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Skodvin SN, Gjessing HK, Jugessur A, Romanowska J, Page CM, Corfield EC, Lee Y, Håberg SE, Gjerdevik M. Statistical methods to detect mother-father genetic interaction effects on risk of infertility: A genome-wide approach. Genet Epidemiol 2023; 47:503-519. [PMID: 37638522 DOI: 10.1002/gepi.22534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023]
Abstract
Infertility is a heterogeneous phenotype, and for many couples, the causes of fertility problems remain unknown. One understudied hypothesis is that allelic interactions between the genotypes of the two parents may influence the risk of infertility. Our aim was, therefore, to investigate how allelic interactions can be modeled using parental genotype data linked to 15,789 pregnancies selected from the Norwegian Mother, Father, and Child Cohort Study. The newborns in 1304 of these pregnancies were conceived using assisted reproductive technologies (ART), and the remainder were conceived naturally. Treating the use of ART as a proxy for infertility, different parameterizations were implemented in a genome-wide screen for interaction effects between maternal and paternal alleles at the same locus. Some of the models were more similar in the way they were parameterized, and some produced similar results when implemented on a genome-wide scale. The results showed near-significant interaction effects in genes relevant to the phenotype under study, such as Dynein axonemal heavy chain 17 (DNAH17) with a recognized role in male infertility. More generally, the interaction models presented here are readily adaptable to the study of other phenotypes in which maternal and paternal allelic interactions are likely to be involved.
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Affiliation(s)
- Siri N Skodvin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Christian M Page
- Department of Physical Health and Ageing, Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Elizabeth C Corfield
- Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
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2
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Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A. The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome? Hum Genomics 2023; 17:35. [PMID: 37085889 PMCID: PMC10122315 DOI: 10.1186/s40246-023-00484-6] [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: 01/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Assisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of epigenome-wide association studies of ART have been published, none have investigated CpGs on the X chromosome. To bridge this knowledge gap, we leveraged one of the largest collections of mother-father-newborn trios of ART and non-ART (natural) conceptions to date to investigate sex-specific DNAm differences on the X chromosome. The discovery cohort consisted of 982 ART and 963 non-ART trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa). To verify our results from the MoBa cohort, we used an external cohort of 149 ART and 58 non-ART neonates from the Australian 'Clinical review of the Health of adults conceived following Assisted Reproductive Technologies' (CHART) study. The Illumina EPIC array was used to measure DNAm in both datasets. In the MoBa cohort, we performed a set of X-chromosome-wide association studies ('XWASs' hereafter) to search for sex-specific DNAm differences between ART and non-ART newborns. We tested several models to investigate the influence of various confounders, including parental DNAm. We also searched for differentially methylated regions (DMRs) and regions of co-methylation flanking the most significant CpGs. Additionally, we ran an analogous model to our main model on the external CHART dataset. RESULTS In the MoBa cohort, we found more differentially methylated CpGs and DMRs in girls than boys. Most of the associations persisted after controlling for parental DNAm and other confounders. Many of the significant CpGs and DMRs were in gene-promoter regions, and several of the genes linked to these CpGs are expressed in tissues relevant for both ART and sex (testis, placenta, and fallopian tube). We found no support for parental DNAm-dependent features as an explanation for the observed associations in the newborns. The most significant CpG in the boys-only analysis was in UBE2DNL, which is expressed in testes but with unknown function. The most significant CpGs in the girls-only analysis were in EIF2S3 and AMOT. These three loci also displayed differential DNAm in the CHART cohort. CONCLUSIONS Genes that co-localized with the significant CpGs and DMRs associated with ART are implicated in several key biological processes (e.g., neurodevelopment) and disorders (e.g., intellectual disability and autism). These connections are particularly compelling in light of previous findings indicating that neurodevelopmental outcomes differ in ART-conceived children compared to those naturally conceived.
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Affiliation(s)
- Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- DeepInsight, 0154, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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Laake I, Skodvin SN, Blix K, Caspersen IH, Gjessing HK, Juvet LK, Magnus P, Mjaaland S, Robertson AH, Starrfelt J, Trogstad L, Feiring B. Effectiveness of mRNA Booster Vaccination Against Mild, Moderate, and Severe COVID-19 Caused by the Omicron Variant in a Large, Population-Based, Norwegian Cohort. J Infect Dis 2022; 226:1924-1933. [PMID: 36259543 PMCID: PMC9620770 DOI: 10.1093/infdis/jiac419] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Understanding how booster vaccination can prevent moderate and severe illness without hospitalization is crucial to evaluate the full advantage of mRNA boosters. METHODS We followed 85 801 participants (aged 31-81 years) in 2 large population-based cohorts during the Omicron BA.1/2 wave. Information on home testing, PCR testing, and symptoms of coronavirus disease 2019 (COVID-19) was extracted from biweekly questionnaires covering the period 12 January 2022 to 7 April 2022. Vaccination status and data on previous SARS-CoV-2 infection were obtained from national registries. Cox regression was used to estimate the effectiveness of booster vaccination compared to receipt of 2-dose primary series >130 days previously. RESULTS The effectiveness of booster vaccination increased with increasing severity of COVID-19 and decreased with time since booster vaccination. The effectiveness against severe COVID-19 was reduced from 80.9% shortly after booster vaccination to 63.4% in the period >90 days after vaccination. There was hardly any effect against mild COVID-19. The effectiveness tended to be lower among subjects aged ≥60 years than those aged <50 years. CONCLUSIONS This is the first population-based study to evaluate booster effectiveness against self-reported mild, moderate, and severe COVID-19. Our findings contribute valuable information on duration of protection and thus timing of additional booster vaccinations.
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Affiliation(s)
- Ida Laake
- Correspondence: Ida Laake, PhD, Norwegian Institute of Public Health, PO Box 222 Skøyen, N-0213 Oslo, Norway ()
| | | | - Kristine Blix
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Lene K Juvet
- Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri Mjaaland
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Anna H Robertson
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Jostein Starrfelt
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Lill Trogstad
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
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Magnus MC, Örtqvist AK, Dahlqwist E, Ljung R, Skår F, Oakley L, Macsali F, Pasternak B, Gjessing HK, Håberg SE, Stephansson O. Association of SARS-CoV-2 Vaccination During Pregnancy With Pregnancy Outcomes. JAMA 2022; 327:1469-1477. [PMID: 35323851 PMCID: PMC8949721 DOI: 10.1001/jama.2022.3271] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
IMPORTANCE Data about the safety of vaccines against SARS-CoV-2 during pregnancy are limited. OBJECTIVE To examine the risk of adverse pregnancy outcomes after vaccination against SARS-CoV-2 during pregnancy. DESIGN, SETTING, AND PARTICIPANTS This registry-based retrospective cohort study included 157 521 singleton pregnancies ending after 22 gestational weeks from January 1, 2021, until January 12, 2022 (Sweden), or January 15, 2022 (Norway). The Pregnancy Register in Sweden and the Medical Birth Registry of Norway were linked to vaccination and other registries for identification of exposure and background characteristics. EXPOSURES Data on mRNA vaccines-BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna)-and 1 viral vector vaccine-AZD1222 (AstraZeneca)-were collected from national vaccination registries. MAIN OUTCOMES AND MEASURES The risk of preterm birth and stillbirth was evaluated using Cox regression models, with gestational day as the time metric and vaccination as a time-dependent exposure variable. The risk of small for gestational age, low Apgar score, and neonatal care admission was evaluated using logistic regression. Random-effects meta-analysis was used to combine results between countries. RESULTS Among the 157 521 singleton births included in the study (103 409 in Sweden and 54 112 in Norway), the mean maternal age at the time of delivery was 31 years, and 28 506 (18%) were vaccinated against SARS-CoV-2 (12.9% with BNT162b2, 4.8% with mRNA-1273, and 0.3% with AZD1222) while pregnant. A total of 0.7%, 8.3%, and 9.1% of individuals delivering were vaccinated during the first, second, and third trimester, respectively. Vaccination against SARS-CoV-2 was not significantly associated with increased risk of preterm birth (6.2 vs 4.9 per 10 000 pregnancy days; adjusted hazard ratio [aHR], 0.98 [95% CI, 0.91 to 1.05]; I2 = 0%; P for heterogeneity = .60), stillbirth (2.1 vs 2.4 per 100 000 pregnancy days; aHR, 0.86 [95% CI, 0.63 to 1.17]), small for gestational age (7.8% vs 8.5%; difference, -0.6% [95% CI, -1.3% to 0.2%]; adjusted OR [aOR], 0.97 [95% CI, 0.90 to 1.04]), low Apgar score (1.5% vs 1.6%; difference, -0.05% [95% CI, -0.3% to 0.1%]; aOR, 0.97 [95% CI, 0.87 to 1.08]), or neonatal care admission (8.5% vs 8.5%; difference, 0.003% [95% CI, -0.9% to 0.9%]; aOR, 0.97 [95% CI, 0.86 to 1.10]). CONCLUSIONS AND RELEVANCE In this population-based study conducted in Sweden and Norway, vaccination against SARS-CoV-2 during pregnancy, compared with no SARS-CoV-2 vaccination during pregnancy, was not significantly associated with an increased risk of adverse pregnancy outcomes. The majority of the vaccinations were with mRNA vaccines during the second and third trimesters of pregnancy, which should be considered in interpreting the findings.
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Affiliation(s)
- Maria C. Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Anne K. Örtqvist
- Clinical Epidemiology Division, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Obstetrics and Gynecology, Visby County Hospital, Visby, Sweden
| | - Elisabeth Dahlqwist
- Clinical Epidemiology Division, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rickard Ljung
- Swedish Medical Products Agency, Uppsala, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Skår
- Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway
| | - Laura Oakley
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ferenc Macsali
- Department of Health Registry Research and Development, Norwegian Institute of Public Health, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Björn Pasternak
- Clinical Epidemiology Division, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Siri E. Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Olof Stephansson
- Clinical Epidemiology Division, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Women’s Health, Division of Obstetrics, Karolinska University Hospital, Stockholm, Sweden
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5
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Håberg SE, Page CM, Lee Y, Nustad HE, Magnus MC, Haftorn KL, Carlsen EØ, Denault WRP, Bohlin J, Jugessur A, Magnus P, Gjessing HK, Lyle R. DNA methylation in newborns conceived by assisted reproductive technology. Nat Commun 2022; 13:1896. [PMID: 35393427 PMCID: PMC8989983 DOI: 10.1038/s41467-022-29540-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Assisted reproductive technology (ART) may affect fetal development through epigenetic mechanisms as the timing of ART procedures coincides with the extensive epigenetic remodeling occurring between fertilization and embryo implantation. However, it is unknown to what extent ART procedures alter the fetal epigenome. Underlying parental characteristics and subfertility may also play a role. Here we identify differences in cord blood DNA methylation, measured using the Illumina EPIC platform, between 962 ART conceived and 983 naturally conceived singleton newborns. We show that ART conceived newborns display widespread differences in DNA methylation, and overall less methylation across the genome. There were 607 genome-wide differentially methylated CpGs. We find differences in 176 known genes, including genes related to growth, neurodevelopment, and other health outcomes that have been associated with ART. Both fresh and frozen embryo transfer show DNA methylation differences. Associations persist after controlling for parents’ DNA methylation, and are not explained by parental subfertility. Timing of assisted reproduction technology (ART) procedures coincides with extensive epigenetic remodeling early after conception. Here the authors identify 176 DNA methylation differences in cord blood of newborns conceived with ART. including genes related to growth, neurodevelopment, and cancer.
