Mining the human phenome using allelic scores that index biological intermediates.

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure these variables in individual disease collections.

Local adaptation maintains clinal variation in melanin-based coloration of European barn owls (Tyto alba).

Ecological parameters vary in space, and the resulting heterogeneity of selective forces can drive adaptive population divergence. Clinal variation represents a classical model to study the interplay of gene flow and selection in the dynamics of this local adaptation process. Although geographic variation in phenotypic traits in discrete populations could be remainders of past adaptation, maintenance of adaptive clinal variation requires recurrent selection. Clinal variation in genetically determined traits is generally attributed to adaptation of different genotypes to local conditions along an environmental gradient, although it can as well arise from neutral processes. Here, we investigated whether selection accounts for the strong clinal variation observed in a highly heritable pheomelanin-based color trait in the European barn owl by comparing spatial differentiation of color and of neutral genes among populations. Barn owl's coloration varies continuously from white in southwestern Europe to reddish-brown in northeastern Europe. A very low differentiation at neutral genetic markers suggests that substantial gene flow occurs among populations. The persistence of pronounced color differentiation despite this strong gene flow is consistent with the hypothesis that selection is the primary force maintaining color variation among European populations. Therefore, the color cline is most likely the result of local adaptation.

Estimating gene flow across hybrid zones: how reliable are microsatellites?

Due to their high polymorphism, microsatellites have become one of the most valued genetic markers in population biology. We review the first two published studies on hybrid zones of the common shrew based on microsatellites. Both reveal surprisingly high interracial gene flow. It can be shown that these are overestimates. Indeed, in classical population genetics models as F-statistics, mutation is neglected. This constitutes an acceptable assumption as long as migration is higher than mutation. However, in hybrid zones where genetic exchanges can be rare, neglecting mutation will lead to strong overestimates of migration when working with microsatellites which display mutation rates up to 10(-3). As there seems to be no straightforward way to correct for this bias, interracial gene flow estimates based on microsatellites should be taken with caution. This problem should however not conceal the enormous potential of microsatellites to unravel the genetics of hybrid zones.

Novel method to estimate the phenotypic variation explained by genome-wide association studies reveals large fraction of the missing heritability.

Genome-wide association studies (GWAS) are conducted with the promise to discover novel genetic variants associated with diverse traits. For most traits, associated markers individually explain just a modest fraction of the phenotypic variation, but their number can well be in the hundreds. We developed a maximum likelihood method that allows us to infer the distribution of associated variants even when many of them were missed by chance. Compared to previous approaches, the novelty of our method is that it (a) does not require having an independent (unbiased) estimate of the effect sizes; (b) makes use of the complete distribution of P-values while allowing for the false discovery rate; (c) takes into account allelic heterogeneity and the SNP pruning strategy. We applied our method to the latest GWAS meta-analysis results of the GIANT consortium. It revealed that while the explained variance of genome-wide (GW) significant SNPs is around 1% for waist-hip ratio (WHR), the observed P-values provide evidence for the existence of variants explaining 10% (CI=[8.5-11.5%]) of the phenotypic variance in total. Similarly, the total explained variance likely to exist for height is estimated to be 29% (CI=[28-30%]), three times higher than what the observed GW significant SNPs give rise to. This methodology also enables us to predict the benefit of future GWA studies that aim to reveal more associated genetic markers via increased sample size.

A comparison of Bayesian and frequentist approaches to incorporating external information for the prediction of prostate cancer risk.

We present the most comprehensive comparison to date of the predictive benefit of genetics in addition to currently used clinical variables, using genotype data for 33 single-nucleotide polymorphisms (SNPs) in 1,547 Caucasian men from the placebo arm of the REduction by DUtasteride of prostate Cancer Events (REDUCE®) trial. Moreover, we conducted a detailed comparison of three techniques for incorporating genetics into clinical risk prediction. The first method was a standard logistic regression model, which included separate terms for the clinical covariates and for each of the genetic markers. This approach ignores a substantial amount of external information concerning effect sizes for these Genome Wide Association Study (GWAS)-replicated SNPs. The second and third methods investigated two possible approaches to incorporating meta-analysed external SNP effect estimates - one via a weighted PCa 'risk' score based solely on the meta analysis estimates, and the other incorporating both the current and prior data via informative priors in a Bayesian logistic regression model. All methods demonstrated a slight improvement in predictive performance upon incorporation of genetics. The two methods that incorporated external information showed the greatest receiver-operating-characteristic AUCs increase from 0.61 to 0.64. The value of our methods comparison is likely to lie in observations of performance similarities, rather than difference, between three approaches of very different resource requirements. The two methods that included external information performed best, but only marginally despite substantial differences in complexity.

