The Central role of KNG1 gene as a genetic determinant of coagulation pathway-related traits: Exploring metaphenotypes

Traditional genetic studies of single traits may be unable to detect the pleiotropic effects involved in complex diseases. To detect the correlation that exists between several phenotypes involved in the same biological process, we introduce an original methodology to analyze sets of correlated phenotypes involved in the coagulation cascade in genome-wide association studies. The methodology consists of a two-stage process. First, we define new phenotypic meta-variables (linear combinations of the original phenotypes), named metaphenotypes, by applying Independent Component Analysis for the multivariate analysis of correlated phenotypes (i.e. the levels of coagulation pathway–related proteins). The resulting metaphenotypes integrate the information regarding the underlying biological process (i.e. thrombus/clot formation). Secondly, we take advantage of a family based Genome Wide Association Study to identify genetic elements influencing these metaphenotypes and consequently thrombosis risk. Our study utilized data from the GAIT Project (Genetic Analysis of Idiopathic Thrombophilia). We obtained 15 metaphenotypes, which showed significant heritabilities, ranging from 0.2 to 0.7. These results indicate the importance of genetic factors in the variability of these traits. We found 4 metaphenotypes that showed significant associations with SNPs. The most relevant were those mapped in a region near the HRG, FETUB and KNG1 genes. Our results are provocative since they show that the KNG1 locus plays a central role as a genetic determinant of the entire coagulation pathway and thrombus/clot formation. Integrating data from multiple correlated measurements through metaphenotypes is a promising approach to elucidate the hidden genetic mechanisms underlying complex diseases.Postprint (published version

Influence of ABO locus on PFA-100 collagen-ADP closure time is not totally dependent on the von willebrand factor. Results of a GWAS on gait-2 project phenotypes

(1) Background: In a previous study, we found that two phenotypes related to platelet reactivity, measured with the PFA-100 system, were highly heritable. The aim of the present study was to identify genetic determinants that influence the variability of these phenotypes: Closure time of collagen-ADP (Col-ADP) and of collagen-epinephrine (Col-Epi). (2) Methods: As part of the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia (2) Project, 935 individuals from 35 large Spanish families were studied. A genome-wide association study (GWAS) with ≈ 10 M single nucleotide polymorphisms (SNPs) was carried out with Col-ADP and Col-Epi phenotypes. (3) Results: The study yielded significant genetic signals that mapped to the ABO locus. After adjusting both phenotypes for the ABO genotype, these signals disappeared. After adjusting for von Willebrand factor (VWF) or for coagulation factor VIII (FVIII), the significant signals disappeared totally for Col-Epi phenotype but only partially for Col-ADP phenotype. (4) Conclusion: Our results suggest that the ABO locus exerts the main genetic influence on PFA-100 phenotypes. However, while the effect of the ABO locus on Col-Epi phenotype is mediated through VWF and/or FVIII, the effect of the ABO locus on Col-ADP phenotype is partly produced through VWF and/or FVIII, and partly through other mechanisms

HGF -rs12536657 and Ocular Biometric Parameters in Hyperopic Children, Emmetropic Adolescents, and Young Adults: A Multicenter Quantitative Trait Study

Introduction. Even though ocular refractive state is highly heritable and under strong genetic control, the identification of susceptibility genes remains a challenge. Several HGF (hepatocyte growth factor) gene variants have been associated with ocular refractive errors and corneal pathology. Purpose. Here, we assess the association of an HGF gene variant, previously reported as associated with hyperopia, and ocular biometric parameters in a multicenter Spanish cohort. Methods. An observational prospective multicenter cross-sectional study was designed, including a total of 403 unrelated subjects comprising 188 hyperopic children (5 to 17 years) and 2 control groups: 52 emmetropic adolescents (13 to 17 years) and 163 emmetropic young adults (18 to 28 years). Each individual underwent a comprehensive eye examination including cycloplegic refraction, and topographic and ocular biometric analysis. Genomic DNA was extracted from oral swabs. HGF single nucleotide polymorphism (SNP) rs12536657 was genotyped. Genotypic, allelic, and logistic regression analyses were performed comparing the different groups. A quantitative trait association test analyzing several biometric parameters was also performed using generalized estimating equations (GEEs) adjusting for age and gender. Results. No association between rs12536657 and hyperopia was found through gender-adjusted logistic regression comparing the hyperopic children with either of the two control groups. Significant associations between mean topographic corneal curvature and rs12536657 for G/A (slope = +0.32; CI 95%: 0.04-0.60; p=0.023) and A/A (slope = +0.76; CI 95%: 0.12-1.40; p=0.020) genotypes were observed with the age- and gender-adjusted univariate GEE model. Both flat and steep corneal topographic meridians were also significantly associated with rs12536657 for the G/A and A/A genotypes. No association was found between rs12536657 and any other topographic or biometric measurements. Conclusions. Our results support a possible role for HGF gene variant rs12536657 in corneal curvature in our population. To our knowledge, this is the first multicenter quantitative trait association study of HGF genotypes and ocular biometric parameters comprising a pediatric cohort