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Affiliation(s)
- Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O box 1032 Blindern, N-0315, Oslo, Norway
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Deepinsight, Karl Johans gate 8, 0154, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway
| | - Ellen Ø Carlsen
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Human Genetics, University of Chicago, 5801S Ellis Ave, Chicago, IL, 60637, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, P.O. box 7804, N-5020, Bergen, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, P.O. box 7804, N-5020, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. box 222 Skøyen, 0213, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, OUS HF, P.O. box 4956 Nydalen, 0424, Oslo, Norway
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6
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Affiliation(s)
| | | | | | - Allen J Wilcox
- National Institute of Environmental Health Sciences, Durham, NC
| | - Deshayne B Fell
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
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7
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Magnus MC, Oakley L, Gjessing HK, Stephansson O, Engjom HM, Macsali F, Juliusson PB, Nybo Andersen AM, Håberg SE. Pregnancy and risk of COVID-19: a Norwegian registry-linkage study. BJOG 2021; 129:101-109. [PMID: 34657368 PMCID: PMC8652518 DOI: 10.1111/1471-0528.16969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/30/2022]
Abstract
Objective To compare the risk of acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection and contact with specialist healthcare services for coronavirus disease 2019 (COVID‐19) between pregnant and non‐pregnant women. Population or sample All women ages 15–45 living in Norway on 1 March 2020 (n = 1 033 699). Methods We linked information from the national birth, patient, communicable diseases and education databases using unique national identifiers. Main outcome measure We estimated hazard ratios (HR) among pregnant compared to non‐pregnant women of having a positive test for SARS‐CoV‐2, a diagnosis of COVID‐19 in specialist healthcare, or hospitalisation with COVID‐19 using Cox regression. Multivariable analyses adjusted for age, marital status, education, income, country of birth and underlying medical conditions. Results Pregnant women were not more likely to be tested for or to a have a positive SARS‐CoV‐2 test (adjusted HR 0.99; 95% CI 0.92–1.07). Pregnant women had higher risk of hospitalisation with COVID‐19 (HR 4.70, 95% CI 3.51–6.30) and any type of specialist care for COVID‐19 (HR 3.46, 95% CI 2.89–4.14). Pregnant women born outside Scandinavia were less likely to be tested, and at higher risk of a positive test (HR 2.37, 95% CI 2.51–8.87). Compared with pregnant Scandinavian‐born women, pregnant women with minority background had a higher risk of hospitalisation with COVID‐19 (HR 4.72, 95% CI 2.51–8.87). Conclusion Pregnant women were not more likely to be infected with SARS‐CoV‐2. Still, pregnant women with COVID‐19, especially those born outside of Scandinavia, were more likely to be hospitalised. Tweetable abstract Pregnant women are at increased risk of hospitalisation for COVID‐19. Pregnant women are at increased risk of hospitalisation for COVID‐19.
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Affiliation(s)
- M C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - L Oakley
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - H K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - O Stephansson
- Division of Clinical Epidemiology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Women's Health, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - H M Engjom
- Department of Health Registry Research and Development, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - F Macsali
- Department of Health Registry Research and Development, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - P B Juliusson
- Department of Health Registry Research and Development, Norwegian Institute of Public Health, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - A-M Nybo Andersen
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - S E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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8
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Denault WRP, Gjessing HK, Juodakis J, Jacobsson B, Jugessur A. Wavelet Screening: a novel approach to analyzing GWAS data. BMC Bioinformatics 2021; 22:484. [PMID: 34620077 PMCID: PMC8499521 DOI: 10.1186/s12859-021-04356-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide polymorphisms (SNPs) simultaneously. Further, by ignoring more complex joint effects of nearby SNPs within a given region, these methods fail to consider the genomic context of an association with the outcome. Results To address these shortcomings, we present a more powerful method for GWAS, coined ‘Wavelet Screening’ (WS), that greatly reduces the number of tests to be performed. This is achieved through the use of a sliding-window approach based on wavelets to sequentially screen the entire genome for associations. Wavelets are oscillatory functions that are useful for analyzing the local frequency and time behavior of signals. The signals can then be divided into different scale components and analyzed separately. In the current setting, we consider a sequence of SNPs as a genetic signal, and for each screened region, we transform the genetic signal into the wavelet space. The null and alternative hypotheses are modeled using the posterior distribution of the wavelet coefficients. WS is enhanced by using additional information from the regression coefficients and by taking advantage of the pyramidal structure of wavelets. When faced with more complex genetic signals than single-SNP associations, we show via simulations that WS provides a substantial gain in power compared to both the traditional GWAS modeling and another popular regional association test called SNP-set (Sequence) Kernel Association Test (SKAT). To demonstrate feasibility, we applied WS to a large Norwegian cohort (N=8006) with genotypes and information available on gestational duration. Conclusions WS is a powerful and versatile approach to analyzing whole-genome data and lends itself easily to investigating various omics data types. Given its broader focus on the genomic context of an association, WS may provide additional insight into trait etiology by revealing genes and loci that might have been missed by previous efforts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway. .,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Julius Juodakis
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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9
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Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor J, Xu Z, Lie RT, Gjessing HK, Jugessur A. Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 2021; 3:lqab035. [PMID: 33987535 PMCID: PMC8092375 DOI: 10.1093/nargab/lqab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch and Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
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10
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Magnus MC, Wilcox AJ, Fadum EA, Gjessing HK, Opdahl S, Juliusson PB, Romundstad LB, Håberg SE. Growth in children conceived by ART. Hum Reprod 2021; 36:1074-1082. [PMID: 33592626 PMCID: PMC7970724 DOI: 10.1093/humrep/deab007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/27/2020] [Indexed: 12/27/2022] Open
Abstract
STUDY QUESTION Is the growth pattern of children conceived by ART different compared to naturally conceived children. SUMMARY ANSWER Both ART and underlying parental subfertility may contribute to differences in early childhood growth between children conceived with and without the use of ART. WHAT IS KNOWN ALREADY Children conceived by ART weigh less and are shorter at the time of delivery. The extent to which differences in growth according to mode of conception persist during childhood, and the role of underlying parental subfertility, remains unclear. STUDY DESIGN, SIZE, DURATION We conducted a prospective study population-based study. We studied 81 461 children participating in the Norwegian Mother, Father and Child Cohort Study (MoBa) and 544 113 adolescents screened for military conscription. PARTICIPANTS/MATERIALS, SETTING, METHODS Conception by ART as registered in the Medical Birth Registry. We compared maternally reported length/height and weight among children in MoBa from mid-pregnancy to age 7 according to mode of conception using mixed-effects linear regression. Differences in self-reported height and weight at 17 years of age at screening for military conscription were assessed with linear regression. MAIN RESULTS AND THE ROLE OF CHANCE At birth, children conceived by ART were shorter (boys −0.3 cm; 95% CI, −0.5 to −0.1), girls −0.4 cm; 95% CI, −0.5 to −0.3) and lighter (boys −113 grams; 95% CI, −201 to −25, girls −107 grams; 95% CI, −197 to −17). After birth, children conceived by ART grew more rapidly, achieving both greater height and weight at age 3. Children conceived by ART had a greater height up to age 7, but did not have a greater height or weight by age 17. Naturally conceived children of parents taking longer time to conceive had growth patterns similar to ART children. Children born after frozen embryo transfer had larger ultrasound measures and were longer and heavier the first 2 years than those born after fresh embryo transfer. LIMITATIONS, REASONS FOR CAUTIONS Selection bias could have been introduced due to the modest participation rate in the MoBa cohort. Our reliance on self-reported measures of length/height and weight could have introduced measurement error. WIDER IMPLICATIONS OF THE FINDINGS : Our findings provide reassurance that offspring conceived by ART are not different in height, weight or BMI from naturally conceived once they reach adolescence. STUDY FUNDING/COMPETING INTEREST(S) Research Council of Norway; Medical Research Council; National Institute of Environmental Health Sciences. The authors have no competing interest. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Bristol Medical School, Population Health Sciences, Bristol, UK
| | - Allen J Wilcox
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway.,Epidemiology Branch, National Institute of Environmental Health Sciences, NC, USA
| | - Elin A Fadum
- Institute of Military Medicine and Epidemiology, Norwegian Armed Forces Joint Medical Services, Sessvollmoen, Norway
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Signe Opdahl
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Petur B Juliusson
- Department of Health Registries, Norwegian Institute of Public Health, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
| | - Liv Bente Romundstad
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, 0213 Oslo, Norway.,Institute of Military Medicine and Epidemiology, Norwegian Armed Forces Joint Medical Services, Sessvollmoen, Norway
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11
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Denault WRP, Romanowska J, Helgeland Ø, Jacobsson B, Gjessing HK, Jugessur A. A fast wavelet-based functional association analysis replicates several susceptibility loci for birth weight in a Norwegian population. BMC Genomics 2021; 22:321. [PMID: 33932983 PMCID: PMC8088671 DOI: 10.1186/s12864-021-07582-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022] Open
Abstract
Background Birth weight (BW) is one of the most widely studied anthropometric traits in humans because of its role in various adult-onset diseases. The number of loci associated with BW has increased dramatically since the advent of whole-genome screening approaches such as genome-wide association studies (GWASes) and meta-analyses of GWASes (GWAMAs). To further contribute to elucidating the genetic architecture of BW, we analyzed a genotyped Norwegian dataset with information on child’s BW (N=9,063) using a slightly modified version of a wavelet-based method by Shim and Stephens (2015) called WaveQTL. Results WaveQTL uses wavelet regression for regional testing and offers a more flexible functional modeling framework compared to conventional GWAS methods. To further improve WaveQTL, we added a novel feature termed “zooming strategy” to enhance the detection of associations in typically small regions. The modified WaveQTL replicated five out of the 133 loci previously identified by the largest GWAMA of BW to date by Warrington et al. (2019), even though our sample size was 26 times smaller than that study and 18 times smaller than the second largest GWAMA of BW by Horikoshi et al. (2016). In addition, the modified WaveQTL performed better in regions of high LD between SNPs. Conclusions This study is the first adaptation of the original WaveQTL method to the analysis of genome-wide genotypic data. Our results highlight the utility of the modified WaveQTL as a complementary tool for identifying loci that might escape detection by conventional genome-wide screening methods due to power issues. An attractive application of the modified WaveQTL would be to select traits from various public GWAS repositories to investigate whether they might benefit from a second analysis. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07582-6).
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway. .,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bo Jacobsson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
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12
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Haftorn KL, Lee Y, Denault WRP, Page CM, Nustad HE, Lyle R, Gjessing HK, Malmberg A, Magnus MC, Næss Ø, Czamara D, Räikkönen K, Lahti J, Magnus P, Håberg SE, Jugessur A, Bohlin J. An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. Clin Epigenetics 2021; 13:82. [PMID: 33875015 PMCID: PMC8056641 DOI: 10.1186/s13148-021-01055-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/11/2021] [Indexed: 01/11/2023] Open
Abstract
Background Gestational age is a useful proxy for assessing developmental maturity, but correct estimation of gestational age is difficult using clinical measures. DNA methylation at birth has proven to be an accurate predictor of gestational age. Previous predictors of epigenetic gestational age were based on DNA methylation data from the Illumina HumanMethylation 27 K or 450 K array, which have subsequently been replaced by the Illumina MethylationEPIC 850 K array (EPIC). Our aims here were to build an epigenetic gestational age clock specific for the EPIC array and to evaluate its precision and accuracy using the embryo transfer date of newborns from the largest EPIC-derived dataset to date on assisted reproductive technologies (ART). Methods We built an epigenetic gestational age clock using Lasso regression trained on 755 randomly selected non-ART newborns from the Norwegian Study of Assisted Reproductive Technologies (START)—a substudy of the Norwegian Mother, Father, and Child Cohort Study (MoBa). For the ART-conceived newborns, the START dataset had detailed information on the embryo transfer date and the specific ART procedure used for conception. The predicted gestational age was compared to clinically estimated gestational age in 200 non-ART and 838 ART newborns using MM-type robust regression. The performance of the clock was compared to previously published gestational age clocks in an independent replication sample of 148 newborns from the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restrictions (PREDO) study—a prospective pregnancy cohort of Finnish women. Results Our new epigenetic gestational age clock showed higher precision and accuracy in predicting gestational age than previous gestational age clocks (R2 = 0.724, median absolute deviation (MAD) = 3.14 days). Restricting the analysis to CpGs shared between 450 K and EPIC did not reduce the precision of the clock. Furthermore, validating the clock on ART newborns with known embryo transfer date confirmed that DNA methylation is an accurate predictor of gestational age (R2 = 0.767, MAD = 3.7 days). Conclusions We present the first EPIC-based predictor of gestational age and demonstrate its robustness and precision in ART and non-ART newborns. As more datasets are being generated on the EPIC platform, this clock will be valuable in studies using gestational age to assess neonatal development. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01055-z.