Recombination is suppressed and variability reduced in a nascent Y chromosome.

Several hypotheses have been elaborated to account for the evolutionary decay commonly observed in full-fledged Y chromosomes. Enhanced drift, background selection and selective sweeps, which are expected to result from reduced recombination, may all share responsibilities in the initial decay of proto-Y chromosomes, but little empirical information has been gathered so far. Here we take advantage of three markers that amplify on both of the morphologically undifferentiated sex chromosomes of the European tree frog (Hyla arborea) to show that recombination is suppressed in males (the heterogametic sex) but not in females. Accordingly, genetic variability is reduced on the Y, but in a way that can be accounted for by merely the number of chromosome copies per breeding pair, without the need to invoke background selection or selective sweeps.

Searching for sex-reversals to explain population demography and the evolution of sex chromosomes.

Sex determination can be purely genetic (as in mammals and birds), purely environmental (as in many reptiles), or genetic but reversible by environmental factors during a sensitive period in life, as in many fish and amphibians (Wallace et al. 1999; Baroiller et al. 2009a; Stelkens & Wedekind 2010). Such environmental sex reversal (ESR) can be induced, for example, by temperature changes or by exposure to hormone-active substances. ESR has long been recognized as a means to produce more profitable single-sex cultures in fish farms (Cnaani & Levavi-Sivan 2009), but we know very little about its prevalence in the wild. Obviously, induced feminization or masculinization may immediately distort population sex ratios, and distorted sex ratios are indeed reported from some amphibian and fish populations (Olsen et al. 2006; Alho et al. 2008; Brykov et al. 2008). However, sex ratios can also be skewed by, for example, segregation distorters or sex-specific mortality. Demonstrating ESR in the wild therefore requires the identification of sex-linked genetic markers (in the absence of heteromorphic sex chromosomes) followed by comparison of genotypes and phenotypes, or experimental crosses with individuals who seem sex reversed, followed by sexing of offspring after rearing under non-ESR conditions and at low mortality. In this issue, Alho et al. (2010) investigate the role of ESR in the common frog (Rana temporaria) and a population that has a distorted adult sex ratio. They developed new sex-linked microsatellite markers and tested wild-caught male and female adults for potential mismatches between phenotype and genotype. They found a significant proportion of phenotypic males with a female genotype. This suggests environmental masculinization, here with a prevalence of 9%. The authors then tested whether XX males naturally reproduce with XX females. They collected egg clutches and found that some had indeed a primary sex ratio of 100% daughters. Other clutches seemed to result from multi-male fertilizations of which at least one male had the female genotype. These results suggest that sex-reversed individuals affect the sex ratio in the following generation. But how relevant is ESR if its prevalence is rather low, and what are the implications of successful reproduction of sex-reversed individuals in the wild?

Inbreeding and selection on sex ratio in the bark beetle Xylosandrus germanus.

ABSTRACT: BACKGROUND: Local Mate Competition (LMC) theory predicts a female should produce a more female-biased sex ratio if her sons compete with each other for mates. Because it provides quantitative predictions that can be experimentally tested, LMC is a textbook example of the predictive power of evolutionary theory. A limitation of many earlier studies in the field is that the population structure and mating system of the studied species are often estimated only indirectly. Here we use microsatellites to characterize the levels of inbreeding of the bark beetle Xylosandrus germanus, a species where the level of LMC is expected to be high. RESULTS: For three populations studied, genetic variation for our genetic markers was very low, indicative of an extremely high level of inbreeding (FIS = 0.88). There was also strong linkage disequilibrium between microsatellite loci and a very strong genetic differentiation between populations. The data suggest that matings among non-siblings are very rare (3%), although sex ratios from X. germanus in both the field and the laboratory have suggested more matings between non-sibs, and so less intense LMC. CONCLUSIONS: Our results confirm that caution is needed when inferring mating systems from sex ratio data, especially when a lack of biological detail means the use of overly simple forms of the model of interest.

