Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort.

BACKGROUND: Genotypes obtained with commercial SNP arrays have been extensively used in many large case-control or population-based cohorts for SNP-based genome-wide association studies for a multitude of traits. Yet, these genotypes capture only a small fraction of the variance of the studied traits. Genomic structural variants (GSV) such as Copy Number Variation (CNV) may account for part of the missing heritability, but their comprehensive detection requires either next-generation arrays or sequencing. Sophisticated algorithms that infer CNVs by combining the intensities from SNP-probes for the two alleles can already be used to extract a partial view of such GSV from existing data sets. RESULTS: Here we present several advances to facilitate the latter approach. First, we introduce a novel CNV detection method based on a Gaussian Mixture Model. Second, we propose a new algorithm, PCA merge, for combining copy-number profiles from many individuals into consensus regions. We applied both our new methods as well as existing ones to data from 5612 individuals from the CoLaus study who were genotyped on Affymetrix 500K arrays. We developed a number of procedures in order to evaluate the performance of the different methods. This includes comparison with previously published CNVs as well as using a replication sample of 239 individuals, genotyped with Illumina 550K arrays. We also established a new evaluation procedure that employs the fact that related individuals are expected to share their CNVs more frequently than randomly selected individuals. The ability to detect both rare and common CNVs provides a valuable resource that will facilitate association studies exploring potential phenotypic associations with CNVs. CONCLUSION: Our new methodologies for CNV detection and their evaluation will help in extracting additional information from the large amount of SNP-genotyping data on various cohorts and use this to explore structural variants and their impact on complex traits.

Gestational diabetes mellitus and the risk of metabolic syndrome: a population-based study in Lausanne, Switzerland

RESUME EN FRANÇAIS BUTS. Étudier les relations entre le diabète gestationnel (GDM) et le syndrome métabolique (MS), comme la résistance à l'insuline est une des caractéristiques des 'deux conditions. Analyser le dépistage du diabète dans le post-partum pour identifier les facteurs de risque associés au développement d'un diabète de type 2 ultérieur. MÉTHODES. Étude rétrospective de toutes les grossesses uniques diagnostiquées avec un diabète gestationnel à l'hôpital universitaire de Lausanne, pendant une durée de trois ans. La présence d'une obésité, d'une hypertension ou d'une dyslipidémie avant la grossesse définissent les composants du syndrome métabolique. RÉSULTATS. Sur 5788 grossesses, 159 patientes (2.7%) présentaient un diabète gestationnel. Des composants du syndrome métabolique étaient présents avant la grossesse chez 26% des patientes (n=37/144) : 84% (n=31/37) étaient obèses, 38% (n=14/37) présentaient une hypertension et 22% (n=8/37) une dyslipidémie. Le développement d'une hypertension gravidique était associé à l'obésité (OR=3.2, p=0.02) et à la dyslipidémie (OR=5.4, p=0.002). Septante-quatre patientes (47%) sont revenues pour l'HGPO dans le post-partum. Celle-ci était anormale chez 20 femmes (27%): 11 % (n=8) présentaient un diabète de type 2 et 16% (n=12) avaient une intolérance au glucose. Les facteurs de risque indépendants associés à une anomalie de la tolérance au glucose dans le post-partum étaient d'avoir plus de 2 valeurs anormales au test diagnostique durant la grossesse et présenter des composants du syndrome métabolique (OR=5.2, CI 1.8-23.2 et OR=5.3, CI 1.3-22.2). CONCLUSIONS. Dans un quart des grossesses avec un diabète gestationnel, des anomalies métaboliques précèdent l'apparition de l'intolérance au glucose. Ces patientes présentent un haut risque de développer un syndrome métabolique et un diabète de type 2 ultérieurement. Là où le dépistage du diabète gestationnel n'est pas systématique, les praticiens devraient être avertis de ces risques métaboliques chez les patiente se présentant avec une obésité, une hypertension ou une dyslipidémie, afin de mieux les diagnostiquer et surtout de mieux les suivre et traiter après leur grossesse.