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Affiliation(s)
- Kristine L Haftorn
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway. .,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Institute of Health and Society, University of Oslo, Oslo, Norway.
| | - Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Mathematics, University of Oslo, Oslo, Norway
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Deepinsight, Karl Johans Gate 8, Oslo, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Anni Malmberg
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Bristol Medical School, Population Health Sciences, Bristol, UK
| | - Øyvind Næss
- Institute of Health and Society, University of Oslo, Oslo, Norway.,Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Division for Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
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13
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Berentsen GD, Azzolini F, Skaug HJ, Lie RT, Gjessing HK. Heritability curves: A local measure of heritability in family models. Stat Med 2020; 40:1357-1382. [PMID: 33336424 DOI: 10.1002/sim.8845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/14/2020] [Accepted: 11/21/2020] [Indexed: 11/07/2022]
Abstract
Classical heritability models for family data split the phenotype variance into genetic and environmental components. For instance, the ACE model in twin studies assumes the phenotype variance decomposes as a2 + c2 + e2 , representing (additive) genetic effects, common (shared) environment, and residual environment, respectively. However, for some phenotypes it is biologically plausible that the genetic and environmental components may vary over the range of the phenotype. For instance, very large or small values of the phenotype may be caused by "sporadic" environmental factors, whereas the mid-range phenotype variation may be more under the control of common genetic factors. This article introduces a "local" measure of heritability, where the genetic and environmental components are allowed to depend on the value of the phenotype itself. Our starting point is a general formula for local correlation between two random variables. For estimation purposes, we use a multivariate Gaussian mixture, which is able to capture nonlinear dependence and respects certain distributional constraints. We derive an analytical expression for the associated correlation curve, and show how to decompose the correlation curve into genetic and environmental parts, for instance, a2 (y) + c2 (y) + e2 (y) for the ACE model, where we estimate the components as functions of the phenotype y. Furthermore, our model allows switching, for instance, from the ACE model to the ADE model within the range of the same phenotype. When applied to birth weight (BW) data on Norwegian mother-father-child trios, we conclude from the model that low and high BW are less heritable traits than medium BW. We also demonstrate switching between the ACE and ADE model when studying body mass index in adult monozygotic and dizygotic twins.
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Affiliation(s)
- Geir D Berentsen
- Department of Business and Management Science, NHH Norwegian School of Economics, Bergen, Norway
| | | | - Hans J Skaug
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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14
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Lee Y, Haftorn KL, Denault WRP, Nustad HE, Page CM, Lyle R, Lee-Ødegård S, Moen GH, Prasad RB, Groop LC, Sletner L, Sommer C, Magnus MC, Gjessing HK, Harris JR, Magnus P, Håberg SE, Jugessur A, Bohlin J. Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array. BMC Genomics 2020; 21:747. [PMID: 33109080 PMCID: PMC7590728 DOI: 10.1186/s12864-020-07168-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina MethylationEPIC BeadChip (EPIC). Thus, it remains unclear to what extent EPIC contributes to increased precision and accuracy in the prediction of chronological age. RESULTS We developed three blood-based epigenetic clocks for human adults using EPIC-based DNA methylation (DNAm) data from the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Gene Expression Omnibus (GEO) public repository: 1) an Adult Blood-based EPIC Clock (ABEC) trained on DNAm data from MoBa (n = 1592, age-span: 19 to 59 years), 2) an extended ABEC (eABEC) trained on DNAm data from MoBa and GEO (n = 2227, age-span: 18 to 88 years), and 3) a common ABEC (cABEC) trained on the same training set as eABEC but restricted to CpGs common to 450 K and EPIC. Our clocks showed high precision (Pearson correlation between chronological and epigenetic age (r) > 0.94) in independent cohorts, including GSE111165 (n = 15), GSE115278 (n = 108), GSE132203 (n = 795), and the Epigenetics in Pregnancy (EPIPREG) study of the STORK Groruddalen Cohort (n = 470). This high precision is unlikely due to the use of EPIC, but rather due to the large sample size of the training set. CONCLUSIONS Our ABECs predicted adults' chronological age precisely in independent cohorts. As EPIC is now the dominant platform for measuring DNAm, these clocks will be useful in further predictions of chronological age, age-related diseases, and mortality.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway. .,Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Kristine L Haftorn
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, N-5020, Bergen, Norway
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Deepinsight, Karl Johans gate 8, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology, Section for Research Support, Oslo University Hospital, Oslo, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,PharmaTox Strategic Research Initiative, School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Sindre Lee-Ødegård
- Department of Internal Medicine, Akershus University Hospital, Kongsvinger, Norway.,Department of transplantation medicine, Institute of Clinical medicine, University of Oslo, Oslo, Norway
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,The University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, QLD, 4102, Australia.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rashmi B Prasad
- Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Leif C Groop
- Department of Clinical Sciences, Clinical Research Centre, Lund University, Malmö, Sweden.,Finnish Institute of Molecular Medicine, Helsinki University, Helsinki, Finland
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Campus AHUS, Lørenskog, Norway
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, N-5020, Bergen, Norway
| | - Jennifer R Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, N-5020, Bergen, Norway
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Division for Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
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15
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Romanowska J, Haaland ØA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clin Epigenetics 2020; 12:109. [PMID: 32678018 PMCID: PMC7367265 DOI: 10.1186/s13148-020-00881-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Current technology allows rapid assessment of DNA sequences and methylation levels at a single-site resolution for hundreds of thousands of sites in the human genome, in thousands of individuals simultaneously. This has led to an increase in epigenome-wide association studies (EWAS) of complex traits, particularly those that are poorly explained by previous genome-wide association studies (GWAS). However, the genome and epigenome are intertwined, e.g., DNA methylation is known to affect gene expression through, for example, genomic imprinting. There is thus a need to go beyond single-omics data analyses and develop interaction models that allow a meaningful combination of information from EWAS and GWAS. RESULTS We present two new methods for genetic association analyses that treat offspring DNA methylation levels as environmental exposure. Our approach searches for statistical interactions between SNP alleles and DNA methylation (G ×Me) and between parent-of-origin effects and DNA methylation (PoO ×Me), using case-parent triads or dyads. We use summarized methylation levels over nearby genomic region to ease biological interpretation. The methods were tested on a dataset of parent-offspring dyads, with EWAS data on the offspring. Our results showed that methylation levels around a SNP can significantly alter the estimated relative risk. Moreover, we show how a control dataset can identify false positives. CONCLUSIONS The new methods, G ×Me and PoO ×Me, integrate DNA methylation in the assessment of genetic relative risks and thus enable a more comprehensive biological interpretation of genome-wide scans. Moreover, our strategy of condensing DNA methylation levels within regions helps overcome specific disadvantages of using sparse chip-based measurements. The methods are implemented in the freely available R package Haplin ( https://cran.r-project.org/package=Haplin ), enabling fast scans of multi-omics datasets.
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Affiliation(s)
- Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway.
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway.
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway.
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, N-0473, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Jack Taylor
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Allen J Wilcox
- National Institute of Environmental Health Sciences, Research Triangle Park, 27709, NC, USA
| | - Inge Jonassen
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, N-0213, Norway
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16
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Gjerdevik M, Gjessing HK, Romanowska J, Haaland ØA, Jugessur A, Czajkowski NO, Lie RT. Design efficiency in genetic association studies. Stat Med 2020; 39:1292-1310. [PMID: 31943314 DOI: 10.1002/sim.8476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/25/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 11/07/2022]
Abstract
Selecting the best design for genetic association studies requires careful deliberation; different study designs can be used to scan for different genetic effects, and each design has its own set of strengths and limitations. A variety of family and unrelated control configurations are amenable to genetic association analyses, including the case-control design, case-parent triads, and case-parent triads in combination with unrelated controls or control-parent triads. Ultimately, the goal is to choose the design that achieves the highest statistical power using the lowest cost. For given parameter values and genotyped individuals, designs can be compared directly by computing the power. However, a more informative and general design comparison can be achieved by studying the relative efficiency, defined as the ratio of variances of two different parameter estimators, corresponding to two separate designs. Using log-linear modeling, we derive the relative efficiency from the asymptotic variance of the parameter estimators and relate it to the concept of Pitman efficiency. The relative efficiency takes into account the fact that different designs impose different costs relative to the number of genotyped individuals. We show that while optimal efficiency for analyses of regular autosomal effects is achieved using the standard case-control design, the case-parent triad design without unrelated controls is efficient when searching for parent-of-origin effects. Due to the potential loss of efficiency, maternal genes should generally not be adjusted for in an initial genome-wide association study scan of offspring genes but instead checked post hoc. The relative efficiency calculations are implemented in our R package Haplin.
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Affiliation(s)
- Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nikolai O Czajkowski
- Department of Psychology, University of Oslo, Oslo, Norway.,Division of Mental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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17
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Ding L, Blitz MJ, Wing DA, Epstein AJ, Gjessing HK, Wilson ML. PHLDA2 gene polymorphisms and risk of HELLP syndrome and severe preeclampsia. Pregnancy Hypertens 2020; 19:190-194. [PMID: 32062476 DOI: 10.1016/j.preghy.2020.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 01/21/2020] [Accepted: 01/26/2020] [Indexed: 10/25/2022]
Abstract
OBJECTIVE Pleckstrin homology-like domain, family A, member 2 (PHLDA2) is a maternally expressed imprinted gene. Loss of imprinting in PHLDA2 is associated with abnormal placental development and fetal growth restriction. Our objective was to determine whether genetic variation in PHLDA2 is also associated with risk of HELLP syndrome and preeclampsia (PE) with severe features. STUDY DESIGN Case (n = 162) and control (n = 33) mother-father-child triads were recruited using an internet-based method. Medical records were reviewed to verify clinical diagnosis of self-reported cases. DNA was genotyped for three polymorphisms in the PHLDA2 gene using TaqMan assays: rs13390, rs1056819, rs2583435. MAIN OUTCOME MEASURES To examine the association between minor alleles and haplotypes with HELLP syndrome and PE with severe features, relative risks and 95% confidence intervals were estimated using log-linear models, adjusting for the correlation between familial genotypes, using HAPLIN. RESULTS There was no association identified between PHLDA2 gene polymorphisms or haplotypes and HELLP syndrome and PE with severe features. No parent-of-origin effects were observed. CONCLUSION Genetic variation in the PHLDA2 gene is not associated with HELLP syndrome or PE with severe features.