On the role of NOS1 ex1f-VNTR in ADHD – allelic, subgroup, and meta-analysis

Attention deficit/hyperactivity disorder (ADHD) is a heritable neurodevelopmental disorder featuring complex genetics with common and rare variants contributing to disease risk. In a high proportion of cases, ADHD does not remit during adolescence but persists into adulthood. Several studies suggest that NOS1, encoding nitric oxide synthase I, producing the gaseous neurotransmitter NO, is a candidate gene for (adult) ADHD. We here extended our analysis by increasing the original sample, adding two further samples from Norway and Spain, and conducted subgroup and co-morbidity analysis. Our previous finding held true in the extended sample, and also meta-analysis demonstrated an association of NOS1 ex1fVNTR short alleles with adult ADHD (aADHD). Association was restricted to females, as was the case in the discovery sample. Subgroup analysis on the single allele level suggested that the repeat allele caused the association. Regarding subgroups, we found that NOS1 was associated with the hyperactive/impulsive ADHD subtype, but not to pure inattention. In terms of comorbidity, major depression, anxiety disorders, cluster C personality disorders and migraine were associated with short repeats, in particular the repeat allele. Also, short allele carriers had significantly lower IQ. Finally, we again demonstrated an influence of the repeat on gene expression in human post-mortem brain samples. These data validate the role of NOS-I in hyperactive/impulsive phenotypes and call for further studies into the neurobiological underpinnings of this association.PostprintPeer reviewe

Diagnosis features of pediatric Gaucher disease patients in the era of enzymatic therapy, a national-base study from the Spanish Registry of Gaucher Disease

Background: The enzymatic replacement therapy (ERT) availability for Gaucher disease (GD) has changed the landscape of the disease, several countries have screening programs. These actions have promoted the early diagnosis and avoided many complications in pediatric patients. In Spain ERT has been available since 1993 and 386 patients have been included in the Spanish Registry of Gaucher Disease (SpRGD). The aim of this study is to analyze the impact of ERT on the characteristics at time of diagnosis and initial complications in pediatric Gaucher disease patients. Aim: To analyze the impact of ERT on the characteristics at time of diagnosis and initial complications in pediatric Gaucher disease patients. Methods: A review of data in SpRGD from patients'' diagnosed before 18 years old was performed. The cohort was split according the year of diagnosis (=1994, cohort A; =1995, cohort B). Results: A total of 98 pediatric patients were included, GD1: 80, GD3: 18; mean age: 7.2 (0.17-16.5) years, 58 (59.2%) males and 40 (40.8%) females. Forty-five were diagnosed = 1994 and 53 = 1995. Genotype: N370S/N370S: 2 (2.0%), N370S/L444P: 27 (27.5%), N370S/other: 47 (48%), L444P/L444P: 7 (7.1%), L444P/D409H: 2 (2.0%), L444P/other: 3 (6.2%), other/other: 10 (10.2%). The mean age at diagnosis was earlier in patients diagnosed after 1995 (p < 0.001) and different between the subtypes, GD1: 8.2 (0.2-16.5) years and GD3: 2.8 (0.17-10.2) years (p < 0.001). There were more severe patients in the group diagnosed before 1994 (p = 0.045) carrying L444P (2), D409H (2), G377S (1), G195W (1) or the recombinant mutation. The patients'' diagnosed =1994 showed worse cytopenias, higher chance of bone vascular complications at diagnosis and previous spleen removal. The patients started ERT at a median time after diagnosis of 5.2 years [cohort A] and 1.6 years [cohort B] (p < 0.001). Conclusions: The early diagnosis of Gaucher disease in the era of ERT availability has permitted to reduce the incidence of severe and irreversible initial complication in pediatric patients, and this has permitted better development of these patients. This is the largest pediatric cohort from a national registry

Pharmacogenetics to Avoid Adverse Drug Reactions

Adverse drug reactions are one of the major constraints when using drugs. These adverse reactions can impact healthcare systems as strongly as many prevalent diseases. Identifying DNA variants associated with adverse drug reactions can help personalize medicine and sustain healthcare systems. This book delves into new advances in pharmacogenetics of cardiovascular, cancer, and nervous system drugs. It may be useful for clinicians and patients to understand the basics of pharmacogenetics