Cardiovascular risk estimation and eligibility for statins in primary prevention comparing different strategies

Recommendations for statin use for primary prevention of coronary heart disease (CHD) are based on estimation of the 10-year CHD risk. It is unclear which risk algorithm and guidelines should be used in European populations. Using data from a population-based study in Switzerland, we first assessed 10-year CHD risk and eligibility for statins in 5,683 women and men 35 to 75 years of age without cardiovascular disease by comparing recommendations by the European Society of Cardiology without and with extrapolation of risk to age 60 years, the International Atherosclerosis Society, and the US Adult Treatment Panel III. The proportions of participants classified as high-risk for CHD were 12.5% (15.4% with extrapolation), 3.0%, and 5.8%, respectively. Proportions of participants eligible for statins were 9.2% (11.6% with extrapolation), 13.7%, and 16.7%, respectively. Assuming full compliance to each guideline, expected relative decreases in CHD deaths in Switzerland over a 10-year period would be 16.4% (17.5% with extrapolation), 18.7%, and 19.3%, respectively; the corresponding numbers needed to treat to prevent 1 CHD death would be 285 (340 with extrapolation), 380, and 440, respectively. In conclusion, the proportion of subjects classified as high risk for CHD varied over a fivefold range across recommendations. Following the International Atherosclerosis Society and the Adult Treatment Panel III recommendations might prevent more CHD deaths at the cost of higher numbers needed to treat compared with European Society of Cardiology guidelines.

LDL-cholesterol concentrations: a genome-wide association study.

BACKGROUND: LDL cholesterol has a causal role in the development of cardiovascular disease. Improved understanding of the biological mechanisms that underlie the metabolism and regulation of LDL cholesterol might help to identify novel therapeutic targets. We therefore did a genome-wide association study of LDL-cholesterol concentrations. METHODS: We used genome-wide association data from up to 11,685 participants with measures of circulating LDL-cholesterol concentrations across five studies, including data for 293 461 autosomal single nucleotide polymorphisms (SNPs) with a minor allele frequency of 5% or more that passed our quality control criteria. We also used data from a second genome-wide array in up to 4337 participants from three of these five studies, with data for 290,140 SNPs. We did replication studies in two independent populations consisting of up to 4979 participants. Statistical approaches, including meta-analysis and linkage disequilibrium plots, were used to refine association signals; we analysed pooled data from all seven populations to determine the effect of each SNP on variations in circulating LDL-cholesterol concentrations. FINDINGS: In our initial scan, we found two SNPs (rs599839 [p=1.7x10(-15)] and rs4970834 [p=3.0x10(-11)]) that showed genome-wide statistical association with LDL cholesterol at chromosomal locus 1p13.3. The second genome screen found a third statistically associated SNP at the same locus (rs646776 [p=4.3x10(-9)]). Meta-analysis of data from all studies showed an association of SNPs rs599839 (combined p=1.2x10(-33)) and rs646776 (p=4.8x10(-20)) with LDL-cholesterol concentrations. SNPs rs599839 and rs646776 both explained around 1% of the variation in circulating LDL-cholesterol concentrations and were associated with about 15% of an SD change in LDL cholesterol per allele, assuming an SD of 1 mmol/L. INTERPRETATION: We found evidence for a novel locus for LDL cholesterol on chromosome 1p13.3. These results potentially provide insight into the biological mechanisms that underlie the regulation of LDL cholesterol and might help in the discovery of novel therapeutic targets for cardiovascular disease.

