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Foss-Skiftesvik J, Li S, Rosenbaum A, Hagen CM, Stoltze UK, Ljungqvist S, Hjalmars U, Schmiegelow K, Morimoto L, de Smith AJ, Mathiasen R, Metayer C, Hougaard D, Melin B, Walsh KM, Bybjerg-Grauholm J, Dahlin AM, Wiemels JL. Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus. Neuro Oncol 2023; 25:1709-1720. [PMID: 36810956 PMCID: PMC10484172 DOI: 10.1093/neuonc/noad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date. METHODS Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes. RESULTS Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8). CONCLUSIONS In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Adam Rosenbaum
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sally Ljungqvist
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Libby Morimoto
- Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - David Hougaard
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kyle M Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | | | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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Stoltze UK, Hagen CM, van Overeem Hansen T, Byrjalsen A, Gerdes AM, Yakimov V, Rasmussen S, Bækvad-Hansen M, Hougaard DM, Schmiegelow K, Hjalgrim H, Wadt K, Bybjerg-Grauholm J. Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants. Genome Med 2023; 15:17. [PMID: 36918911 PMCID: PMC10013285 DOI: 10.1186/s13073-023-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but the costs associated with screening millions of humans remain prohibitive. New methods for population genetic testing that lower the costs of NGS without compromising diagnostic power are needed. METHODS We developed double batched sequencing where DNA samples are batch-sequenced twice - directly pinpointing individuals with rare variants. We sequenced batches of at-birth blood spot DNA using a commercial 113-gene panel in an explorative (n = 100) and a validation (n = 100) cohort of children who went on to develop pediatric cancers. All results were benchmarked against individual whole genome sequencing data. RESULTS We demonstrated fully replicable detection of cancer-causing germline variants, with positive and negative predictive values of 100% (95% CI, 0.91-1.00 and 95% CI, 0.98-1.00, respectively). Pathogenic and clinically actionable variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches indicated that our approach is highly scalable, yielding more than 95% cost reduction or less than 3 cents per gene screened for rare disease-causing mutations. We also show that double batched sequencing could cost-effectively prevent childhood cancer deaths through broad genomic testing. CONCLUSIONS Our ultracheap genetic diagnostic method, which uses existing sequencing hardware and standard newborn blood spots, should readily open up opportunities for population-wide risk stratification using genetic screening across many fields of clinical genetics and genomics.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark. .,Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.,Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Victor Yakimov
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark.,Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark
| | - Henrik Hjalgrim
- Department of Clinical Medicine, Copenhagen University, Blegdamsvej 3B, 2200, KBH N, Denmark.,Danish Cancer Society Research Centre, Danish Cancer Society, Strandboulevarden 49, 2100, KBH Ø, Denmark.,Department of Epidemiology Research, Statens Serum Institut, 2300, KBH S, Artillerivej 5, Denmark.,Department of Haematology, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, 2100, KBH Ø, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institute, 2300, KBH S, Artillerivej 5, Denmark.
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3
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Foss-Skiftesvik J, Hagen CM, Mathiasen R, Adamsen D, Bækvad-Hansen M, Børglum AD, Nordentoft M, Werge T, Christiansen M, Schmiegelow K, Juhler M, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J. Genome-wide association study across pediatric central nervous system tumors implicates shared predisposition and points to 1q25.2 (PAPPA2) and 11p12 (LRRC4C) as novel candidate susceptibility loci. Childs Nerv Syst 2021; 37:819-830. [PMID: 33226468 DOI: 10.1007/s00381-020-04946-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Central nervous system (CNS) tumors constitute the most common form of solid neoplasms in children, but knowledge on genetic predisposition is sparse. In particular, whether susceptibility attributable to common variants is shared across CNS tumor types in children has not been investigated. The purpose of this study was to explore potential common genetic risk variants exhibiting pleiotropic effects across pediatric CNS tumors. We also investigated whether such susceptibility differs between early and late onset of disease. METHOD A Danish nationwide genome-wide association study (GWAS) of 1,097 consecutive patients (< 15 years of age) with CNS tumors and a cohort of 4,745 population-based controls. RESULTS For both the overall cohort and patients diagnosed after the age of four, the strongest association was rs12064625 which maps to PAPPA2 at 1q25.2 (p = 3.400 × 10-7 and 9.668 × 10-8, respectively). PAPPA2 regulates local bioavailability of insulin-like growth factor I (IGF-I). IGF-I is fundamental to CNS development and is involved in tumorigenesis across a wide range of different cancers. For the younger children, the strongest association was provided by rs11036373 mapping to LRRC4C at 11p12 (p = 7.620 × 10-7), which encoded protein acts as an axon guidance molecule during CNS development and has not formerly been associated with brain tumors. DISCUSSION This GWAS indicates shared susceptibility attributable to common variants across pediatric CNS tumor types. Variations in genetic loci with roles in CNS development appear to be involved, possibly via altered IGF-I related pathways.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark.