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Affiliation(s)
- Li Ding
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Matthew J Blitz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, North Shore University Hospital, Manhasset, NY, USA
| | - Deborah A Wing
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of California, Irvine, Orange, CA, USA
| | - Aaron J Epstein
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Melissa L Wilson
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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Borgan Ø, Gjessing HK. Special issue dedicated to Odd O. Aalen. Lifetime Data Anal 2019; 25:587-592. [PMID: 31463654 DOI: 10.1007/s10985-019-09483-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Ørnulf Borgan
- Department of Mathematics, University of Oslo, Oslo, Norway.
| | - Håkon K Gjessing
- Norwegian Institute of Public Health, Oslo, Norway
- Department for Global Health and Primary Care, University of Bergen, Bergen, Norway
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19
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Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, Marsit C, Lu AT, Ritz B, Bohlin J, Gjessing HK, Harris JR, Magnus P, Binder AM, Robinson WP, Jugessur A, Horvath S. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY) 2019; 11:4238-4253. [PMID: 31235674 PMCID: PMC6628997 DOI: 10.18632/aging.102049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
The human pan-tissue epigenetic clock is widely used for estimating age across the entire lifespan, but it does not lend itself well to estimating gestational age (GA) based on placental DNAm methylation (DNAm) data. We replicate previous findings demonstrating a strong correlation between GA and genome-wide DNAm changes. Using substantially more DNAm arrays (n=1,102 in the training set) than a previous study, we present three new placental epigenetic clocks: 1) a robust placental clock (RPC) which is unaffected by common pregnancy complications (e.g., gestational diabetes, preeclampsia), and 2) a control placental clock (CPC) constructed using placental samples from pregnancies without known placental pathology, and 3) a refined RPC for uncomplicated term pregnancies. These placental clocks are highly accurate estimators of GA based on placental tissue; e.g., predicted GA based on RPC is highly correlated with actual GA (r>0.95 in test data, median error less than one week). We show that epigenetic clocks derived from cord blood or other tissues do not accurately estimate GA in placental samples. While fundamentally different from Horvath's pan-tissue epigenetic clock, placental clocks closely track fetal age during development and may have interesting applications.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samantha L. Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Victor Yuan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amber Burt
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Carmen Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra M. Binder
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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Gjerdevik M, Jugessur A, Haaland ØA, Romanowska J, Lie RT, Cordell HJ, Gjessing HK. Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls. BMC Bioinformatics 2019; 20:165. [PMID: 30940094 PMCID: PMC6444579 DOI: 10.1186/s12859-019-2727-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 01/22/2023] Open
Abstract
Background Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-parent configurations. Although the calculation of statistical power or sample size is an important first step in the planning of any scientific study, there is currently a lack of software for genetic power calculations in family-based study designs. Here, we address this shortcoming through new implementations of power calculations in the R package Haplin, which is a flexible and robust software for genetic epidemiological analyses. Power calculations in Haplin can be performed analytically using the asymptotic variance-covariance structure of the parameter estimator, or else by a straightforward simulation approach. Haplin performs power calculations for child, parent-of-origin and maternal effects, as well as for gene-environment interactions. The power can be calculated for both single SNPs and haplotypes, either autosomal or X-linked. Moreover, Haplin enables power calculations for different child-parent configurations, including (but not limited to) case-parent triads, case-mother dyads, and case-parent triads in combination with unrelated control-parent triads. Results We compared the asymptotic power approximations to the power of analysis attained with Haplin. For external validation, the results were further compared to the power of analysis attained by the EMIM software using data simulations from Haplin. Consistency observed between Haplin and EMIM across various genetic scenarios confirms the computational accuracy of the inference methods used in both programs. The results also demonstrate that power calculations in Haplin are applicable to genetic association studies using either log-linear or multinomial modeling approaches. Conclusions Haplin provides a robust and reliable framework for power calculations in genetic association analyses for a wide range of genetic effects and etiologic scenarios, based on genotype data from a variety of child-parent configurations. Electronic supplementary material The online version of this article (10.1186/s12859-019-2727-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway. .,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, UK
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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Gjessing HK, Skaug HJ. Editorial. Scand Stat Theory Appl 2019. [DOI: 10.1111/sjos.12386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Hans J. Skaug
- Department of MathematicsUniversity of Bergen Bergen Norway
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22
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Dale MTG, Magnus P, Leirgul E, Holmstrøm H, Gjessing HK, Brodwall K, Haugen M, Stoltenberg C, Øyen N. Intake of sucrose-sweetened soft beverages during pregnancy and risk of congenital heart defects (CHD) in offspring: a Norwegian pregnancy cohort study. Eur J Epidemiol 2019; 34:383-396. [DOI: 10.1007/s10654-019-00480-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/05/2019] [Indexed: 01/13/2023]
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23
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Haaland ØA, Lie RT, Romanowska J, Gjerdevik M, Gjessing HK, Jugessur A. A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG. Front Genet 2018. [PMID: 29535761 PMCID: PMC5834486 DOI: 10.3389/fgene.2018.00060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry. A GxE effect is present if the relative risk estimates for gene-effects in the offspring are different across exposure strata. We tested this using the relative risk ratio (RRR). Besides analyzing all ethnicities combined ("pooled analysis"), separate analyses were conducted on Europeans and Asians to investigate ethnicity-specific effects. To control for multiple testing, q-values were calculated from the p-values. Results: We identified significant GxVitamin interactions with three SNPs in "Estrogen-related receptor gamma" (ESRRG) in the pooled analysis. The RRRs (95% confidence intervals) were 0.56 (0.45-0.69) with rs1339221 (q = 0.011), 0.57 (0.46-0.70) with rs11117745 (q = 0.011), and 0.62 (0.50-0.76) with rs2099557 (q = 0.037). The associations were stronger when these SNPs were analyzed as haplotypes composed of two-SNP and three-SNP combinations. The strongest effect was with the "t-t-t" haplotype of the rs1339221-rs11117745-rs2099557 combination [RRR = 0.50 (0.40-0.64)], suggesting that the effects observed with the other SNP combinations, including those in the single-SNP analyses, were mainly driven by this haplotype. Although there were potential GxVitamin effects with rs17734557 and rs1316471 and GxAlcohol effects with rs9653456 and rs921876 in the European sample, respectively, none of the SNPs was located in or near genes with strong links to orofacial clefts. GxAlcohol and GxSmoke effects were not assessed in the Asian sample because of a lack of observations for these exposures. Discussion/Conclusion: We identified significant interactions between vitamin use and variants in ESRRG in the pooled analysis. These GxE effects are novel and warrant further investigations to elucidate their roles in orofacial clefting. If validated, they could provide prospects for exploring the impact of estrogens and vitamins on clefting, with potential translational applications.
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Affiliation(s)
- Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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24
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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Gjerdevik M, Haaland ØA, Romanowska J, Lie RT, Jugessur A, Gjessing HK. Parent-of-origin-environment interactions in case-parent triads with or without independent controls. Ann Hum Genet 2017; 82:60-73. [PMID: 29094765 PMCID: PMC5813215 DOI: 10.1111/ahg.12224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/05/2017] [Indexed: 01/31/2023]
Abstract
With case–parent triad data, one can frequently deduce parent of origin of the child's alleles. This allows a parent‐of‐origin (PoO) effect to be estimated as the ratio of relative risks associated with the alleles inherited from the mother and the father, respectively. A possible cause of PoO effects is DNA methylation, leading to genomic imprinting. Because environmental exposures may influence methylation patterns, gene–environment interaction studies should be extended to allow for interactions between PoO effects and environmental exposures (i.e., PoOxE). One should thus search for loci where the environmental exposure modifies the PoO effect. We have developed an extensive framework to analyze PoOxE effects in genome‐wide association studies (GWAS), based on complete or incomplete case–parent triads with or without independent control triads. The interaction approach is based on analyzing triads in each exposure stratum using maximum likelihood estimation in a log‐linear model. Interactions are then tested applying a Wald‐based posttest of parameters across strata. Our framework includes a complete setup for power calculations. We have implemented the models in the R software package Haplin. To illustrate our PoOxE test, we applied the new methodology to top hits from our previous GWAS, assessing whether smoking during the periconceptional period modifies PoO effects on cleft palate only.
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Affiliation(s)
- Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetic Research and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computional Biology Unit, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Health Registries, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetic Research and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
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Gjessing HK. Svangerskapsdatering. Nor J Epidemiol 2017. [DOI: 10.5324/nje.v27i1-2.2397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
SAMMENDRAGSvangerskapsdatering er et komplekst felt med mange aspekter. Minst tre svært forskjellige metoder fordatering er i bruk: siste menstruasjon, ultralyd samt tidspunkt for fertilisering eller overføring av embryoved in vitro-fertilisering. Bare innenfor ultralyddatering finnes en stor mengde forskjellige “formler” fordatering. Jeg gir her en kort oversikt over de forskjellige tilnærmingene til svangerskapsdatering og visernoen av prinsippene bak populasjonsbasert ultralyddatering.ENGLISH ABSTRACTPregnancy dating is a complex and multifaceted field. At least three very different methods for dating arecommonly used: last menstrual period, ultrasound, and date of fertilization or embryo transfer during invitro fertilization. Within ultrasound dating alone there is a wide range of different “formulas” for dating. Ipresent a short overview over the different approaches to pregnancy dating and show some of the principlesbehind population-based ultrasound dating.
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Moreno Uribe LM, Fomina T, Munger RG, Romitti PA, Jenkins MM, Gjessing HK, Gjerdevik M, Christensen K, Wilcox AJ, Murray JC, Lie RT, Wehby GL. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts. J Dent Res 2017; 96:1322-1329. [PMID: 28662356 DOI: 10.1177/0022034517716914] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. Prior samples were also small for investigating effects by cleft type and exclusively studied isolated clefts (those occurring without other birth defects). We estimated the effects of 17 top loci on cleft types in both isolated and nonisolated cases in the largest consortium to date of European-descent population-based studies. Our analytic approach focused on a mother-child dyad case-control design, but it also allowed analyzing mother-only or child-only genotypes to maximize power. Our total sample included 1,875 cases with isolated clefts, 459 cases with nonisolated clefts, and 3,749 controls. After correcting for multiple testing, we observed significant associations between fetal single-nucleotide polymorphisms (SNPs) at IRF6, PAX7, 8q21.3, 8q24, KIAA1598-VAX1, and MAFB and isolated cleft lip only (CLO) and cleft lip and palate (CLP). Significant associations were observed between isolated CLO and fetal SNPs near TPM1 and NOG1 and between CLP and fetal SNPs at ABCA4-ARHGAP29, THADA, FOXE1, and SPRY2. Overall, effects were similar for isolated CLO and CLP, except for ABCA4-ARHGAP29. A protective effect was observed for the fetal NOG1 SNP on cleft palate only, opposite in direction to the effect on CLO. For most fetal SNPs, a dose-response allelic effect was observed. No evidence of parent-of-origin or maternal genome effects was observed. Overall, effect direction and magnitude were similar between isolated and nonisolated clefts, suggesting that several loci are modifiers of cleft risk in both isolated and nonisolated forms. Our results provide reliable estimates of the effects of top loci on risks of oral clefts in a population of European descent.