Blood pressure modifies the association between serum adiponectin and uric acid, in a sex-dependent manner

Purpose: Plasma adiponectin and serum uric acid (SUA) levels are negatively correlated. To better understand the possible mechanisms linking adiponectin and uric acid, we analyzed whether the association between adiponectin and SUA differed by hypertension status (or blood pressure level) and by sex. Methods and materials: We analyzed data from the populationbased CoLaus study (Switzerland). Fasting plasma adiponectin levels were assessed by ELISA and SUA by uricase-PAP. Blood pressure (BP) was measured using a validated automated device and hypertension was defined as having office BP 140/90 mm Hg or being on current antihypertensive treatment. Results: In the 2897 men and 3181 women, aged 35-74, BMI (mean ± SD) was 26.6 ± 4.0 and 25.1 ± 4.8 Kg/m2, systolic blood pressure (SBP) was 132.2 ± 16.6 and 124.8 ± 18.3 mm Hg, median (interquartile range) plasma adiponectin was 6.2 (4.1-9.2) and 10.6 (6.9-15.4) mg/dL, and hypertension prevalence was 42.0% and 30.2%, respectively. The age- and BMI- adjusted partial correlation coefficients between log-adiponectin and SUA were 0.09 and 0.06 in normotensive men and women (P <0.01), and 0.004 (P = 0.88) and 0.15 (P <0.001) in hypertensive men and women, respectively. In median regression adjusted for BMI, insulin, smoking, alcohol consumption, menopausal status and HDL-cholesterol, there was a significant three-way interaction between SUA, SBP and sex for their effect on adiponectin (dependent variable, P = 0.005), as well as interactions between SBP and sex (P = 0.014) and between SUA and sex (P = 0.033). Conclusion: Plasma adiponectin and SUA are negatively associated, independently of BMI and insulin, in a population-based study in Caucasians. However, BP modifies this inverse relationship, as it was significant mainly in women with elevated BP. This observation suggests that the link between adiponectin and SUA may be mediated by sex hormones and the hypertension status.

Metabolic syndrome according to different definitions in a rapidly developing country of the African region

Rapport de synthèseLe syndrome métabolique représente un ensemble de facteurs de risque métaboliques souvent présents simultanément et il est associé à un risque accru de développer des maladies cardiovasculaires. La prevalence du syndrome métabolique est à la hausse au niveau mondial comme cela a souvent été documenté, en particulier dans les pays développés. Pourtant, les données concernant le syndrome métabolique dans les pays de la région sub-saharienne restent rares.Au cours des dernières années, plusieurs définitions du syndrome métabolique ont été formulées, dont celle du 'National Cholesterol Education Program Adult Treatment Panel III', celle de 1 Organisation Mondiale de la Santé et celle du 'International Diabetes Federation'. Parmi les controverses au sujet du syndrome métabolique persiste la question de l'utilité de rechercher la présence du syndrome métabolique chez les patients diabétiques, étant donné que la présence d'un diabète en soit suffit pour identifier un individu à haut risque de faire un événement cardiovasculaire.L'objectif de ce travail de thèse a été de déterminer la prévalence du syndrome métabolique selon les trois définitions majeures mentionnées ci-dessus, grâce à une étude de population transversale, réalisée aux Seychelles en 2004 dans un échantillon représentatif de la population âgée de 24-65 ans (n=1255, taux de participation de 80.3%). L'intérêt d'examiner cette question dans ce pays était d'obtenir des informations dans un pays en transition épidémiologique.Les résultats de ce travail montrent que la prévalence du syndrome métabolique aux Seychelles est élevée, quelque soit la définition utilisée. Selon la définition utilisée, cette prévalence était d'environ 25% chez les hommes et variant entre 25 et 35% chez les femmes.Cependant, malgré des prévalences semblables selon ces trois définitions, la concordance entre ces définitions n'était pas bonne, impliquant que ces différentes définitions classifient, à un certain degré, des individus différents comme étant porteurs du syndrome métabolique.En outre, la plupart (environ 80%) des individus diabétiques avaient un syndrome métabolique. Après exclusion des individus diabétiques, la prévalence du syndrome métabolique dans la population est réduite d'environ un tiers, à environ 20-25%.Ces résultats montrent que, d'une part, le fardeau de maladie dû au syndrome métabolique aux Seychelles, un pays en voie de développement, est considérable. Cette observation peut potentiellement s'appliquer à d'autres pays à un stade de développement semblable. Cela renforce le besoin de mettre en oeuvre des stratégies de santé publique afin de cibler les causes de ces désordres métaboliques, tels que le surpoids et la sédentarité. D'un point de vue du diagnostic, les trois définitions du syndrome métabolique semblent classifier un nombre semblable de personnes atteints du syndrome métabolique dans cette population. Par contre, la relativement mauvaise concordance entre ces définitions - certaines personnes identifiés comme porteurs du syndrome métabolique selon une définition ne le sont pas selon une autre - confirme la nécessité de clarifier la signification de ces différentes définitions et/ou éventuellement de développer une définition unifiée et fiable du syndrome métabolique.