Population genetics of Capercaillie (Tetrao urogallus) in the Jura and the Pyrenees: a non-invasive approach to avian conservation genetics

RÉSUMÉ Le Grand tétras est un galliforme de montagne apparenté au faisan et au tétras lyre. Il est distribué de manière continue à travers la toundra et les montagnes de moyenne altitude en Europe de l'ouest. Toutefois, les populations d'Europe de l'ouest ont subi un déclin constant au cours des derniers siècles. Les causes de ce déclin sont probablement liées à l'activité humaine, telle .que l'élevage ou le tourisme, qui ont engendré une modification et une fragmentation de l'habitat de l'espèce. Malheureusement, les populations soumises à de forts déclins démographiques peuvent subir des effets génétiques (augmentation de la consanguinité et perte de diversité génétique) pouvant diminuer leur potentiel de reproduction et conduire irrémédiablement à l'extinction. Cette thèse présente les analyses conduites dans le but d'estimer l'impact du déclin démographique des populations de Grand tétras sur l'étendue et la distribution de leur variabilité génétique dans le Jura et dans les Pyrénées. Du fait de la législation locale protégeant les tétraonidés en général, mais également en raison de la biologie très cryptique du Grand tétras, l'ensemble des analyses de cette étude a été réalisé à partir de matériel génétique extrait des fientes (ou échantillonnage génétique non invasif). Dans la première partie de l'étude, je détaille les protocoles d'extraction. d'ADN et d'amplification par PCR modifiés à partir des protocoles classiques utilisant des échantillons conventionnels, riches en ADN. L'utilisation d'ADN fécal impose des contraintes dues à la mauvaise qualité et à la faible quantité du matériel génétique à disposition dans les fientes. Ces contraintes ont pu être partiellement contournées en réalisant des répétitions multiples du génotypage afin d'obtenir un degré de fiabilité suffisante. J'ai également analysé les causes de la dégradation de l'ADN dans les excréments. Parmi les causes les plus communes, telles que l'activité bactérienne, l'hydrolyse spontanée et la dégradation enzymatique par les DNases libres, c'est ce dernier facteur qui apparaît comme étant la cause majeure et la plus rapide responsable de la dégradation de la qualité des échantillons. La rapidité de l'action enzymatique suggère que les plans d'échantillonnages de excréments sur le terrain pourraient être optimisés en les réalisant dans des conditions climatiques froides et sèches, favorisant ainsi l'inhibition des DNases. La seconde partie de la thèse est une étude par simulation visant à déterminer la capacité du logiciel Structure à identifier les structures génétiques complexes et hiérarchiques fréquemment rencontrées dans les populations naturelles, et ce en utilisant différents types de marqueurs génétiques. Les troisième et quatrième parties de cette thèse décrivent le statut génétique des populations résiduelles du Jura et des Pyrénées à partir de l'analyse de 11 loci microsatellites. Nous n'avons pas pu mettre en évidence dans les deux populations des effets liés à la consanguinité ou à la réduction de la diversité génétique. De plus, la différenciation génétique entre les patches d'habitats favorables reste modérée et corrélée à la distance géographique, ce qui suggère que la dispersion d'individus entre les patches a été importante au moins pendant ces dernières générations. La comparaison des paramètres de la diversité génétique avec ceux d'autres populations de Grand tétras, ou d'autres espèces proches, indique que la population du Jura a retenu une proportion importante de sa diversité originelle. Ces résultats suggèrent que le déclin récent des populations a jusqu'ici eu un impact modéré sur les facteurs génétiques et que ces populations semblent avoir conservé le potentiel génétique nécessaire à leur survie à long terme. Finalement, en cinquième partie, l'analyse de l'apparentement entre les mâles qui participent à la parade sur les places de chant (leks) indique que ces derniers sont distribués en agrégats de manière non aléatoire, préférentiellement entre individus apparentés. De plus, la corrélation entre les distances génétique et géographique entre les leks est en accord avec les motifs d'isolement par la distance mis en évidence à d'autres niveaux hiérarchiques (entre patches d'habitat et populations), ainsi qu'avec les études menées sur d'autres espèces ayant choisi ce même système de reproduction. En conclusion, cette première étude basée uniquement sur de l'ADN nucléaire aviaire extrait à partir de fèces a fourni des informations nouvelles qui n'auraient pas