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Affiliation(s)
- L M Moreno Uribe
- 1 Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Fomina
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - R G Munger
- 3 Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA
| | - P A Romitti
- 4 Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - M M Jenkins
- 5 National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - H K Gjessing
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - M Gjerdevik
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - K Christensen
- 7 Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - A J Wilcox
- 8 Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - J C Murray
- 9 Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - R T Lie
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - G L Wehby
- 10 Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA
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McGinnis R, Steinthorsdottir V, Williams NO, Thorleifsson G, Shooter S, Hjartardottir S, Bumpstead S, Stefansdottir L, Hildyard L, Sigurdsson JK, Kemp JP, Silva GB, Thomsen LCV, Jääskeläinen T, Kajantie E, Chappell S, Kalsheker N, Moffett A, Hiby S, Lee WK, Padmanabhan S, Simpson NAB, Dolby VA, Staines-Urias E, Engel SM, Haugan A, Trogstad L, Svyatova G, Zakhidova N, Najmutdinova D, Dominiczak AF, Gjessing HK, Casas JP, Dudbridge F, Walker JJ, Pipkin FB, Thorsteinsdottir U, Geirsson RT, Lawlor DA, Iversen AC, Magnus P, Laivuori H, Stefansson K, Morgan L. Variants in the fetal genome near FLT1 are associated with risk of preeclampsia. Nat Genet 2017. [PMID: 28628106 DOI: 10.1038/ng.3895] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Preeclampsia, which affects approximately 5% of pregnancies, is a leading cause of maternal and perinatal death. The causes of preeclampsia remain unclear, but there is evidence for inherited susceptibility. Genome-wide association studies (GWAS) have not identified maternal sequence variants of genome-wide significance that replicate in independent data sets. We report the first GWAS of offspring from preeclamptic pregnancies and discovery of the first genome-wide significant susceptibility locus (rs4769613; P = 5.4 × 10-11) in 4,380 cases and 310,238 controls. This locus is near the FLT1 gene encoding Fms-like tyrosine kinase 1, providing biological support, as a placental isoform of this protein (sFlt-1) is implicated in the pathology of preeclampsia. The association was strongest in offspring from pregnancies in which preeclampsia developed during late gestation and offspring birth weights exceeded the tenth centile. An additional nearby variant, rs12050029, associated with preeclampsia independently of rs4769613. The newly discovered locus may enhance understanding of the pathophysiology of preeclampsia and its subtypes.
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Affiliation(s)
| | | | | | | | | | - Sigrun Hjartardottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | | | | | - John P Kemp
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Gabriela B Silva
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Liv Cecilie V Thomsen
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Tiina Jääskeläinen
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki, Finland.,Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Susan Hiby
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wai Kwong Lee
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Nigel A B Simpson
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Vivien A Dolby
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Eleonora Staines-Urias
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Nuffield Department of Obstetrics &Gynaecology, University of Oxford, Oxford, UK
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anita Haugan
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Gulnara Svyatova
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan
| | - Nodira Zakhidova
- Institute of Immunology, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | - Dilbar Najmutdinova
- Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology, Tashkent, Uzbekistan
| | | | | | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Håkon K Gjessing
- Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Juan P Casas
- Farr Institute of Health Informatics, University College London, London, UK
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - James J Walker
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ann-Charlotte Iversen
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Linda Morgan
- School of Life Sciences, University of Nottingham, Nottingham, UK
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Gjessing HK, Grøttum P, Økland I, Eik-Nes SH. Fetal size monitoring and birth-weight prediction: a new population-based approach. Ultrasound Obstet Gynecol 2017; 49:500-507. [PMID: 27130245 DOI: 10.1002/uog.15954] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 04/04/2016] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To develop a complete, population-based system for ultrasound-based fetal size monitoring and birth-weight prediction for use in the second and third trimesters of pregnancy. METHODS Using 31 516 ultrasound examinations from a population-based Norwegian clinical database, we constructed fetal size charts for biparietal diameter, femur length and abdominal circumference from 24 to 42 weeks' gestation. A reference curve of median birth weight for gestational age was estimated using 45 037 birth weights. We determined how individual deviations from the expected ultrasound measures predicted individual percentage deviations from expected birth weight. The predictive quality was assessed by explained variance of birth weight and receiver-operating characteristics curves for prediction of small-for-gestational age. A curve for intrauterine estimated fetal weight was constructed. Charts were smoothed using the gamlss non-linear regression method. RESULTS The population-based approach, using bias-free ultrasound gestational age, produces stable estimates of size-for-age and weight-for-age curves in the range 24-42 weeks' gestation. There is a close correspondence between percentage deviations and percentiles of birth weight by gestational age, making it easy to convert between the two. The variance of birth weight that can be 'explained' by ultrasound increases from 8% at 20 weeks up to 67% around term. Intrauterine estimated fetal weight is 0-106 g higher than median birth weight in the preterm period. CONCLUSIONS The new population-based birth-weight prediction model provides a simple summary measure, the 'percentage birth-weight deviation', to be used for fetal size monitoring throughout the third trimester. Predictive quality of the model can be measured directly from the population data. The model computes both median observed birth weight and intrauterine estimated fetal weight. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- H K Gjessing
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - P Grøttum
- Section of Medical Informatics, University of Oslo, Oslo, Norway
| | - I Økland
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - S H Eik-Nes
- National Center for Fetal Medicine, Department of Obstetrics and Gynecology, St Olav's University Hospital, Trondheim, Norway
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
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30
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Clark MM, Chazara O, Sobel EM, Gjessing HK, Magnus P, Moffett A, Sinsheimer JS. Human Birth Weight and Reproductive Immunology: Testing for Interactions between Maternal and Offspring KIR and HLA-C Genes. Hum Hered 2017; 81:181-193. [PMID: 28214848 DOI: 10.1159/000456033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 06/24/2016] [Accepted: 01/11/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND/AIMS Maternal and offspring cell contact at the site of placentation presents a plausible setting for maternal-fetal genotype (MFG) interactions affecting fetal growth. We test hypotheses regarding killer cell immunoglobulin-like receptor (KIR) and HLA-C MFG effects on human birth weight by extending the quantitative MFG (QMFG) test. METHODS Until recently, association testing for MFG interactions had limited applications. To improve the ability to test for these interactions, we developed the extended QMFG test, a linear mixed-effect model that can use multi-locus genotype data from families. RESULTS We demonstrate the extended QMFG test's statistical properties. We also show that if an offspring-only model is fit when MFG effects exist, associations can be missed or misattributed. Furthermore, imprecisely modeling the effects of both KIR and HLA-C could result in a failure to replicate if these loci's allele frequencies differ among populations. To further illustrate the extended QMFG test's advantages, we apply the extended QMFG test to a UK cohort study and the Norwegian Mother and Child Cohort (MoBa) study. CONCLUSION We find a significant KIR-HLA-C interaction effect on birth weight. More generally, the QMFG test can detect genetic associations that may be missed by standard genome-wide association studies for quantitative traits.
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Affiliation(s)
- Michelle M Clark
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
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31
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Pay ASD, Frøen JF, Staff AC, Jacobsson B, Gjessing HK. Symfyse-fundus-mål – prediktiv verdi av ny referansekurve. Tidsskriftet 2017; 137:717-720. [DOI: 10.4045/tidsskr.16.1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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32
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Abstract
The field of traditional biometrical genetics uses mixed-effects models to quantify the influence of genetic and environmental factors on a biological trait, based essentially on estimating within-family trait correlations. Such analyses provide a useful preview of what may be discovered with the emerging full-scale genotyping strategies. However, biometrical analyses require unrealistically large sample sizes to obtain a reasonable precision, particularly for dichotomous traits. In addition, it may be very difficult to separate genetic and environmental effects because environmental correlations are poorly understood. We illustrate these and other difficulties using population-based cousins and nuclear family data for birth weight, collected from the Medical Birth Registry of Norway.
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Affiliation(s)
- Håkon K Gjessing
- Divison of Epidemiology, Norwegian Institute of Public Health, Norway.
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33
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Eggebø TM, Klefstad OA, Økland I, Lindtjørn E, Eik-Nes SH, Gjessing HK. Estimation of fetal weight in pregnancies past term. Acta Obstet Gynecol Scand 2016; 96:183-189. [PMID: 27743479 DOI: 10.1111/aogs.13044] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/10/2016] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The aim of the study was to investigate the accuracy of estimating fetal weight with ultrasound in pregnancies past term, using the eSnurra algorithm. MATERIAL AND METHODS In all, 419 women with pregnancy length of 290 days, attending a specialist consultation at Stavanger University Hospital, Norway, were included in a prospective observational study. Fetal weight was estimated using biparietal diameter (BPD) and abdominal circumference (AC). The algorithm implemented in an electronic calculation (eSnurra) was used to compute estimated fetal weight (EFW). Results were compared with birthweight (BW). RESULTS The mean interval between the ultrasound examination and birth was 2 days (SD 1.4). The median difference between BW and EFW was -6 g (CI -40 to +25 g) and the median percentage error was -0.1% (95% CI -1.0 to 0.6%). The median absolute difference was 190 g (95% CI 170-207 g). The BW was within 10% of EFW in 83% (95% CI 79-87%) of cases and within 15% of EFW in 94% (95% CI 92-96%) of cases. Limits of agreement (95%) were from -553 g to +556 g. Using 5% false-positive rates, the sensitivity in detecting macrosomic and small for gestational age fetuses was 54% (95% CI 35-72%) and 49% (95% CI 35-63%), respectively. CONCLUSION The accuracy of fetal weight estimation was good. Clinicians should be aware of limitations related to prediction at the upper and lower end, and the importance of choosing appropriate cut-off levels.
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Affiliation(s)
- Torbjørn M Eggebø
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway.,National Center for Fetal Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olav A Klefstad
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - Inger Økland
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - Elsa Lindtjørn
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - Sturla H Eik-Nes
- National Center for Fetal Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Håkon K Gjessing
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway.,Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway
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Bohlin J, Håberg SE, Magnus P, Reese SE, Gjessing HK, Magnus MC, Parr CL, Page CM, London SJ, Nystad W. Prediction of gestational age based on genome-wide differentially methylated regions. Genome Biol 2016; 17:207. [PMID: 27717397 PMCID: PMC5054559 DOI: 10.1186/s13059-016-1063-4] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/14/2016] [Indexed: 01/09/2023] Open
Abstract
Background We explored the association between gestational age and cord blood DNA methylation at birth and whether DNA methylation could be effective in predicting gestational age due to limitations with the presently used methods. We used data from the Norwegian Mother and Child Birth Cohort study (MoBa) with Illumina HumanMethylation450 data measured for 1753 newborns in two batches: MoBa 1, n = 1068; and MoBa 2, n = 685. Gestational age was computed using both ultrasound and the last menstrual period. We evaluated associations between DNA methylation and gestational age and developed a statistical model for predicting gestational age using MoBa 1 for training and MoBa 2 for predictions. The prediction model was additionally used to compare ultrasound and last menstrual period-based gestational age predictions. Furthermore, both CpGs and associated genes detected in the training models were compared to those detected in a published prediction model for chronological age. Results There were 5474 CpGs associated with ultrasound gestational age after adjustment for a set of covariates, including estimated cell type proportions, and Bonferroni-correction for multiple testing. Our model predicted ultrasound gestational age more accurately than it predicted last menstrual period gestational age. Conclusions DNA methylation at birth appears to be a good predictor of gestational age. Ultrasound gestational age is more strongly associated with methylation than last menstrual period gestational age. The CpGs linked with our gestational age prediction model, and their associated genes, differed substantially from the corresponding CpGs and genes associated with a chronological age prediction model. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1063-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Bohlin
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway.
| | - S E Håberg
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - P Magnus
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - S E Reese
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, PO Box 12233, MD A3-05, Research Triangle Park, Durham, NC, 27709, USA
| | - H K Gjessing
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - M C Magnus
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - C L Parr
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - C M Page
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
| | - S J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, PO Box 12233, MD A3-05, Research Triangle Park, Durham, NC, 27709, USA
| | - W Nystad
- Norwegian Institute of Public Health, P.O. Box 4404, 0456, Oslo, Norway
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Abstract
We consider a risk process with stochastic interest rate, and show that the probability of eventual ruin and the Laplace transform of the time of ruin can be found by solving certain boundary value problems involving integro-differential equations. These equations are then solved for a number of special cases. We also show that a sequence of such processes converges weakly towards a diffusion process, and analyze the above-mentioned ruin quantities for the limit process in some detail.
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Abstract
Generalizing the standard frailty models of survival analysis, we propose to model frailty as a weighted Lévy process. Hence, the frailty of an individual is not a fixed quantity, but develops over time. Formulae for the population hazard and survival functions are derived. The power variance function Lévy process is a prominent example. In many cases, notably for compound Poisson processes, quasi-stationary distributions of survivors may arise. Quasi-stationarity implies limiting population hazard rates that are constant, in spite of the continual increase of the individual hazards. A brief discussion is given of the biological relevance of this finding.