Associations of serum uric acid and SLC2A9 variant with depressive and anxiety disorders: a population-based study

Background: Limited information exists regarding the association between serum uric acid (SUA) and psychiatric disorders. We explored the relationship between SUA and subtypes of major depressive disorder (MDD) and specific anxiety disorders. Additionally, we examined the association of SLC2A9 rs6855911 variant with anxiety disorders. Methods: We conducted a cross-sectional analysis on 3,716 individuals aged 35-66 years previously selected for the population-based CoLaus survey and who agreed to undergo further psychiatric evaluation. SUA was measured using uricase-PAP method. The French translation of the semi-structured Diagnostic Interview for Genetic Studies was used to establish lifetime and current diagnoses of depression and anxiety disorders according to the DSM-IV criteria. Results: Men reported significantly higher levels of SUA compared to women (357}74 μmol/L vs. 263}64 μmol/L). The prevalence of lifetime and current MDD was 44% and 18% respectively while the corresponding estimates for any anxiety disorders were 18% and 10% respectively. A quadratic hockey-stick shaped curve explained the relationship between SUA and social phobia better than a linear trend. However, with regards to the other specific anxiety disorders and other subtypes of MDD, there was no consistent pattern of association. Further analyses using SLC2A9 rs6855911 variant, known to be strongly associated with SUA, supported the quadratic relationship observed between SUA phenotype and social phobia. Conclusions: A quadratic relationship between SUA and social phobia was observed consistent with a protective effect of moderately elevated SUA on social phobia, which disappears at higher concentrations. Further studies are needed to confirm our observations.

Prevalence of obesity and abdominal obesity in the Lausanne population.

BACKGROUND: Obesity can be defined using body mass index (BMI) or waist (abdominal obesity). Little information exists regarding its prevalence and determinants in Switzerland. Hence, we assessed the levels of obesity as defined by BMI or waist circumference in a Swiss population-based sample. METHODS: Cross-sectional, population-based non-stratified random sample of 3,249 women and 2,937 men aged 35-75 years living in Lausanne, Switzerland. Overall participation rate was 41%. RESULTS: In men, the prevalences of overweight (BMI > or =25 kg/m2) and obesity (BMI > or =30 kg/m2) were 45.5% and 16.9%, respectively, higher than in women (28.3% and 14.3%, respectively). The prevalence of abdominal obesity (waist > or =102 in men and > or =88 cm in women) was higher in women than in men (30.6% vs. 23.9%). Obesity and abdominal obesity increased with age and decreased with higher educational level in both genders. In women, the prevalence of obesity was lower among former and current smokers, whereas in men the prevalence of obesity was higher in former smokers but did not differ between current and never smokers. Multivariate analysis showed age to be positively related, and education and physical activity to be negatively related with obesity and abdominal obesity in both genders, whereas differential effects of smoking were found between genders. CONCLUSION: The prevalence of abdominal obesity is higher than BMI-derived obesity in the Swiss population. Women presented with more abdominal obesity than men. The association between smoking and obesity levels appears to differ between genders.