pu être obtenues par une méthode d'observation sur le terrain ou d'échantillonnage génétique classique. Aucun oiseau n'a été dérangé ou capturé, et les résultats sont comparables à d'autres études concernant des espèces proches. Néanmoins, la taille de ces populations approche des niveaux au-dessous desquels la survie à long terme est fortement incertaine. La persistance de la diversité génétique pour les prochaines générations reste en conséquence liée à la survie des adultes et à une reprise du succès de la reproduction. ABSTRACT Capercaillie (Tetrao urogallus) is a large grouse that is continuously distributed across the tundra and the mid-high mountains of Western Europe. However, the populations in Western Europe have been showing a constant decline during the last decades. The causes for this decline are possibly related to human activities, such as cattle breeding and tourism that have both led to habitat modification and fragmentation. Unfortunately, populations that have undergone drastic demographic bottlenecks often go through genetic processes of inbreeding and loss of diversity that decrease their fitness and eventually lead to extinction. This thesis presents the investigations conducted to estimate the impact of the demographic decline of capercaillie populations on the extent and distribution of their genetic variability in the Jura and in the Pyrenees mountains. Because grouse are protected by wildlife legislation, and also because of the cryptic behaviour of capercaillie, all DNA material used in this study was extracted from faeces (non-invasive genetic sampling). In the first part of my thesis, I detail the protocols of DNA extraction and PCR amplification adapted from classical methods using conventional DNA-rich samples. The use of faecal DNA imposes specific constraints due to the low quantity and the highly degraded genetic material available. These constraints are partially overcome by performing multiple genotyping repetitions to obtain sufficient reliability. I also investigate the causes of DNA degradation in faeces. Among the main degraders, namely bacterial activity, spontaneous hydrolysis, and free-¬DNase activities, the latter was pointed out as the most important according to our experiments. These enzymes degrade DNA very rapidly, and, as a consequence, faeces sampling schemes must be planned preferably in cold and dry weather conditions, allowing for enzyme activity inhibition. The second part of the thesis is a simulation study aiming to assess the capacity of the software Structure to detect population structure in hierarchical models relevant to situations encountered in wild populations, using several genetic markers. The methods implemented in Structure appear efficient in detecting the highest hierarchical structure. The third and fourth parts of the thesis describe the population genetics status of the remaining Jura and Pyrenees populations using 11 microsatellite loci. In either of these populations, no inbreeding nor reduced genetic diversity was detected. Furthermore, the genetic differentiation between patches defined by habitat suitability remains moderate and correlated with geographical distance, suggesting that significant dispersion between patches was at work at least until the last generations. The comparison of diversity indicators with other species or other populations of capercaillie indicate that population in the Jura has retained a large part of its original genetic diversity. These results suggest that the recent decline has had so forth a moderate impact on• genetic factors and that these populations might have retained the potential for long term survival, if the decline is stopped. Finally, in the fifth part, the analysis of relatedness between males participating in the reproduction parade, or lek, indicate that capercaillie males, like has been shown for some other grouse species, gather on leks• among individuals that are more related than the average of the population. This pattern appears to be due to both population structure and kin-association. As a conclusion, this first study relying exclusively on nuclear DNA extracted from faeces has provided novel information that was not available through field observation or classical genetic sampling. No bird has been captured or disturbed, and the results are consistent with other studies of closely related species. However, the size of these populations is approaching thresholds below which long-term survival is unlikely. The persistence of genetic diversity for the forthcoming generations remains therefore bond to adult survival and to the increase of reproduction success.