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark.
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.
| | - Christian Munch Hagen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Dea Adamsen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Department of Biomedicine, Aarhus University and Centre for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Aarhus Genome Center, Aarhus, Denmark
| | - Merete Nordentoft
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Michael Christiansen
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Juhler
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
- Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neurosurgery, Aarhus University Hospital, Aarhus, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - David Michael Hougaard
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen, Denmark
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Ahlberg G, Hadji-Turdeghal K, Andreasen L, Hagen CM, Ghouse J, Baekvad-Hansen M, Bybjerg-Grauholm J, Hougaard DM, Hedley P, Haunsoe S, Svendsen JH, Jepps TA, Skov MW, Christiansen M, Olesen MS. 4259Discovery of the first genome-wide significant risk loci for syncope and collapse. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz745.0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Syncope is a common condition in the general population causing frequent hospitalisation and visits to the emergency department. Family aggregation and twin studies have previously indicated that syncope and collapse has a heritable component.
Purpose
We investigated whether common genetic variants predispose to syncope and collapse.
Methods
We used genome-wide association data on syncope and collapse for 408,961 individuals with European ancestry from the UK Biobank study. In a replication study, the Integrative Psychiatric Research Consortium (iPSYCH) cohort (n=86,189) was used to investigate the risk of incident syncope stratified by genotype carrier status.
Results
We report on a genome-wide significant locus on chromosome 2q32.1 with the lead SNP rs12465214 (odds ratio [OR] = 1.13, 95% confidence interval [CI] = 1.10–1.17, P=5.8x10–15; Figure 1a). This association was replicated in the iPSYCH cohort, where homozygous carriers of the C allele conferred an increased hazard ratio (HR=1.30, CI: 1.15–1.46, P=1.68x10–5; Figure 1b). LD score regression demonstrated a significant genetic correlation (rg) with coronary artery disease (rg=0.41, P=6.99x10–15) and related phenotypes such as angina and hypertension (Figure 1c). Analyses of eQTL (P=4x10–8) and epigenetic chromatin states revealed that variation in this locus likely affects expression of the gene ZNF804A, which resides in its proximity (Figure 1d). A qPCR analysis showed that ZNF804A was mostly expressed in the brain. A lower level of ZNF804A expression was also detected in the cerebral arteries. ZNF804A was not expressed in heart tissue.
Figure 1
Conclusion
rs12465214 is associated with syncope and collapse. Variation in this locus likely modulates the expression of the nearby gene ZNF804A through eQTLs and chromatin interactions. ZNF804A is mainly expressed in the brain and cerebral arteries. However, the precise function of ZNF804A is unknown. Furthermore, syncope and collapse is a polygenetic trait and share a significant genetic overlap with coronary artery disease, angina and hypertension.