Maternal ABO Blood Phenotype and Factors Associated with Preeclampsia Subtype

Preeclampsia affects 3-8% of all pregnancies and is a global issue that significantly effects the short and long-term health of women and neonates. The pathophysiology of preeclampsia remains unclear and there seems to be two distinct subtypes, early and late onset. Each subtype may have a unique pathophysiology and set of risk factors. Preeclampsia is linked to long-term risk of cardiovascular disease in previously affected women. Subsequently, risk factors shared between preeclampsia and cardiovascular disease should be explored. The main aim of this study was to determine the strength of association between maternal ABO blood type and preeclampsia subtype. This hospital-based case control study was completed at one community hospital in the Mid Atlantic, United States. The study included 126 female subjects with early onset preeclampsia (≤ 33 6/7 weeks gestation), 126 female subjects with late onset preeclampsia (≥ 34 weeks gestation) and 259 control subjects with no history of preeclampsia. Strict diagnostic criteria were used and preeclamptic subjects were classified by subtype based on gestational age at diagnosis. Data on ABO blood type, as well other physical and socio-demographic variables were extracted from the electronic health record. No significant association was noted between preeclampsia subtype and non-O blood type (p=.456) and ABO blood phenotype trended towards significance (p=.062). After exclusion of subjects with comorbidities (CHTN, GDM and DM) from the sample (n=403), there was a significant association noted between ABO blood type and preeclampsia subtype (p=.001). A significant association was also noted between preeclamptic subjects with growth restriction and ABO blood type (p= \u3c.001). Preeclamptic subjects with the B blood type had OR=3.44, 95% CI 1.58, 7.50 of having a growth-restricted fetus than did those with other blood types. Finally, when adjusting for race only, subjects with AB blood type had the following odds (OR=3.03, 95% CI 1.04, 8.80; OR=3.35, 95% CI 1.02, 11.03.) of developing pre-eclampsia and late onset preeclampsia respectively. When other clinical risk factors of preeclampsia are included in the model, AB blood type significantly predicts membership in the early onset preeclampsia subtype (OR=5.41, 95% CI, 1.19, 24.55) and was trend-level in the late onset group (p=.053). Preeclamptic women with B blood type had three times the odds of having a growth-restricted fetus, subsequently; they may require close ultrasound surveillance. AB blood type was significantly associated with three times increased odds of late onset preeclampsia. When included in a model with other common risk factors of preeclampsia, ABO blood type only accounted for a small amount of variability in the model. ABO blood type may not be a valuable addition to a preeclampsia-screening algorithm that already includes common clinical risk factors of preeclampsia. However, when controlling for other common clinical risk factors of preeclampsia, women with AB blood type had over 5 times the odds of developing early onset preeclampsia. Further research is necessary to examine if blood type regulates biomarkers that mediate the development of each preeclampsia subtype or in some way is associated with severe features of the disease

Genetic determinants of rare disorders and complex traits : insights into the genetics of dilated cardiomyopathy and blood cell traits

