Kirsti Kvaløy

Genetic Heterogeneity in Latent Autoimmune Diabetes Is Linked to Various Degrees of Autoimmune Activity: Results From the Nord-Trøndelag Health Study

OBJECTIVE Previous studies have indicated that the latent autoimmune diabetes in adults (LADA) phenotype is heterogeneous and that LADA patients share features of type 1 and type 2 diabetes in various proportions. We tested for association of known type 1 and type 2 diabetes susceptibility genes in LADA subjects and analyzed relationships to a marker of autoimmune activity (titers of anti-GAD) and a phenotypic risk factor of type 2 diabetes (BMI). RESEARCH DESIGN AND METHODS Data were assembled from the Nord-Trøndelag Health Study (HUNT) study, which comprises the adult population of an entire county in Norway. We genotyped 60 single nucleotide polymorphisms (SNPs) known to be associated with type 1 or type 2 diabetes, including 14 tag SNPs used for HLA haplotyping in 120 type 1 diabetic, 126 LADA, and 1,090 type 2 diabetic patients and 1,503 age- and sex-matched nondiabetic subjects. RESULTS The majority of the strongly associated HLA haplotypes for type 1 diabetes were significantly associated with LADA in general, but mainly with high anti-GAD LADA patients. Two distinct HLA haplotypes were associated only with LADA and mainly in low anti-GAD LADA patients. There were no associations of non-HLA type 1 diabetes loci with LADA. Of type 2 diabetes–associated genes, the CC/CT genotypes of rs7961581 (TSPAN8) and the obesity-linked AA/AC genotypes of rs8050136 (FTO) were associated with LADA in general, but mainly in low anti-GAD LADA patients (P = 0.004 and P = 0.004, respectively). CONCLUSIONS Genetic heterogeneity in LADA is linked to various degrees of autoimmune activity and may be partly distinct from both type 1 and type 2 diabetes.

DataSHIELD: taking the analysis to the data, not the data to the analysis

Background: Research in modern biomedicine and social science requires sample sizes so large that they can often only be achieved through a pooled co-analysis of data from several studies. But the pooling of information from individuals in a central database that may be queried by researchers raises important ethico-legal questions and can be controversial. In the UK this has been highlighted by recent debate and controversy relating to the UK’s proposed ‘care.data’ initiative, and these issues reflect important societal and professional concerns about privacy, confidentiality and intellectual property. DataSHIELD provides a novel technological solution that can circumvent some of the most basic challenges in facilitating the access of researchers and other healthcare professionals to individual-level data. Methods: Commands are sent from a central analysis computer (AC) to several data computers (DCs) storing the data to be co-analysed. The data sets are analysed simultaneously but in parallel. The separate parallelized analyses are linked by non-disclosive summary statistics and commands transmitted back and forth between the DCs and the AC. This paper describes the technical implementation of DataSHIELD using a modified R statistical environment linked to an Opal database deployed behind the computer firewall of each DC. Analysis is controlled through a standard R environment at the AC. Results: Based on this Opal/R implementation, DataSHIELD is currently used by the Healthy Obese Project and the Environmental Core Project (BioSHaRE-EU) for the federated analysis of 10 data sets across eight European countries, and this illustrates the opportunities and challenges presented by the DataSHIELD approach. Conclusions: DataSHIELD facilitates important research in settings where: (i) a co-analysis of individual-level data from several studies is scientifically necessary but governance restrictions prohibit the release or sharing of some of the required data, and/or render data access unacceptably slow; (ii) a research group (e.g. in a developing nation) is particularly vulnerable to loss of intellectual property—the researchers want to fully share the information held in their data with national and international collaborators, but do not wish to hand over the physical data themselves; and (iii) a data set is to be included in an individual-level co-analysis but the physical size of the data precludes direct transfer to a new site for analysis.

Data harmonization and federated analysis of population-based studies: the BioSHaRE project

AbstractsBackgroundIndividual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses.MethodsEight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis.ResultsRetrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method.ConclusionNew Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.

Being Normal Weight but Feeling Overweight in Adolescence May Affect Weight Development into Young Adulthood—An 11-Year Followup: The HUNT Study, Norway

Objectives. To explore if self-perceived overweight in normal weight adolescents influence their weight development into young adulthood and if so, whether physical activity moderates this association. Methods. A longitudinal study of 1196 normal weight adolescents (13–19 yrs) who were followed up as young adults (24–30 yrs) in the HUNT study. Lifestyle and health issues were assessed employing questionnaires, and standardized anthropometric measurements were taken. Chi square calculations and regression analyses were performed to investigate the associations between self-perceived overweight and change in BMI or waist circumference (WC) adjusted for age, age squared, sex, and other relevant cofactors. Results. Adolescents, defined as being normal weight, but who perceived themselves as overweight had a larger weight gain into young adulthood than adolescents who perceived themselves as normal weight (difference in BMI: 0.66 units [CI95%: 0.1, 1.2] and in WC: 3.46 cm [CI95%: 1.8, 5.1]). Level of physical activity was not found to moderate this association. Conclusions. This study reveals that self-perceived overweight during adolescence may affect development of weight from adolescence into young adulthood. This highlights the importance of also focusing on body image in public health interventions against obesity, favouring a “healthy” body weight taking into account natural differences in body shapes.