Prevalence of normal weight obesity in Switzerland: effect of various definitions

BACKGROUND: Normal weight obesity (NWO) is defined as an excessive body fat associated with a normal body mass index (BMI < 25 kg/m(2)), but its prevalence in the general population is unknown. AIM OF THE STUDY: To assess the prevalence of NWO in Switzerland according to different cut points used to define excess body fat. METHODS: Cross-sectional study including 3,213 women and 2,912 men aged 35-75 years. Body fat was assessed by bioelectrical impedance analysis and prevalence of NWO was assessed using four previously published definitions for excess body fat. RESULTS: Percent body fat increased with age: in men, the values (mean +/- SD) were 20.2 +/- 5.4, 23.0 +/- 5.4, 26.3 +/- 5.2 and 28.2 +/- 4.6 for age groups 35-44, 45-54, 55-64 and 65-75 years, respectively; the corresponding values for women were 29.9 +/- 7.8, 33.1 +/- 7.4, 36.7 +/- 7.5 and 39.6 +/- 6.9. In men, prevalence of NWO was <1% irrespective of the definition used. Conversely, in women, a 1- to 20-fold difference (from 1.4 to 27.8%) in NWO prevalence was found. The prevalence of NWO increased with age when age-independent cut points were used in women, but not in men. CONCLUSIONS: Prevalence of NWO is low in the general population and higher in women than in men. The prevalence is highly dependent on the criteria used to define excess body fat, namely in women. The use of gender- and age-specific cut points to define excess body fat is better than fixed or gender-specific only cut points.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

OBJECTIVE: Plasma adiponectin is strongly associated with various components of metabolic syndrome, type 2 diabetes and cardiovascular outcomes. Concentrations are highly heritable and differ between men and women. We therefore aimed to investigate the genetics of plasma adiponectin in men and women. METHODS: We combined genome-wide association scans of three population-based studies including 4659 persons. For the replication stage in 13795 subjects, we selected the 20 top signals of the combined analysis, as well as the 10 top signals with p-values less than 1.0 x 10(-4) for each the men- and the women-specific analyses. We further selected 73 SNPs that were consistently associated with metabolic syndrome parameters in previous genome-wide association studies to check for their association with plasma adiponectin. RESULTS: The ADIPOQ locus showed genome-wide significant p-values in the combined (p=4.3 x 10(-24)) as well as in both women- and men-specific analyses (p=8.7 x 10(-17) and p=2.5 x 10(-11), respectively). None of the other 39 top signal SNPs showed evidence for association in the replication analysis. None of 73 SNPs from metabolic syndrome loci exhibited association with plasma adiponectin (p>0.01). CONCLUSIONS: We demonstrated the ADIPOQ gene as the only major gene for plasma adiponectin, which explains 6.7% of the phenotypic variance. We further found that neither this gene nor any of the metabolic syndrome loci explained the sex differences observed for plasma adiponectin. Larger studies are needed to identify more moderate genetic determinants of plasma adiponectin.

Genetic polymorphisms of the main transcription factors for adiponectin gene promoter in regulation of adiponectin levels: association analysis in three European cohorts.

Adiponectin serum concentrations are an important biomarker in cardiovascular epidemiology with heritability etimates of 30-70%. However, known genetic variants in the adiponectin gene locus (ADIPOQ) account for only 2%-8% of its variance. As transcription factors are thought to play an under-acknowledged role in carrying functional variants, we hypothesized that genetic polymorphisms in genes coding for the main transcription factors for the ADIPOQ promoter influence adiponectin levels. Single nucleotide polymorphisms (SNPs) at these genes were selected based on the haplotype block structure and previously published evidence to be associated with adiponectin levels. We performed association analyses of the 24 selected SNPs at forkhead box O1 (FOXO1), sterol-regulatory-element-binding transcription factor 1 (SREBF1), sirtuin 1 (SIRT1), peroxisome-proliferator-activated receptor gamma (PPARG) and transcription factor activating enhancer binding protein 2 beta (TFAP2B) gene loci with adiponectin levels in three different European cohorts: SAPHIR (n = 1742), KORA F3 (n = 1636) and CoLaus (n = 5355). In each study population, the association of SNPs with adiponectin levels on log-scale was tested using linear regression adjusted for age, sex and body mass index, applying both an additive and a recessive genetic model. A pooled effect size was obtained by meta-analysis assuming a fixed effects model. We applied a significance threshold of 0.0033 accounting for the multiple testing situation. A significant association was only found for variants within SREBF1 applying an additive genetic model (smallest p-value for rs1889018 on log(adiponectin) = 0.002, β on original scale = -0.217 µg/ml), explaining ∼0.4% of variation of adiponectin levels. Recessive genetic models or haplotype analyses of the FOXO1, SREBF1, SIRT1, TFAPB2B genes or sex-stratified analyses did not reveal additional information on the regulation of adiponectin levels. The role of genetic variations at the SREBF1 gene in regulating adiponectin needs further investigation by functional studies.