Les facteurs génétiques peuvent apporter des réponses à plusieurs questions que nous nous posons sur les traits humains, les maladies et la réaction aux médicaments, entre autres. Avec le temps, le développement continu d'outils d'analyse génétique nous a permis d'examiner ces facteurs et de trouver des explications pertinentes. Cette thèse explore plusieurs méthodes et outils génétiques, tels que le séquençage pan-exomique et le génotypage sur puce, dans un contexte d'analyse familial et populationnel pour étudier ces facteurs génétiques qui jouent un rôle dans une maladie rare, la cardiomyopathie dilatée (DCM), et dans deux traits complexes soient les globules rouges et les plaquettes. DCM est une maladie rare qui est définie par un ventricule gauche dilaté et une dysfonction systolique. Environ 30% des cas de DCM sont héréditaires, et plus de 50 gènes ont été associés à un rôle dans la pathogénicité de DCM. Le dépistage génétique est un outil de référence dans la gestion clinique de DCM familiale. Par contre, pour la majorité des patients, les tests génétiques ne parviennent pas à identifier une mutation causale dans un gène candidat. Les cellules sanguines remplissent une variété de fonctions biologiques, incluant le transport de l'oxygène, les fonctions immunologiques, ainsi que la guérison de plaies. Les niveaux de ces cellules et leurs paramètres auxiliaires sont mesurés par un test sanguin, et une différence avec les valeurs optimales peut signifier certains troubles. De plus, ces traits sont étudiés méticuleusement dans le contexte des maladies cardiovasculaires (CVD) où différents niveaux sont associés avec un risque variable de CVD ou sont des prédicteurs de complications de CVD. iii J'ai examiné la DCM et les traits sanguins avec comme objectif de découvrir des nouvelles associations de mutations génétiques. Pour la DCM, j'ai évalué la pertinence d'un séquençage pan-exomique dans un environnement clinique. Je rapporte plusieurs nouvelles mutations dans des gènes candidats (DSP, LMNA, MYH7, MYPN, RBM20, TNNT2) et des mutations nonsenses dans deux gènes nouvellement associés (TTN et BAG3), et je démontre que les mutations nonsenses influencent la maladie d'une manière différente des autres mutations causales. Je rapporte aussi une mutation dans un nouveau gène, FLNC, qui cause une forme rare et distincte de cardiomyopathie. Pour l'étude des traits complexes, dans le grand consortium Blood Cell Consortium (BCX), j'ai utilisé l’exomechip pour disséquer le rôle des variantes rares et communes dans les globules rouges et les plaquettes. J'ai identifié 16 nouvelles régions génomiques associées avec les globules rouges et 15 avec les plaquettes, parmi lesquelles se retrouvent plusieurs variantes de basses fréquences (MAP1A, HNF4A, ITGA2B, APOH), et j'ai démontré un chevauchement significatif de régions associées avec d'autres traits, incluant les lipides. Mes résultats sur la DCM ont mis en évidence le rôle de plusieurs gènes candidats, et suggèrent un traitement différent au niveau de la gestion clinique des patients qui portent des mutations dans BAG3 et FLNC. En ce qui concerne les traits sanguins, mes résultats contribuent à enrichir le répertoire de régions associées avec ces traits, soulignant l'importance de l'utilisation de grands ensembles de données pour détecter les variantes rares ou de basses fréquences. La découverte de gènes dans les maladies rares et les traits complexes contribue à la compréhension des mécanismes sous-jacents qui ultimement favorisera de meilleurs diagnostics, gestions et traitements de maladies.Genetic factors hold within them the answers to many questions we have on human traits, disease, and drug response among others. With time, the continuously advancing genetic tools have enabled us to examine those factors and provided and continue to provide astonishing answers. This thesis utilizes various methods of genetic tools such as exome sequencing and chip-based genotyping data in the context of both family and population-based analyses to interrogate the genetic factors that play a role in a rare disease, dilated cardiomyopathy (DCM), and in two complex traits, red blood cells and platelets. DCM is a rare disease that is defined by a dilated left ventricle and systolic dysfunction. It is estimated that 30% of DCM cases are hereditary and more than 50 genes have been linked to play a role in the pathogenesis of DCM. Genetic screening of known genes is a gold standard tool in the clinical management of familial DCM. However, in the majority of probands, genetic testing fails to identify the causal mutation. Blood cells play a variety of biological functions including oxygen transport, immunological functions, and wound healing. Levels of these cells and their associated indices are measured by a blood test, and deviation from optimal values may indicate certain disorders. Additionally, these traits are heavily studied in the context of cardiovascular disease (CVD) where different levels associate with a variable risk of CVD or are predictors of CVD complications or outcomes (for example, a higher level of white blood cells or lower level of hemoglobin). I examined both DCM and blood cell traits and aimed to discover new mutations and variants that are associated with each. For DCM, I evaluated the value of whole exome vi sequencing in a clinical setting, and I report a number of novel mutations in candidate genes (DSP, LMNA, MYH7, MYPN, RBM20, TNNT2) and truncating mutations in two newly established genes, TTN and BAG3, and I demonstrate that truncating mutations in the latter influence disease differently than other causal mutations. I also report a mutation in a novel gene, FLNC that causes a rare and distinct form of cardiomyopathy. In examining complex traits, I dissected the role of common and rare variants in red blood cells and platelets within a large consortium, the Blood Cell Consortium (BCX) using the ExomeChip, and identified 16 novel loci associated with red blood cell traits and 15 with platelet traits, some of which harbored low-frequency variants (MAP1A, HNF4A, ITGA2B, APOH), and demonstrated a substantial overlap with other phenotypes predominantly lipids. My results on DCM establish the role of a number of candidate genes in this disorder and suggest a different course of clinical management for patients that carry mutations in BAG3 and FLNC. As for blood cell traits, my results contributed to expanding the repertoire of loci associated with red blood cell and platelet traits and illustrate the importance of using large datasets to discover low-frequency or rare variants. Gene discovery in rare disease and complex traits gives insight into the underlying mechanisms which ultimately contributes to a better diagnosis, management, and treatment of disease