Common Variants Show Predicted Polygenic Effects on Height in the Tails of the Distribution, Except in Extremely Short Individuals

Common genetic variants have been shown to explain a fraction of the inherited variation for many common diseases and quantitative traits, including height, a classic polygenic trait. The extent to which common variation determines the phenotype of highly heritable traits such as height is uncertain, as is the extent to which common variation is relevant to individuals with more extreme phenotypes. To address these questions, we studied 1,214 individuals from the top and bottom extremes of the height distribution (tallest and shortest ∼1.5%), drawn from ∼78,000 individuals from the HUNT and FINRISK cohorts. We found that common variants still influence height at the extremes of the distribution: common variants (49/141) were nominally associated with height in the expected direction more often than is expected by chance (p<5×10−28), and the odds ratios in the extreme samples were consistent with the effects estimated previously in population-based data. To examine more closely whether the common variants have the expected effects, we calculated a weighted allele score (WAS), which is a weighted prediction of height for each individual based on the previously estimated effect sizes of the common variants in the overall population. The average WAS is consistent with expectation in the tall individuals, but was not as extreme as expected in the shortest individuals (p<0.006), indicating that some of the short stature is explained by factors other than common genetic variation. The discrepancy was more pronounced (p<10−6) in the most extreme individuals (height<0.25 percentile). The results at the extreme short tails are consistent with a large number of models incorporating either rare genetic non-additive or rare non-genetic factors that decrease height. We conclude that common genetic variants are associated with height at the extremes as well as across the population, but that additional factors become more prominent at the shorter extreme.

The association of air pollution and depressed mood in 70,928 individuals from four European cohorts

BACKGROUND Exposure to ambient air pollution may be associated with impaired mental health, including depression. However, evidence originates mainly from animal studies and epidemiological studies in specific subgroups. We investigated the association between air pollution and depressed mood in four European general population cohorts. METHODS Data were obtained from LifeLines (the Netherlands), KORA (Germany), HUNT (Norway), and FINRISK (Finland). Residential exposure to particles (PM2.5, PM2.5absorbance, PM10) and nitrogen dioxide (NO2) was estimated using land use regression (LUR) models developed for the European Study of Cohorts for Air Pollution Effects (ESCAPE) and using European wide LUR models. Depressed mood was assessed with interviews and questionnaires. Logistic regression analyses were used to investigate the cohort specific associations between air pollution and depressed mood. RESULTS A total of 70,928 participants were included in our analyses. Depressed mood ranged from 1.6% (KORA) to 11.3% (FINRISK). Cohort specific associations of the air pollutants and depressed mood showed heterogeneous results. For example, positive associations were found for NO2 in LifeLines (odds ratio [OR]=1.34; 95% CI: 1.17, 1.53 per 10 μg/m(3) increase in NO2), whereas negative associations were found in HUNT (OR=0.79; 95% CI: 0.66, 0.94 per 10 μg/m(3) increase in NO2). CONCLUSIONS Our analyses of four European general population cohorts found no consistent evidence for an association between ambient air pollution and depressed mood.

Sequence variation in the human uracil-DNA glycosylase (UNG) gene.

Spontaneous deamination of cytosine results in a premutagenic G:U mismatch that may result in a GC-->AT transition during replication. The human UNG-gene encodes the major uracil-DNA glycosylase (UDG or UNG) which releases uracil from DNA, thus, initiating base excision repair to restore the correct DNA sequence. Bacterial and yeast mutants lacking the homologous UDG exhibit elevated spontaneous mutation frequencies. Hence, mutations in the human UNG gene could presumably result in a mutator phenotype. We screened all seven exons including exon-intron boundaries, both promoters, and one intron of the UNG gene and identified considerable sequence variation in cell lines derived from normal fibroblasts and tumour tissue. None of the sequence variants was accompanied by significantly reduced UDG activity. In the UNG gene from 62 sources, we identified 12 different variant alleles, with allele frequencies ranging from 0.01 to 0.23. We identified one variant allele per 3.8kb in non-coding regions, but none in the coding region of the gene. In promoter B we identified four different variants. A substitution within an AP2 element was observed in tumour cell lines only and had an allele frequency of 0.10. Introduction of this substitution into chimaeric promoter-luciferase constructs affected transcription from the promoter. UDG-activity varied little in fibroblasts, but widely between tumour cell lines. This variation did not however correlate with the presence of any of the variant alleles. In conclusion, mutations affecting the function of human UNG gene are seemingly infrequent in human tumour cell lines.