Acknowledgement/Funding
This work was supported by grants from The John and Birthe Meyer Foundation, The Research Foundation of the Heart Centre, Rigshospitalet, The Research
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Affiliation(s)
- G Ahlberg
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - K Hadji-Turdeghal
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - L Andreasen
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - C M Hagen
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - J Ghouse
- University of Copenhagen, Biomedical Science, Copenhagen, Denmark
| | - M Baekvad-Hansen
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - J Bybjerg-Grauholm
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - D M Hougaard
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - P Hedley
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - S Haunsoe
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - J H Svendsen
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - T A Jepps
- University of Copenhagen, Biomedical Science, Copenhagen, Denmark
| | - M W Skov
- Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - M Christiansen
- Statens Serum Institut, Department of Congenital Disorders, Copenhagen, Denmark
| | - M S Olesen
- University of Copenhagen, Biomedical Science, Copenhagen, Denmark
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5
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Duhn PH, Sode J, Hagen CM, Christiansen M, Locht H. Mitochondrial haplogroups in patients with rheumatoid arthritis: No association with disease and disease manifestations. PLoS One 2017; 12:e0188492. [PMID: 29261674 PMCID: PMC5737896 DOI: 10.1371/journal.pone.0188492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE To describe the distribution of specific mitochondrial DNA (mtDNA) haplogroups (hgs) in a cohort of patients with rheumatoid arthritis (RA). METHODS Two-hundred nineteen consecutive patients with RA had mtDNA isolated from their blood, sequenced and haplotyped. Patients were diagnosed according to the American College of Rheumatology (ACR)/European league against Rheumatism (EULAR) criteria. Demographic and clinical data were retrieved from the Danish nationwide database (DANBIO). Logistic regression analyses were performed to test for associations. RESULTS One-hundred eighty-four patients were eligible for analysis. Haplogroup frequencies were: H (n = 88; 47.8%), U (n = 37; 20.1%), T (n = 22; 12.0%), J (n = 16; 8.7%), K (n = 11; 5.9%), HV (n = 6; 3.3%) and V (n = 4; 2.2%). The distribution of individual hgs was identical to the background population. Radiographic erosions were significantly associated with hg clusters JT (OR = 2.37, 95% confidence interval (CI): 1.07-5.53, p = 0.038). Significantly fewer patients from hg cluster JT received biological treatment (OR = 0.17, 95% CI: 0.03-0.87, p = 0.038). Albeit, none of these associations were significant when corrected for multiple tests. CONCLUSION There was no significant association between mtDNA hgs and presence of RA or disease manifestations. There was an, albeit insignificant, overrepresentation of patients with hg JT among patients with erosive disease; however, slightly fewer patients in the JT group were treated with biological drugs.
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Affiliation(s)
- Pernille Hurup Duhn
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
- * E-mail:
| | - Jacob Sode
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
- Institute of Regional Health Research, Center Sønderjylland, University of Southern Denmark, Campusvej, Odense M, Denmark
| | - Christian Munch Hagen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej, Copenhagen S, Denmark
- Department of Biomedical Sciences, Faculty of Health and Life Science, University of Copenhagen, Blegdamsvej, Copenhagen N, Denmark
| | - Henning Locht
- Department of Rheumatology Frederiksberg Hospital, Nordre Fasanvej, Frederiksberg, Denmark
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6
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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8
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Denti P, Jeremiah K, Chigutsa E, Faurholt-Jepsen D, PrayGod G, Range N, Castel S, Wiesner L, Hagen CM, Christiansen M, Changalucha J, McIlleron H, Friis H, Andersen AB. Pharmacokinetics of Isoniazid, Pyrazinamide, and Ethambutol in Newly Diagnosed Pulmonary TB Patients in Tanzania. PLoS One 2015; 10:e0141002. [PMID: 26501782 PMCID: PMC4621059 DOI: 10.1371/journal.pone.0141002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/02/2015] [Indexed: 12/31/2022] Open
Abstract
Exposure to lower-than-therapeutic levels of anti-tuberculosis drugs is likely to cause selection of resistant strains of Mycobacterium tuberculosis and treatment failure. The first-line anti-tuberculosis (TB) regimen consists of rifampicin, isoniazid, pyrazinamide, and ethambutol, and correct management reduces risk of TB relapse and development of drug resistance. In this study we aimed to investigate the effect of standard of care plus nutritional supplementation versus standard care on the pharmacokinetics of isoniazid, pyrazinamide and ethambutol among sputum smear positive TB patients with and without HIV. In a clinical trial in 100 Tanzanian TB patients, with or without HIV infection, drug concentrations were determined at 1 week and 2 months post initiation of anti-TB medication. Data was analysed using population pharmacokinetic modelling. The effect of body size was described using allometric scaling, and the effects of nutritional supplementation, HIV, age, sex, CD4+ count, weight-adjusted dose, NAT2 genotype, and time on TB treatment were investigated. The kinetics of all drugs was well characterised using first-order elimination and transit compartment absorption, with isoniazid and ethambutol described by two-compartment disposition models, and pyrazinamide by a one-compartment model. Patients with a slow NAT2 genotype had higher isoniazid exposure and a lower estimate of oral clearance (15.5 L/h) than rapid/intermediate NAT2 genotype (26.1 L/h). Pyrazinamide clearance had an estimated typical value of 3.32 L/h, and it was found to increase with time on treatment, with a 16.3% increase after the first 2 months of anti-TB treatment. The typical clearance of ethambutol was estimated to be 40.7 L/h, and was found to decrease with age, at a rate of 1.41% per year. Neither HIV status nor nutritional supplementations were found to affect the pharmacokinetics of these drugs in our cohort of patients.