Mise en place d'un protocole d'insulinothérapie intraveineuse sûr et efficace hors des soins intensifs. [Establishing a protocol for safe intravenous insulin therapy and effective outside intensive care.]

Introductionþ: L'insulinothérapie intraveineuse est la mieux adaptée pour obtenirun contrôle glycémique rapidement efficace ou lors de besoins en insulinechangeants de façon peu prévisible, mais son emploi hors des soins intensifs seheurte souvent aux manque de formation et réticences des soignants. L'inclusionL'inclusiondu contrôle glycémique rapide dans nos standards institutionnels de priseen charge de l'AVC aigu a suscité une demande de protocole thérapeutiqueadapté aux besoins de l'Unité cérébrovasculaire.Patients et méthodesþ: Le protocole d'insulinothérapie a été dérivé d'algorithmespubliés intégrant glycémie actuelle, cinétique glycémique et sensibilité àl'insuline du patient. Aux repas, une augmentation du débit d'insuline iv. pendant1 h a été ajoutée. Les objectifs glycémiques étaient 4-6þmmol/l en préprandialetþ< 8þmmol/l en postprandial. L'implémentation s'est faite à travers unprocessus de co-construction (outils de gestion, documents et activités de formation)avec les responsables médico-infirmiers du service.Résultatsþ: Les données des 90 premiers patients ont été analysées (diabète connuþ:38, hyperglycémie nouvelleþ: 52, 2715h de traitement cumulées). Les duréesd'insulinothérapie iv. étaient de 34,5 h [interquartile 24-39] et 26,5 h [21-36,3] respectivement(pþ=þ0,03), les délais d'atteinte de l'objectif de 5 h [4.0-8.25] et 7 h[4.0-9.75] (pþ=þns.). Pendant les 24 h suivantes, les taux de glycémies dans la cibleétaient de 70,4þ%/81,3þ% (90,3þ%/94,6þ% entre 4-8þmmol/l), avec un faible tauxd'hypoglycémies (3,9þ%/3,1þ%þ< 4,0þmmol/l, 0,4þ%/0,2þ%þ<þ3,3þmmol/l) et un contrôleglycémique postprandial comparable (excursions +2,6þmmol/l [0,7-3,9] et+1,7þmmol/l [0,6-3,7]þ; Nþ=þ75þ; pþ=þns.).Conclusionþ: L'insulinothérapie intraveineuse hors des soins intensifs est faisable,hautement sûre et efficace, même avec des objectifs glycémiques particulièrementstricts. Outre la fiabilité perçue de l'outil de gestion, la démarche departenariat adoptée avec les soignants, permettant la prise en compte de leurspréoccupations à chaque étape du processus, a été un facteur de succès importantpour son implémentation.

Vieillissement: éléments pour une politique de santé publique

[Table des matières] 1. Résumé. 2. Introduction. 3. Evolution démographique. 4. Evolution épidémiologique : infarctus du myocarde, insuffisance cardiaque, accident vasculaire cérébral, diabète, bronchopneumopathie chronique obstructive, cancer en général, cancer pulmonaire, cancer colorectal, cancer du sein, cancer de la prostate, dépression, démence sénile de type Alzheimer et autres démences, syndrome parkinsonien et maladie de Parkinson, maladie rhumatismale, arthrose, lombalgie, ostéoporose et fractures, déficit et dépendance fonctionnels. 5. Réponses sanitaires. 6. Recommandations. 7. Lexique. 8. Index des tableaux. 9. Index des figures. 10-11. Annexes.