norway
| | - Kaare M Gautvik
- b Lovisenberg Diakonale Hospital, Unger-Vetlesen Institute , Oslo , Norway.,c University of Oslo, Institute of Basic Medical Sciences , Oslo , Norway
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