Species or subspecies? The dilemma of taxonomic ranking of some South-East Asian hawk-eagles (genus Spizaetus )

Summary A molecular phylogeny of the Spizaetus cirrhatus complex is presented in this study, based on two sections of the mitochondrial genome: partial sequences of the cytochrome b gene and of the control region (CR). The topologies derived from the two sequences are in agreement. Within S. cirrhatus distances are rather low (0–1.5% in cytochrome b). Among the cirrhatus subspecies the island taxa floris, vanheurni and andamanensis form distinct haplogroups in the CR trees, conforming to the earlier subspecific divisions which were based on morphological characters. On the other hand, the most widespread subspecies, limnaeetus, does not represent a monophyletic group in the gene trees and its haplogroups do not cluster according to geographic affinities. An unambiguous resolution of relationships among haplotypes and haplogroups, respectively, was not achieved, suggesting a more recent radiation of this group of hawk-eagles in the course of the last ice ages. Concerning the outgroup taxa Spizaetus philippensis and Spizaetus lanceolatus, our data indicate a clear genetic distinction between the two subspecies S. p. philippensis and S. p. pinskeri, suggesting that they should be treated as distinct species. Yet the phylogenetic relationships of the three outgroup taxa with respect to S. cirrhatus are ambiguous in our trees. The taxonomic consequences of applying different species concepts (BSC, PSC) are discussed. The species concept chosen would result in different conservation strategies.

Sex-specific effects of weight-affecting gene variants in a life course perspective-The HUNT Study, Norway

Objective:The impact of previously identified genetic variants directly or indirectly associated with obesity, were investigated at birth, adolescence and adulthood to provide knowledge concerning timing and mechanisms of obesity susceptibility with focus on sex differences.Design:Twenty four previously identified obesity- and eating disorder susceptibility loci were tested for association with adiposity traits at birth (ponderal index (PI)), adolescence and young adulthood (body mass index (BMI), waist circumference (WC) and waist-hip ratio (WHR)) in 1782 individuals from the HUNT study. Single-nucleotide polymorphism (SNPs) were evaluated individually and by haplotype sliding-window approach for windows⩽50 kb (near-MC4R, FTO and near-BDNF). The analyses were performed on the total and sex stratified samples.Results:The most substantial effect on BMI was observed for the near-MC4R variants at adolescence and adulthood (adjusted P-values in adolescence: 0.002 and 0.003 for rs17782313 and rs571312, respectively). The same variants showed inverse association with PI in males (adjusted P-values: 0.019–0.036). Furthermore, significant effects were observed at adolescence with BMI for the near-KCTD15 variant (rs11084753) (adjusted P=0.038) in the combined sample. The near-INSIG2 (rs7566605) was significantly associated to WHR in males and near-BDNF (rs925946) in the combined sample (adjusted P=0.027 and P=0.033, respectively). The OPRD1 locus was associated to BMI and WC in males both at adolescence and adulthood with highest effect in adults (adjusted P=0.058). Interaction with sex was identified for near-MC4R, OPRD1, COMT, near-BDNF and DRD2.Conclusions:Most obesity susceptibility variants show stronger effect at adolescence than at birth and adulthood with a clear sex-specific effect at some loci. The near-MC4R locus exhibit inverse effect on weight at birth in boys compared with findings at adolescence and adulthood. Some variants less known for obesity-susceptibility such as OPRD1 were found to be associated to weight with strongest effects in males.

Prevalence of ZnT8 antibody in relation to phenotype and SLC30A8 polymorphism in adult autoimmune diabetes. Results from the HUNT study, Norway

Zinc transporter 8 (ZnT8), a product of the SLC30A8 gene, is a target-antigen in autoimmune diabetes. Associations between ZnT8 antibody (ZnT8A), phenotype and the genetic variant rs13266634 in the SLC30A8 gene have primarily been studied in patients with young-onset diabetes. We explored such associations in adult-onset autoimmune diabetes identified from the all-population based Nord-Trøndelag health Study (HUNT) ZnT8A (assayed by a fusion probe of C-terminal Arg325 and Trp325), and antibodies against glutamic decarboxylase (GADA) and tyrosine phosphatase-like protein insulinoma antigen-2 (IA-2A) were analysed in 266 subjects classified as having adult-onset autoimmune diabetes ( ≥ 25 years of age at diagnosis). Of these, 161 subjects fulfilled the criteria of latent autoimmune diabetes in adults (LADA), whereas 105 subjects were termed “classical” type 1 diabetes. Ten out of 161 LADA (6.2%) and 23 out of 105 adult-onset “classical” type 1 diabetic patients (22%) were ZnT8A positive. Adult-onset diabetic subjects positive both for GADA and IA-2A (n = 17), had lower waist circumference (p = 0.024) and higher fasting glucose levels (p = 0.023) than those positive both for GADA and ZnT8A (n = 13). Genotyping results of rs13266634 (available in 178 adult-onset diabetic subjects), showed a tendency for association between ZnT8A positivity and the TT- and CC genotypes of SNP rs13266634 (p = 0.101) using the standard cut-off level of 0.06ai, and a significant association at a lower cut-off level of 0.01ai (p = 0.005). We conclude that ZnT8A positivity in a population of adult-onset autoimmune diabetes is a less strong marker of autoimmunity than IA-2A. Further, positivity could be influenced by polymorphism of the SLC30A8 gene.