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Affiliation(s)
- Paolo Denti
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kidola Jeremiah
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- National Institute for Medical Research, Mwanza Medical Research Centre, Mwanza, Tanzania
- * E-mail:
| | - Emmanuel Chigutsa
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniel Faurholt-Jepsen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - George PrayGod
- National Institute for Medical Research, Mwanza Medical Research Centre, Mwanza, Tanzania
| | - Nyagosya Range
- National Institute for Medical Research, Muhimbili Research Centre, Dar Es Salaam, Tanzania
| | - Sandra Castel
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - John Changalucha
- National Institute for Medical Research, Mwanza Medical Research Centre, Mwanza, Tanzania
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Henrik Friis
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Aase Bengaard Andersen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
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9
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Abdissa A, Olsen MF, Yilma D, Tesfaye M, Girma T, Christiansen M, Hagen CM, Wiesner L, Castel S, Aseffa A, McIlleron H, Pedersen C, Friis H, Andersen AB. Lipid-based nutrient supplements do not affect efavirenz but lower plasma nevirapine concentrations in Ethiopian adult HIV patients. HIV Med 2015; 16:403-11. [PMID: 25974723 DOI: 10.1111/hiv.12225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2015] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Lipid-based nutrient supplements (LNSs) are increasingly used in HIV programmes in resource-limited settings. However, the possible effects of LNSs on the plasma concentrations of antiretroviral drugs have not been assessed. Here, we aimed to assess the effects of LNSs on plasma efavirenz and nevirapine trough concentrations in Ethiopian adult HIV-infected patients. METHODS The effects of LNSs were studied in adults initiating antiretroviral therapy (ART) in a randomized trial. Patients with body mass index (BMI) > 17 kg/m(2) (n = 282) received daily supplementation of an LNS containing whey (LNS/w), an LNS containing soy (LNS/s) or no LNS. Trough plasma concentrations of efavirenz and nevirapine were measured at 1 and 2 months. Genotyping for 516 G>T and 983 T>C polymorphisms of the cytochrome P450 (CYP) 2B6 locus was performed. Multilevel linear mixed-effects models were used to assess the associations between LNS and plasma efavirenz and nevirapine concentrations. RESULTS In patients with BMI > 17 kg/m(2), nevirapine concentrations were lower in the LNS/w and LNS/s groups by a median of -2.3 μg/mL [interquartile range (IQR) -3.9; -0.9 μg/mL; P = 0.002] and -2.1 μg/mL (IQR -3.9; -0.9 μg/mL; P = 0.01), respectively, compared with the group not receiving supplements. There were no differences between groups with respect to efavirenz plasma concentrations. The CYP2B6 516 G>T polymorphism was associated with a 5 μg/mL higher plasma efavirenz concentration compared with the wild type (P < 0.0001), while it was not associated with plasma nevirapine concentrations. CONCLUSIONS Intake of an LNS was associated with lower plasma nevirapine trough concentrations, indicating possible drug-LNS interactions. The clinical relevance of such reductions in nevirapine exposure is not clear. Plasma efavirenz concentration was not affected by the LNS.