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Andersen GL, Krzywinski K, Gjessing HK, Pierce RH. Seed viability and germination success of Acacia tortilis along land-use and aridity gradients in the Eastern Sahara. Ecol Evol 2015; 6:256-66. [PMID: 26811790 PMCID: PMC4716523 DOI: 10.1002/ece3.1851] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/24/2015] [Accepted: 10/03/2015] [Indexed: 11/05/2022] Open
Abstract
Our study focuses on the keystone species Acacia tortilis and is the first to investigate the effect of domestic ungulates and aridity on seed viability and germination over an extensive part of the Eastern Sahara. Bruchids infest its seeds and reduce their viability and germination, but ingestion by ruminant herbivores diminishes infestation levels and enhances/promotes seed viability and germination. The degree of these effects seems to be correlated with animal body mass. Significantly reduced numbers of wild ruminant ungulates have increased the potential importance of domestic animals and pastoral nomadism for the functionality of arid North African and Middle Eastern ecosystems. We sampled seeds (16,543) from A. tortilis in eight areas in three regions with different aridity and land use. We tested the effect of geography and sampling context on seed infestation using random effects logistic regressions. We did a randomized and balanced germination experiment including 1193 seeds, treated with different manure. Germination time and rates across geography, sampling context, and infestation status were analyzed using time-to-event analyses, Kaplan-Meier curves and proportional hazards Cox regressions. Bruchid infestation is very high (80%), and the effects of context are significant. Neither partial infestation nor adding manure had a positive effect on germination. There is a strong indication that intact, uningested seeds from acacia populations in the extremely arid Western Desert germinate more slowly and have a higher fraction of hard seeds than in the Eastern Desert and the Red Sea Hills. For ingested seeds in the pastoralist areas we find that intact seeds from goat dung germinate significantly better than those from camel dung. This is contrary to the expected body-mass effect. There is no effect of site or variation in tribal management.
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Affiliation(s)
- Gidske Leknæs Andersen
- UNI Research Environment P O Box 7810 5020 Bergen Norway; Department of Geography University of Bergen P O Box 7802 5020 Bergen Norway
| | - Knut Krzywinski
- UNI Research Environment P O Box 7810 5020 Bergen Norway; Department of Biology University of Bergen P O Box 7800 5020 Bergen Norway
| | - Håkon K Gjessing
- Norwegian Institute of Public Health P O Box 4404 Nydalen 0403 Oslo Norway; Department of Global Public Health and Primary Care University of Bergen Bergen Norway
| | - Richard Holton Pierce
- Department of Linguistic, Literary and Aesthetic Studies University of Bergen Sydnesplassen 7 5007 Bergen Norway
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38
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Pay A, Frøen JF, Staff AC, Jacobsson B, Gjessing HK. Prediction of small-for-gestational-age status by symphysis-fundus height: a registry-based population cohort study. BJOG 2015; 123:1167-73. [PMID: 26644370 DOI: 10.1111/1471-0528.13727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 09/07/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To develop a chart for risk of small-for-gestational-age (SGA) at birth depending on deviations in symphysis-fundus (SF) height values for gestational age during pregnancy weeks 24-42. DESIGN Registry-based population cohort study. SETTING Antenatal clinics, Västra Götaland County, Sweden, 2005-2010. POPULATION The study included 42 018 women with ultrasound-dated singleton pregnancies who delivered at Sahlgrenska University Hospital. Data (including 282 713 SF height measurements) were extracted from the hospital's computerised obstetric database. METHODS Linear and binary regression analyses were used to derive prediction models with deviations in birthweight (BW) and SF height by gestational age as dependent and independent variables, respectively. Receiver operating characteristic curves were generated to evaluate the predictive value of the model in detecting SGA. MAIN OUTCOME MEASURES Birthweight and small-for-gestational-age. RESULTS Symphysis-fundus height accounted for 3% of individual BW variance at 24 weeks, increasing gradually to 20% at 40 weeks. Maternal factors explained an additional 10 percentage points of BW variance. Receiver operating characteristic curves confirmed that SF height was a stronger SGA predictor in late than in early pregnancy. Using an SGA relative risk cut-off limit of ≥2-fold, the overall sensitivity was 50% and the overall specificity 80%. Only the most recent SF measurement was useful in predicting BW deviation; previous measurements added nothing to the predictive value. CONCLUSIONS The ability of SF measurements to detect SGA status at birth increases with gestational age. Only the most recent SF measurement has predictive value; a static or falling pattern of SF values did not increase SGA likelihood. TWEETABLE ABSTRACT New SF curves predict SGA best in late pregnancy; only the most recent SF measurement has predictive value.
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Affiliation(s)
- Asd Pay
- Departments of Obstetrics and Gynaecology, Women's and Children's Division, Oslo University Hospital, Oslo, Norway.,Department of International Public Health, Norwegian Institute of Public Health, Oslo, Norway
| | - J F Frøen
- Department of International Public Health, Norwegian Institute of Public Health, Oslo, Norway
| | - A C Staff
- Departments of Obstetrics and Gynaecology, Women's and Children's Division, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - B Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg, Sweden.,Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway
| | - H K Gjessing
- Department of Genes and Environment, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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Witsø E, Cinek O, Tapia G, Brorsson CA, Stene LC, Gjessing HK, Rasmussen T, Bergholdt R, Pociot FM, Rønningen KS. Genetic Determinants of Enterovirus Infections: Polymorphisms in Type 1 Diabetes and Innate Immune Genes in the MIDIA Study. Viral Immunol 2015; 28:556-63. [DOI: 10.1089/vim.2015.0067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
| | - Ondrej Cinek
- Department of Pediatrics, University Hospital Motol, and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - German Tapia
- Norwegian Institute of Public Health, Oslo, Norway
| | - Caroline A. Brorsson
- Department of Pediatrics E, Copenhagen Diabetes Research Centre (CPH-DIRECT), Herlev University Hospital, Herlev, Denmark
| | | | - Håkon K. Gjessing
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | | | | | - Flemming M. Pociot
- Department of Pediatrics E, Copenhagen Diabetes Research Centre (CPH-DIRECT), Herlev University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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40
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Farrell LE, Hiby SE, Apps R, Chazara O, Trogstad L, Gjessing HK, Magnus P, Carrington M, Moffett A. KIR and HLA-C: Immunogenetic regulation of human birth weight. Nor J Epidemiol 2014. [DOI: 10.5324/nje.v24i1-2.1810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Pregnancies resulting in very small or very large babies are at higher risk of obstetric complications with increased morbidity for both mother and baby. Using data from the Medical Birth Registry of Norway we have shown how human birth weight is still subject to stabilizing selection. Particular combinations of maternal/fetal immune genes have been implicated in pregnancies resulting in a low birth weight baby (<5th birth weight centile). More specifically, an inhibitory maternal KIRAA genotype with a paternally derived fetal HLA-C2 ligand. At the other end of the birth weight spectrum the presence of an activating maternal KIR2DS1 gene is associated with increased birth weight in linear or logistic regression analyses of all pregnancies >5th centile (p=0.005, OR=2.65). Thus, inhibitory maternal KIR combined with fetal HLA-C2 is more frequently associated with low birth weight, whereas activating maternal KIR with fetal HLA-C2 ligand is associated with increasing birth weight. Our findings using the MoBa cohort have replicated the association of KIR and HLA-C seen in poor placentation, and confirm the importance of maternal/fetal immune gene interactions in determining the outcome of pregnancy.
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Hiby SE, Apps R, Chazara O, Farrell LE, Magnus P, Trogstad L, Gjessing HK, Carrington M, Moffett A. Maternal KIR in combination with paternal HLA-C2 regulate human birth weight. J Immunol 2014; 192:5069-73. [PMID: 24778445 DOI: 10.4049/jimmunol.1400577] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Human birth weight is subject to stabilizing selection; babies born too small or too large are less likely to survive. Particular combinations of maternal/fetal immune system genes are associated with pregnancies where the babies are ≤ 5th birth weight centile, specifically an inhibitory maternal KIR AA genotype with a paternally derived fetal HLA-C2 ligand. We have now analyzed maternal KIR and fetal HLA-C combinations at the opposite end of the birth weight spectrum. Mother/baby pairs (n = 1316) were genotyped for maternal KIR as well as fetal and maternal HLA-C. Presence of a maternal-activating KIR2DS1 gene was associated with increased birth weight in linear or logistic regression analyses of all pregnancies >5th centile (p = 0.005, n = 1316). Effect of KIR2DS1 was most significant in pregnancies where its ligand, HLA-C2, was paternally but not maternally inherited by a fetus (p = 0.005, odds ratio = 2.65). Thus, maternal KIR are more frequently inhibitory with small babies but activating with big babies. At both extremes of birth weight, the KIR associations occur when their HLA-C2 ligand is paternally inherited by a fetus. We conclude that the two polymorphic immune gene systems, KIR and HLA-C, contribute to successful reproduction by maintaining birth weight between two extremes with a clear role for paternal HLA.
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Affiliation(s)
- Susan E Hiby
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Olympe Chazara
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Lydia E Farrell
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Per Magnus
- Division of Epidemiology, Norwegian Institute of Public Health, 0403 Oslo, Norway; and
| | - Lill Trogstad
- Division of Infectious Disease Control, Norwegian Institute of Public Health, 0403 Oslo, Norway
| | - Håkon K Gjessing
- Division of Epidemiology, Norwegian Institute of Public Health, 0403 Oslo, Norway; and
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
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42
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Sommerfelt H, Steinsland H, van der Merwe L, Blackwelder WC, Nasrin D, Farag TH, Kotloff KL, Levine MM, Gjessing HK. Case/control studies with follow-up: Constructing the source population to estimate effects of risk factors on development, disease, and survival. Clin Infect Dis 2013; 55 Suppl 4:S262-70. [PMID: 23169939 PMCID: PMC3502318 DOI: 10.1093/cid/cis802] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
If individuals in a case/control study are subsequently observed as a cohort of cases and a cohort of controls, weighted regression analyses can be used to estimate the association between the exposures initially recorded and events occurring during the follow-up of the 2 cohorts. Such analyses can be conceptualized as being undertaken on a reconstructed source population from which cases and controls stem. To simulate this population, the cohort of cases is added to the cohort of controls expanded with the reciprocal of the case disease incidence odds (the sampling weight) to include all individuals in the source population who did not develop the case disease. We use a simulated dataset to illustrate how weighted generalized linear model regression can be used to estimate the association between an exposure captured during the case/control study component and an outcome that occurs during follow-up.
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Affiliation(s)
- Halvor Sommerfelt
- Centre for International Health, University of Bergen, Bergen, Norway.