Sex-chromosome differentiation and 'sex races' in the common frog (Rana temporaria).

Sex-chromosome differentiation was recently shown to vary among common frog populations in Fennoscandia, suggesting a trend of increased differentiation with latitude. By rearing families from two contrasted populations (respectively, from northern and southern Sweden), we show this disparity to stem from differences in sex-determination mechanisms rather than in XY-recombination patterns. Offspring from the northern population display equal sex ratios at metamorphosis, with phenotypic sexes that correlate strongly with paternal LG2 haplotypes (the sex chromosome); accordingly, Y haplotypes are markedly differentiated, with male-specific alleles and depressed diversity testifying to their smaller effective population size. In the southern population, by contrast, a majority of juveniles present ovaries at metamorphosis; only later in development do sex ratios return to equilibrium. Even at these later stages, phenotypic sexes correlate only mildly with paternal LG2 haplotypes; accordingly, there are no recognizable Y haplotypes. These distinct patterns of gonadal development fit the concept of 'sex races' proposed in the 1930s, with our two populations assigned to the 'differentiated' and 'semi-differentiated' races, respectively. Our results support the suggestion that 'sex races' differ in the genetic versus epigenetic components of sex determination. Analysing populations from the 'undifferentiated race' with high-density genetic maps should help to further test this hypothesis.

Evaluation of serum myostatin and sclerostin levels in chronic spinal cord injured patients.

STUDY DESIGN: Case-control study. OBJECTIVES: To assess serum myostatin levels, bone mineral density (BMD), appendicular skeletal muscle mass (ASMM) and serum sclerostin levels in chronic spinal cord injured (SCI) patients and healthy controls. SETTING: SCI centre in Italy. METHODS: Blood samples, whole-body bioelectrical impedance analysis and BMD measurement with the ultrasound technique at the calcaneus level were taken from patients suffering from chronic SCI (both motor complete and incomplete) and healthy control subjects. RESULTS: A total of 28 SCI patients and 15 healthy controls were enrolled. Serum myostatin levels were statistically higher (P<0.01) in SCI patients compared with healthy controls. Similar results were found comparing both the motor complete and the motor incomplete SCI subgroups to healthy controls. Serum sclerostin was significantly higher in patients with SCI compared with healthy controls (P<0.01). BMD, stiffness and mean T-score values in SCI patients were significantly lower than those in healthy controls. Serum myostatin concentrations in the motor complete SCI subgroups correlated only with serum sclerostin levels (r(2)=0.42; P=0.001) and ASMM (r(2)=0.70; P=0.002) but not in healthy controls. DISCUSSION: Serum myostatin and serum sclerostin are significantly higher in chronic SCI patients compared with healthy controls. They are potential biomarkers of muscle and bone modifications after SCI. This is the first study reporting an increase in serum myostatin in patients suffering from chronic SCI and a correlation with ASMM.

Genetics-Based Population Pharmacokinetics and Pharmacodynamics of Risperidone in a Psychiatric Cohort.

BACKGROUND: High interindividual variability in plasma concentrations of risperidone and its active metabolite, 9-hydroxyrisperidone, may lead to suboptimal drug concentration. OBJECTIVE: Using a population pharmacokinetic approach, we aimed to characterize the genetic and non-genetic sources of variability affecting risperidone and 9-hydroxyrisperidone pharmacokinetics, and relate them to common side effects. METHODS: Overall, 150 psychiatric patients (178 observations) treated with risperidone were genotyped for common polymorphisms in NR1/2, POR, PPARα, ABCB1, CYP2D6 and CYP3A genes. Plasma risperidone and 9-hydroxyrisperidone were measured, and clinical data and common clinical chemistry parameters were collected. Drug and metabolite concentrations were analyzed using non-linear mixed effect modeling (NONMEM(®)). Correlations between trough concentrations of the active moiety (risperidone plus 9-hydroxyrisperidone) and common side effects were assessed using logistic regression and linear mixed modeling. RESULTS: The cytochrome P450 (CYP) 2D6 phenotype explained 52 % of interindividual variability in risperidone pharmacokinetics. The area under the concentration-time curve (AUC) of the active moiety was found to be 28 % higher in CYP2D6 poor metabolizers compared with intermediate, extensive and ultrarapid metabolizers. No other genetic markers were found to significantly affect risperidone concentrations. 9-hydroxyrisperidone elimination was decreased by 26 % with doubling of age. A correlation between trough predicted concentration of the active moiety and neurologic symptoms was found (p = 0.03), suggesting that a concentration >40 ng/mL should be targeted only in cases of insufficient, or absence of, response. CONCLUSIONS: Genetic polymorphisms of CYP2D6 play an important role in risperidone, 9-hydroxyrisperidone and active moiety plasma concentration variability, which were associated with common side effects. These results highlight the importance of a personalized dosage adjustment during risperidone treatment.