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Affiliation(s)
- A Abdissa
- Department of Medical Laboratory Sciences & Pathology, Jimma University, Jimma, Ethiopia.,Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | - M F Olsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - D Yilma
- Department of Internal Medicine, Jimma University, Jimma, Ethiopia
| | - M Tesfaye
- Department of Psychiatry, Jimma University, Jimma, Ethiopia
| | - T Girma
- Department of Pediatrics and Child Health, Jimma University, Jimma, Ethiopia
| | - M Christiansen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institute, Copenhagen, Denmark
| | - C M Hagen
- Department of Clinical Biochemistry and Immunology, Statens Serum Institute, Copenhagen, Denmark
| | - L Wiesner
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - S Castel
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - A Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - H McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - C Pedersen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | - H Friis
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - A B Andersen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
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10
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Lausten-Thomsen U, Gamborg M, Bøjsøe C, Hedley PL, Hagen CM, Christiansen M, Holm JC. Longitudinal changes in C-reactive protein, proform of eosinophil major basic protein, and pregnancy-associated plasma protein-A during weight changes in obese children. J Pediatr Endocrinol Metab 2015; 28:393-8. [PMID: 25460282 DOI: 10.1515/jpem-2014-0249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/29/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND Childhood obesity is associated with several complications, including cardiovascular comorbidity. Several biomarkers, such as high-sensitive C-reactive protein (hs-CRP), proform of eosinophil major basic protein (Pro-MBP) and pregnancy associated plasma protein-A (PAPP-A), have equally been linked to increased cardiovascular susceptibility. This study investigates these biomarkers during weight loss and regain in obese children. MATERIALS AND METHODS A longitudinal study during a 12-week weight loss program with a 28 months follow-up was conducted. Anthropometrics and plasma concentrations of hs-CRP, Pro-MBP, and PAPP-A were measured at baseline; at days 14, 33 and 82 during weight loss; and at months 10, 16, and 28 during follow-up. RESULTS Fifty-three boys and 62 girls aged 8-15 years with a median body mass index (BMI) standard deviation score (SDS) at baseline of 2.78 (boys), and 2.70 (girls) were included. Ninety children completed the weight loss program and 68 children entered the follow-up program. Pro-MBP and PAPP-A, but not hs-CRP, exhibited individual-specific levels (tracking) during weight loss and regain. The PAPP-A/Pro-MBP correlation was strong, whereas the hs-CRP/PAPP-A correlation was weak during weight fluctuations. CONCLUSION Hs-CRP changes reflect weight changes. PAPP-A and Pro-MBP exhibited tracking during weight perturbations and may contribute as early risk markers of cardiovascular susceptibility.
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11
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Aidt FH, Nielsen SMB, Kanters J, Pesta D, Nielsen TT, Nørremølle A, Hasholt L, Christiansen M, Hagen CM. Dysfunctional mitochondrial respiration in the striatum of the Huntington's disease transgenic R6/2 mouse model. PLoS Curr 2013; 5. [PMID: 23568011 PMCID: PMC3614423 DOI: 10.1371/currents.hd.d8917b4862929772c5a2f2a34ef1c201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolic dysfunction and mitochondrial involvement are recognised as part of the pathology in Huntington's Disease (HD). Post-mortem examinations of the striatum from end-stage HD patients have shown a decrease in the in vitro activity of complexes II, III and IV of the electron transport system (ETS). In different models of HD, evidence of enzyme defects have been reported in complex II and complex IV using enzyme assays. However, such assays are highly variable and results have been inconsistent.
We investigated the integrated ETS function ex vivo using a sensitive high-resolution respirometric (HRR) method. The O2 flux in a whole-cell sample combined with the addition of mitochondrial substrates, uncouplers and inhibitors enabled us to accurately quantitate the function of individual mitochondrial complexes in intact mitochondria, while retaining mitochondrial regulation and compensatory mechanisms.
We used HRR to examine the mitochondrial function in striata from 12-week old R6/2 mice expressing exon 1 of human HTT with 130 CAG repeats. A significant reduction in complex II and complex IV flux control ratios was found in the R6/2 mouse striatum at 12 weeks of age compared to controls, confirming previous findings obtained with spectrophotometric enzyme assays.
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Affiliation(s)
- Frederik Heurlin Aidt
- Institute of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen; Section of Molecular Medicine, Department of Clinical Biochemistry, Genetics and Immunology, Statens Serum Institut, Copenhagen, Denmark
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