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43
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Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, Martin NW, Westra HJ, Shakhbazov K, Abdellaoui A, Agrawal A, Albrecht E, Alizadeh BZ, Amin N, Barnard J, Baumeister SE, Benke KS, Bielak LF, Boatman JA, Boyle PA, Davies G, de Leeuw C, Eklund N, Evans DS, Ferhmann R, Fischer K, Gieger C, Gjessing HK, Hägg S, Harris JR, Hayward C, Holzapfel C, Ibrahim-Verbaas CA, Ingelsson E, Jacobsson B, Joshi PK, Jugessur A, Kaakinen M, Kanoni S, Karjalainen J, Kolcic I, Kristiansson K, Kutalik Z, Lahti J, Lee SH, Lin P, Lind PA, Liu Y, Lohman K, Loitfelder M, McMahon G, Vidal PM, Meirelles O, Milani L, Myhre R, Nuotio ML, Oldmeadow CJ, Petrovic KE, Peyrot WJ, Polašek O, Quaye L, Reinmaa E, Rice JP, Rizzi TS, Schmidt H, Schmidt R, Smith AV, Smith JA, Tanaka T, Terracciano A, van der Loos MJ, Vitart V, Völzke H, Wellmann J, Yu L, Zhao W, Allik J, Attia JR, Bandinelli S, Bastardot F, Beauchamp J, Bennett DA, Berger K, Bierut LJ, Boomsma DI, Bültmann U, Campbell H, Chabris CF, Cherkas L, Chung MK, Cucca F, de Andrade M, De Jager PL, De Neve JE, Deary IJ, Dedoussis GV, Deloukas P, Dimitriou M, Eiriksdottir G, Elderson MF, Eriksson JG, Evans DM, Faul JD, Ferrucci L, Garcia ME, Grönberg H, Gudnason V, Hall P, Harris JM, Harris TB, Hastie ND, Heath AC, Hernandez DG, Hoffmann W, Hofman A, Holle R, Holliday EG, Hottenga JJ, Iacono WG, Illig T, Järvelin MR, Kähönen M, Kaprio J, Kirkpatrick RM, Kowgier M, Latvala A, Launer LJ, Lawlor DA, Lehtimäki T, Li J, Lichtenstein P, Lichtner P, Liewald DC, Madden PA, Magnusson PKE, Mäkinen TE, Masala M, McGue M, Metspalu A, Mielck A, Miller MB, Montgomery GW, Mukherjee S, Nyholt DR, Oostra BA, Palmer LJ, Palotie A, Penninx B, Perola M, Peyser PA, Preisig M, Räikkönen K, Raitakari OT, Realo A, Ring SM, Ripatti S, Rivadeneira F, Rudan I, Rustichini A, Salomaa V, Sarin AP, Schlessinger D, Scott RJ, Snieder H, Pourcain BS, Starr JM, Sul JH, Surakka I, Svento R, Teumer A, Tiemeier H, Rooij FJA, Van Wagoner DR, Vartiainen E, Viikari J, Vollenweider P, Vonk JM, Waeber G, Weir DR, Wichmann HE, Widen E, Willemsen G, Wilson JF, Wright AF, Conley D, Davey-Smith G, Franke L, Groenen PJF, Hofman A, Johannesson M, Kardia SL, Krueger RF, Laibson D, Martin NG, Meyer MN, Posthuma D, Thurik AR, Timpson NJ, Uitterlinden AG, van Duijn CM, Visscher PM, Benjamin DJ, Cesarini D, Koellinger PD. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 2013; 340:1467-71. [PMID: 23722424 PMCID: PMC3751588 DOI: 10.1126/science.1235488] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
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Affiliation(s)
- Cornelius A. Rietveld
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Sarah E. Medland
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Jaime Derringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309–0447, USA
| | - Jian Yang
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Nicolas W. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia,School of Psychology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Konstantin Shakhbazov
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - John Barnard
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Kelly S. Benke
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jeffrey A. Boatman
- Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patricia A. Boyle
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Gail Davies
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Christiaan de Leeuw
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Niina Eklund
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA 94107–1728, USA
| | - Rudolf Ferhmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Håkon K. Gjessing
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Sara Hägg
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jennifer R. Harris
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Christina Holzapfel
- Else Kroener-Fresenius-Centre for Nutritional Medicine, Technische Universität München, 81675 Munich, Germany,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Carla A. Ibrahim-Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands,Department of Neurology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Erik Ingelsson
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Bo Jacobsson
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway,Department of Obstetrics and Gynecology, Institute of Public Health, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Peter K. Joshi
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Astanand Jugessur
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marika Kaakinen
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland,Biocenter Oulu, University of Oulu, Oulu 90014, Finland
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Juha Karjalainen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Kati Kristiansson
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jari Lahti
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Sang H. Lee
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Peng Lin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Penelope A. Lind
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Marisa Loitfelder
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - George McMahon
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Pedro Marques Vidal
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1005 Lausanne, Switzerland
| | - Osorio Meirelles
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Ronny Myhre
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Christopher J. Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Katja E. Petrovic
- Division of General Neurology, Department of Neurology, General Hospital and Medical University of Graz, Graz 8036, Austria
| | - Wouter J. Peyrot
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Ozren Polašek
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - John P. Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thais S. Rizzi
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz 8036, Austria
| | - Reinhold Schmidt
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur 201, Iceland,Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Antonio Terracciano
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA,College of Medicine, Florida State University, Tallahassee, FL 32306–4300, USA
| | - Matthijs J.H.M. van der Loos
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Veronique Vitart
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jüri Allik
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - John R. Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | | | - François Bastardot
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | | | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Ute Bültmann
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, 9700 AD Groningen, The Netherlands
| | - Harry Campbell
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Lynn Cherkas
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Mina K. Chung
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy,Dipartimento di Scienze Biomediche, Università di Sassari, 07100 SS, Italy
| | - Mariza de Andrade
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Philip L. De Jager
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jan-Emmanuel De Neve
- School of Public Policy, University College London, London WC1H 9QU, UK,Centre for Economic Performance, London School of Economics, London WC2A 2AE, UK
| | - Ian J. Deary
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK,Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Maria Dimitriou
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | | | - Martin F. Elderson
- LifeLines Cohort Study, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki 00014, Finland,Unit of General Practice, Helsinki University Central Hospital, Helsinki 00280, Finland,Folkhälsan Research Center, Helsinki 00250, Finland,Vaasa Central Hospital, Vaasa 65130, Finland
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Melissa E. Garcia
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur 201, Iceland,Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Juliette M. Harris
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Nicholas D. Hastie
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew C. Heath
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63110–1093, USA
| | - Dena G. Hernandez
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Wolfgang Hoffmann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Adriaan Hofman
- Faculty of Behavioral and Social Sciences, University of Groningen, 9747 AD Groningen, The Netherlands
| | - Rolf Holle
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Elizabeth G. Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Marjo-Riitta Järvelin
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland,Biocenter Oulu, University of Oulu, Oulu 90014, Finland,Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, Imperial College London, London W2 1PG, UK,Unit of Primary Care, Oulu University Hospital, Oulu 90220, Finland,Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu 90101, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere 33520, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Department of Public Health, University of Helsinki, 00014 Helsinki, Finland,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | | | - Matthew Kowgier
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Antti Latvala
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | - Lenore J. Launer
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Debbie A. Lawlor
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere University Hospital, Tampere 33520, Finland
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David C. Liewald
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Pamela A. Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Tomi E. Mäkinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andreas Mielck
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Michael B. Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Grant W. Montgomery
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Sutapa Mukherjee
- Western Australia Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Perth, Western Australia 6009, Australia,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada,Women’s College Research Institute, University of Toronto, Toronto, Ontario M5G 1N8, Canada
| | - Dale R. Nyholt
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Ben A. Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK,Department of Medical Genetics, University of Helsinki, 00014 Helsinki, Finland
| | - Brenda Penninx
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Martin Preisig
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Katri Räikkönen
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Anu Realo
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - Susan M. Ring
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands,Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Aldo Rustichini
- Department of Economics, University of Minnesota, Minneapolis, MN 55455–0462, USA
| | - Veikko Salomaa
- Chronic Disease Epidemiology Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Rodney J. Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Beate St Pourcain
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK,School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - John M. Starr
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK,Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Jae Hoon Sul
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Ida Surakka
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland,Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Rauli Svento
- Department of Economics, Oulu Business School, University of Oulu, Oulu 90014, Finland
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald 17487, Germany
| | | | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands,Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
| | - Frank JAan Rooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - David R. Van Wagoner
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Erkki Vartiainen
- Division of Welfare and Health Promotion, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Jorma Viikari
- Department of Medicine, Turku University Hospital, Turku 20520, Finland
| | - Peter Vollenweider
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Judith M. Vonk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - H.-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany,Klinikum Grosshadern, 81377 Munich, Germany,Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Alan F. Wright
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Dalton Conley
- Department of Sociology, New York University, New York, NY 10012, USA
| | - George Davey-Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Patrick J. F. Groenen
- Econometric Institute, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam 3000 DR, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm 113 83, Sweden
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Robert F. Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - David Laibson
- Department of Economics, Harvard University, Cambridge, MA 02138, USA
| | - Nicholas G. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Michelle N. Meyer
- Petrie-Flom Center for Health Law Policy, Biotechnology, & Bioethics, Harvard Law School, Cambridge, MA 02138, USA,Nelson A. Rockefeller Institute of Government, State University of New York, Albany, NY 12203–1003, USA
| | - Danielle Posthuma
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands,Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands,Department of Clinical Genetics, VU University Medical Centrer, 1081 BT Amsterdam, The Netherlands
| | - A. Roy Thurik
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands,Panteia, Zoetermeer 2701 AA, Netherlands,GSCM-Montpellier Business School, Montpellier 34185, France
| | - Nicholas J. Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands,Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands,Centre for Medical Systems Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter M. Visscher
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia,University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia,Corresponding author. (D.J.B.); (D.C.); (P.D.K.); (P.M.V.)
| | - Daniel J. Benjamin
- Department of Economics, Cornell University, Ithaca, NY 14853, USA,Corresponding author. (D.J.B.); (D.C.); (P.D.K.); (P.M.V.)
| | - David Cesarini
- Center for Experimental Social Science, Department of Economics, New York University, New York, NY 10012, USA,Division of Social Science, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, UAE,Research Institute of Industrial Economics, Stockholm 102 15, Sweden,Corresponding author. (D.J.B.); (D.C.); (P.D.K.); (P.M.V.)
| | - Philipp D. Koellinger
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands,Corresponding author. (D.J.B.); (D.C.); (P.D.K.); (P.M.V.)
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Pay ASD, Frøen JF, Staff AC, Jacobsson B, Gjessing HK. A new population-based reference curve for symphysis-fundus height. Acta Obstet Gynecol Scand 2013; 92:925-33. [PMID: 23611757 DOI: 10.1111/aogs.12157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 04/17/2013] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To present a new gestational-age-specific percentile curve for symphysis-fundus (SF) height and to determine the effects of maternal and fetal covariates. DESIGN A population-based register study. SETTING Antenatal clinics in Västra Götaland County, Sweden, between 2005 and 2010. POPULATION A total of 42 018 women with ultrasound-dated singleton pregnancies who delivered at Sahlgrenska University Hospital. MAIN OUTCOME MEASURES Measurement of SF height. METHODS A non-linear regression of SF height on day of pregnancy was used to construct a reference chart for the median and other percentiles of SF height. RESULTS The new reference curve for SF height showed almost linear growth until term. The median value was considerably larger at each gestational age compared with the curves for SF height used in Norway and Denmark. Compared with the curve currently used in Sweden, higher median values were observed only at gestational ages >34 weeks, accompanied by an upward shift in all percentiles. The only notably influential covariates were maternal pre-pregnancy weight and height. CONCLUSIONS The new reference curve for SF height shows a pattern that is different from the Scandinavian reference curves of older origin, reflecting changes in the pregnant population, as well as methodological differences. The new curve can be adjusted for maternal and fetal covariates to suit individual pregnancies.
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Affiliation(s)
- Aase Serine D Pay
- Women and Children's Division, Department of Obstetrics and Gynecology, Oslo University Hospital, Oslo, Norway.