Pharmacogenetic and clinical study on adverse effects induced by psychotropic drugs

Second-generation antipsychotics (SGAs) have become the first-line antipsychotic treatment for psychotic disorders due to their better overall tolerance compared to classical antipsychotics. However, metabolic side effects such as weight gain are frequently described during treatment with SGAs and/or other psychotropic drugs including some antidepressants and mood stabilizers, which may also result in poor adherence to treatment. The aim of this work was to investigate different methods to predict common side effects, in particular weight gain during treatment with weight gain inducing psychotropic drugs. Firstly, clinical data were used to determine the potential predictive power of a one month weight gain on weight increase after three and 12 months of treatment (n=351 patients). A fast and strong weight gain of >5% after a period of one month (>5%WG) was found to be the best predictor for an important weight gain at three (>15%) and 12 months (>20%). Similar analyses in an independent cohort of psychiatric adolescents (n=42), showed that a comparable >4% weight gain at one month is the best predictor for an important weight gain at three months (>15%). Secondly, we aimed to determine whether an extensive analysis of genes could be used, in addition to clinical factors, to predict patients at risk for >5%WG or for type 2 diabetes (T2D). Adding genetic markers to clinical variables to predict >5%WG increased significantly the area under the curve (AUC) of the analysis (AUCfinai:0.92, AUCdmicai:0.75, pcO.OOOl, n=248). Conversely, genetic risk scores were found to be associated with T2D (OR: 2.5, p=0.03, n=285) but without a significant increase of AUC'when compared to the prediction based to clinical factors alone. Finally, therapeutic drug monitoring was used to predict extrapyramidal symptoms during risperidone treatment (n=150). Active moiety (sum of risperidone and of its active metabolite 9- hydroxyrisperidone plasma concentrations) of >40 ng/ml should be targeted only in case of insufficient response. These results highlight different approaches for personalizing psychotropic treatments in order to reduce related side effects. Further research is needed, in particular on the identification of genetic markers, to improve the implementation of these results into clinical practice. Résumé Les antipsychotiques atypiques (APA) sont devenus le traitement antipsychotique de première intention pour le traitement des psychoses, grâce à un profil d'effets secondaires plus favorables comparé aux antipsychotiques typiques. Néanmoins, d'autres effets indésirables d'ordre métabolique (ex. prise pondérale) sont observés sous APA, stabilisateurs de l'humeur et/ou certains antidépresseurs, pouvant aussi limiter l'adhérence au traitement. L'objectif de ce travail est d'explorer différentes méthodes permettant de prédire des effets secondaires courants, en particulier la prise de poids durant un traitement avec des psychotropes pouvant induire un tel effet. Dans une première partie, des données cliniques ont été évaluées pour leurs potentiels prédictifs d'une prise de poids à un mois sur une prise de poids à trois et 12 mois de traitement (n=351 patients). Une prise de poids rapide et forte >5% à un mois (PP>5%) s'est avérée être le meilleur prédicteur pour une prise pondérale importante à trois (>15%) et 12 (>20%) mois de traitement. Des analyses similaires dans une cohorte pédiatrique (n=42) ont indiqué une prise de poids >4% à un mois comme le meilleur prédicteur pour une prise pondérale importante (>15%) à trois mois de traitement. Dans une deuxième partie, des marqueurs génétiques, en complément aux données cliniques, ont été analysés pour leur contribution potentielle à la prédiction d'une PP>5% et au dépistage du diabète de type 2 (DT2). L'ajout de variants génétiques aux données cliniques afin de prédire une PP>5% a augmenté significativement l'aire sous la courbe (ASC) de l'analyse (ASCflnai:0.92, ASCC|inique:0.75, p<0.0001, n=248). Concernant le DT2, un score génétique est associé au DT2 (OR: 2.5, p=0.03, n=285), néanmoins aucune augmentation significative de l'ASC n'a été observée par rapport à l'analyse avec les données cliniques seules. Finalement, des mesures de concentrations plasmatiques de médicaments ont été utilisées pour prédire la survenue de symptômes extrapyramidaux sous rispéridone (n=150). Cette analyse nous a permis d'établir qu'une concentration plasmatique de rispéridone associée à son métabolite actif >40 ng/ml ne devrait être recherchée qu'en cas de réponse clinique insuffisante. Ces différents résultats soulignent différentes approches pour personnaliser la prescription de psychotropes afin de réduire la survenue d'effets secondaires. Des études supplémentaires sont néanmoins nécessaires, en particulier sur l'identification de marqueurs génétiques, afin d'améliorer l'implémentation de ces résultats en pratique clinique. Résumé large publique Les antipsychotiques atypiques et autres traitements psychotropes sont couramment utilisés pour traiter les symptômes liés à la schizophrénie et aux troubles de l'humeur. Comme pour tout médicament, des effets secondaires sont observés. L'objectif de ce travail est d'explorer différentes méthodes qui permettraient de prédire la survenue de certains effets indésirables, en particulier une prise de poids et la survenue d'un diabète. Dans une première partie, nous avons évalué l'effet d'une prise de poids précoce sur une prise de poids au long terme sous traitement psychotrope. Les analyses ont mis en évidence dans une population psychiatrique qu'une prise de poids à un mois >5% par rapport au poids initial permettait de prédire une prise pondérale importante après trois (>15%) et 12 (>20%) mois de traitement. Un résultat semblable a. été observé dans un autre groupe de patients exclusivement pédiatriques. Dans une deuxième partie, nous avons évalué la contribution potentielle de marqueurs génétiques à la prédiction d'une prise pondérale de >5% après un mois de traitement ainsi que dans la survenue d'un diabète de type 2. Pour la prise de poids, la combinaison des données génétiques aux données cliniques a permis d'augmenter de 17% la précision de la prédiction, en passant de 70% à 87%. Concernant la survenue d'un diabète, les données génétiques n'ont pas amélioré la prédiction. Finalement, nous avons analysé la relation possible entre les concentrations sanguines d'un antipsychotique atypique couramment utilisé, la rispéridone, et la survenue d'effets secondaires (ici les tremblements). Il est ressorti de cette étude qu'une concentration plasmatique du médicament supérieure à 40 ng/ml ne devrait être dépassée qu'en cas de réponse thérapeutique insuffisante, au risque de voir augmenter la survenue d'effets secondaires du type tremblements. Ces résultats démontrent la possibilité de prédire avec une bonne précision la survenue de certains effets secondaires. Cependant, en particulier dans le domaine de la génétique, d'autres études sont nécessaires afin de confirmer les résultats obtenus dans nos analyses. Une fois cette étape franchie, il serait possible d'utiliser ces outils dans la pratique clinique. A terme, cela pourrait permettre au prescripteur de sélectionner les traitements les mieux adaptés aux profils spécifiques de chaque patient.

Clinical and genetic investigation of a large Tunisian family with complete achromatopsia: identification of a new nonsense mutation in GNAT2 gene.

Complete achromatopsia is a rare autosomal recessive disease associated with CNGA3, CNGB3, GNAT2 and PDE6C mutations. This retinal disorder is characterized by complete loss of color discrimination due to the absence or alteration of the cones function. The purpose of the present study was the clinical and the genetic characterization of achromatopsia in a large consanguineous Tunisian family. Ophthalmic evaluation included a full clinical examination, color vision testing and electroretinography. Linkage analysis using microsatellite markers flanking CNGA3, CNGB3, GNAT2 and PDE6C genes was performed. Mutations were screened by direct sequencing. A total of 12 individuals were diagnosed with congenital complete achromatopsia. They are members of six nuclear consanguineous families belonging to the same large consanguineous family. Linkage analysis revealed linkage to GNAT2. Mutational screening of GNAT2 revealed three intronic variations c.119-69G>C, c.161+66A>T and c.875-31G>C that co-segregated with a novel mutation p.R313X. An identical GNAT2 haplotype segregating with this mutation was identified, indicating a founder mutation. All patients were homozygous for the p.R313X mutation. This is the first report of the clinical and genetic investigation of complete achromatopsia in North Africa and the largest family with recessive achromatopsia involving GNAT2; thus, providing a unique opportunity for genotype-phenotype correlation for this extremely rare condition.