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Håberg SE, Trogstad L, Gunnes N, Wilcox AJ, Gjessing HK, Samuelsen SO, Skrondal A, Cappelen I, Engeland A, Aavitsland P, Madsen S, Buajordet I, Furu K, Nafstad P, Vollset SE, Feiring B, Nøkleby H, Magnus P, Stoltenberg C. Risk of fetal death after pandemic influenza virus infection or vaccination. N Engl J Med 2013; 368:333-40. [PMID: 23323868 PMCID: PMC3602844 DOI: 10.1056/nejmoa1207210] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND During the 2009 influenza A (H1N1) pandemic, pregnant women were at risk for severe influenza illness. This concern was complicated by questions about vaccine safety in pregnant women that were raised by anecdotal reports of fetal deaths after vaccination. METHODS We explored the safety of influenza vaccination of pregnant women by linking Norwegian national registries and medical consultation data to determine influenza diagnosis, vaccination status, birth outcomes, and background information for pregnant women before, during, and after the pandemic. We used Cox regression models to estimate hazard ratios for fetal death, with the gestational day as the time metric and vaccination and pandemic exposure as time-dependent exposure variables. RESULTS There were 117,347 eligible pregnancies in Norway from 2009 through 2010. Fetal mortality was 4.9 deaths per 1000 births. During the pandemic, 54% of pregnant women in their second or third trimester were vaccinated. Vaccination during pregnancy substantially reduced the risk of an influenza diagnosis (adjusted hazard ratio, 0.30; 95% confidence interval [CI], 0.25 to 0.34). Among pregnant women with a clinical diagnosis of influenza, the risk of fetal death was increased (adjusted hazard ratio, 1.91; 95% CI, 1.07 to 3.41). The risk of fetal death was reduced with vaccination during pregnancy, although this reduction was not significant (adjusted hazard ratio, 0.88; 95% CI, 0.66 to 1.17). CONCLUSIONS Pandemic influenza virus infection in pregnancy was associated with an increased risk of fetal death. Vaccination during pregnancy reduced the risk of an influenza diagnosis. Vaccination itself was not associated with increased fetal mortality and may have reduced the risk of influenza-related fetal death during the pandemic. (Funded by the Norwegian Institute of Public Health.).
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Jugessur A, Skare Ø, Lie RT, Wilcox AJ, Christensen K, Christiansen L, Nguyen TT, Murray JC, Gjessing HK. X-linked genes and risk of orofacial clefts: evidence from two population-based studies in Scandinavia. PLoS One 2012; 7:e39240. [PMID: 22723972 PMCID: PMC3378529 DOI: 10.1371/journal.pone.0039240] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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: 02/27/2012] [Accepted: 05/17/2012] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Orofacial clefts are common birth defects of complex etiology, with an excess of males among babies with cleft lip and palate, and an excess of females among those with cleft palate only. Although genes on the X chromosome have been implicated in clefting, there has been no association analysis of X-linked markers. METHODOLOGY/PRINCIPAL FINDINGS We added new functionalities in the HAPLIN statistical software to enable association analysis of X-linked markers and an exploration of various causal scenarios relevant to orofacial clefts. Genotypes for 48 SNPs in 18 candidate genes on the X chromosome were analyzed in two population-based samples from Scandinavia (562 Norwegian and 235 Danish case-parent triads). For haplotype analysis, we used a sliding-window approach and assessed isolated cleft lip with or without cleft palate (iCL/P) separately from isolated cleft palate only (iCPO). We tested three statistical models in HAPLIN, allowing for: i) the same relative risk in males and females, ii) sex-specific relative risks, and iii) X-inactivation in females. We found weak but consistent associations with the oral-facial-digital syndrome 1 (OFD1) gene (formerly known as CXORF5) in the Danish iCL/P samples across all models, but not in the Norwegian iCL/P samples. In sex-specific analyses, the association with OFD1 was in male cases only. No analyses showed associations with iCPO in either the Norwegian or the Danish sample. CONCLUSIONS The association of OFD1 with iCL/P is plausible given the biological relevance of this gene. However, the lack of replication in the Norwegian samples highlights the need to verify these preliminary findings in other large datasets. More generally, the novel analytic methods presented here are widely applicable to investigations of the role of X-linked genes in complex traits.
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Affiliation(s)
- Astanand Jugessur
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway.
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Strand TA, Sharma PR, Gjessing HK, Ulak M, Chandyo RK, Adhikari RK, Sommerfelt H. Risk factors for extended duration of acute diarrhea in young children. PLoS One 2012; 7:e36436. [PMID: 22590543 PMCID: PMC3348155 DOI: 10.1371/journal.pone.0036436] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 11/23/2011] [Accepted: 04/02/2012] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE AND BACKGROUND We sought to identify predictors of extended duration of diarrhea in young children, which contributes substantially to the nearly 1 1/2 million annual diarrheal deaths globally. METHODS We followed 6-35 month old Nepalese children enrolled in the placebo-arm of a randomized controlled trial with 391 episodes of acute diarrhea from the day they were diagnosed until cessation of the episode. Using multiple logistic regression analysis, we identified independent risk factors for having diarrhea for more than 7 days after diagnosis. RESULTS Infants had a 17 (95% CI 3.5, 83)-fold and toddlers (12 to 23 month olds) a 9.9 (95% CI 2.1, 47)-fold higher odds of having such illness duration compared to the older children. Not being breastfed was associated with a 9.3 (95% CI 2.4, 35.7)-fold increase in the odds for this outcome. The odds also increased with increasing stool frequency. Furthermore, having diarrhea in the monsoon season also increased the risk of prolonged illness. CONCLUSION We found that high stool frequency, not being breastfed, young age and acquiring diarrhea in the rainy season were risk factors for prolonged diarrhea. In populations such as ours, breastfeeding may be the most important modifiable risk factor for extended duration of diarrhea.
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Affiliation(s)
- Tor A Strand
- Centre for International Health, University of Bergen, Bergen, Norway.
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Økland I, Nakling J, Gjessing HK, Grøttum P, Eik-Nes SH. Advantages of the population-based approach to pregnancy dating: results from 23,020 ultrasound examinations. Ultrasound Obstet Gynecol 2012; 39:563-568. [PMID: 21898635 DOI: 10.1002/uog.10081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To confirm the results from two previous evaluations of term prediction models, including two sample-based models and one population-based model, in a third population. METHODS In a study population of 23,020 second-trimester ultrasound examinations, data were prospectively collected and registered over the period 1988-2009. Three different models for ultrasonically estimated date of delivery were applied to the measurements of fetal biparietal diameter (BPD) and two models were applied to the femur length (FL) measurements; the resulting term estimations were compared with the actual time of delivery. The difference between the actual and the predicted dates of delivery (the median bias) was calculated for each of the models, for three BPD/FL-measurement subgroups and for the study population as a whole. RESULTS For the population-based model, the median bias was + 0.4 days for the BPD-based predictions and - 0.4 days for the FL-based predictions, and the biases were stable over the inclusion ranges. The biases of the two traditional models varied with the size of the fetus at examination; median biases were - 0.87 and + 2.2 days, respectively, with extremes - 4.2 and + 4.8 days for the BPD-based predictions, and the median bias was + 1.72 days with range - 0.8 to + 4.5 days for FL-based predictions. The disagreement between the two sample-based models was never less than 2 days for the BPD-based predictions. CONCLUSION This study confirms the results from previous studies; median biases were negligible with term predictions from the population-based model, while those from the traditional models varied substantially. The biases, which have clinical implications, seem inevitable with the sample-based models, which, even if overall biases were removed, will perform unsatisfactorily.
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Affiliation(s)
- I Økland
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway.
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Jugessur A, Wilcox AJ, Murray JC, Gjessing HK, Nguyen TT, Nilsen RM, Lie RT. Assessing the impact of nicotine dependence genes on the risk of facial clefts: An example of the use of national registry and biobank data. Nor Epidemiol 2012; 21:241-250. [PMID: 26451072 DOI: 10.5324/nje.v21i2.1500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy has been associated with risk of facial clefts in offspring, but causation has not yet been established. It is possible that the effect of maternal smoking on facial clefts is mediated through genes that are involved in nicotine dependence. Gamma-aminobutyric acid B receptor 2 (GABBR2), dopa decarboxylase (DDC), and cholinergic receptor nicotinic alpha 4 (CHRNA4) are three examples of genes that have previously shown strong associations with nicotine dependence. METHODS We used a population-based sample of 377 case-parent trios of cleft lip with or without cleft palate (CL/P) and 762 control-parent trios from Norway (1996-2001) to investigate whether variants in GABBR2, DDC and CHRNA4 are associated with maternal first-trimester smoking and with clefting risk. We used HAPLIN (Gjessing et al. 2006), a statistical software tailored for family-based association tests, to perform haplotype-based analyses on 12 SNPs in these genes (rs10985765, rs1435252, rs3780422, rs2779562, and rs3750344 in GABBR2; rs2060762, rs3757472, rs1451371, rs3735273, and rs921451 in DDC; rs4522666 and rs1044393 in CHRNA4). RESULTS When analyzed one at a time, there was little evidence of association between any of the 12 SNPs and maternal first-trimester smoking. In haplotype analyses, however, one copy of the maternal G-G-c-G-c haplotype in DDC was linked with smoking prevalence (odds ratio: 1.5; 95% confidence interval: 1.0-2.1). This same haplotype also increased the risk of isolated CL/P in offspring by 1.5-fold with one copy and 2.4-fold with two copies (Ptrend = 0.06). No statistically significant associations were detected with GABBR2 and CHRNA4. CONCLUSIONS Despite strong associations previously reported between nicotine dependence and variants in GABBR2, DDC and CHRNA4, these genes were poor predictors of maternal first-trimester smoking in our data. The direct association of the DDC haplotype with CL/P suggests that this haplotype may either have direct effects on clefts or it may influence clefting risks through other yet unexplored risk behavior(s).
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Affiliation(s)
- Astanand Jugessur
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway ; Craniofacial Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, North Carolina, USA
| | - Jeffrey C Murray
- Departments of Pediatrics, Epidemiology and Biological Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Håkon K Gjessing
- Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway ; Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway
| | - Truc Trung Nguyen
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Roy M Nilsen
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Rolv T Lie
- Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway ; Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
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50
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Myking S, Myhre R, Gjessing HK, Morken NH, Sengpiel V, Williams SM, Ryckman KK, Magnus P, Jacobsson B. Candidate gene analysis of spontaneous preterm delivery: new insights from re-analysis of a case-control study using case-parent triads and control-mother dyads. BMC Med Genet 2011; 12:174. [PMID: 22208904 PMCID: PMC3260094 DOI: 10.1186/1471-2350-12-174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 12/30/2011] [Indexed: 11/10/2022]
Abstract
Background Spontaneous preterm delivery (PTD) has a multifactorial etiology with evidence of a genetic contribution to its pathogenesis. A number of candidate gene case-control studies have been performed on spontaneous PTD, but the results have been inconsistent, and do not fully assess the role of how two genotypes can impact outcome. To elucidate this latter point we re-analyzed data from a previously published case-control candidate gene study, using a case-parent triad design and a hybrid design combining case-parent triads and control-mother dyads. These methods offer a robust approach to genetic association studies for PTD compared to traditional case-control designs. Methods The study participants were obtained from the Norwegian Mother and Child Cohort Study (MoBa). A total of 196 case triads and 211 control dyads were selected for the analysis. A case-parent triad design as well as a hybrid design was used to analyze 1,326 SNPs from 159 candidate genes. We compared our results to those from a previous case-control study on the same samples. Haplotypes were analyzed using a sliding window of three SNPs and a pathway analysis was performed to gain biological insight into the pathophysiology of preterm delivery. Results The most consistent significant fetal gene across all analyses was COL5A2. The functionally similar COL5A1 was significant when combining fetal and maternal genotypes. PON1 was significant with analytical approaches for single locus association of fetal genes alone, but was possibly confounded by maternal effects. Focal adhesion (hsa04510), Cell Communication (hsa01430) and ECM receptor interaction (hsa04512) were the most constant significant pathways. Conclusion This study suggests a fetal association of COL5A2 and a combined fetal-maternal association of COL5A1 with spontaneous PTD. In addition, the pathway analysis implied interactions of genes affecting cell communication and extracellular matrix.
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Affiliation(s)
- Solveig Myking
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway.
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