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Öğe A study of cancer-related genes: Prevalence of polymorphic GSTT1 and GSTM1 deletions in Turkey(2013) Karaca, Şefayet; Karaca, Mehmet; Kaymaz, AyşeThe major burden of cancer in the general population is results from the complex interactions of multiple genetic and environmental factors over time. Population based studies support the involvement of GSTM1 and GSTT1 deletion in susceptibility to commonly occurring forms of cancer. The aim of this study was to determine frequency of GSTM1 and GSTT1 deletion variants in Turkish population. Deletion polymorphisms were screened in a collection of samples n=507 for GSTM1 and n=464 for GSTT1. After isolation of DNAs from whole blood, sequences of interest were amplified and then analyzed by electrophoretic methods in the presence of positive and negative controls. Allele frequencies were detected as 52% for GSTM1 and 24% for GSTT1 deletion polymorphisms. The obtained frequencies were consistent with the values that reported for different populations. Cancer is a disease of the genome and identification of the genetic characteristics of healthy individuals is important in determining of current risks, developing of preventive health care models and medical follow-up programs to reducing risk of diseases. However, during the treatment process it allows the selection of optimal therapy.Öğe Allergy-specific phenome-wide association study for ımmunogenes in Turkish children(Nature Publishing Group, 2016) Karaca, Şefayet; Civelek, Ersoy; Karaca, Mehmet; Şahiner, Ümit M.; Özgul, Rıza K.; Kocabaş, Can N.; Polimanti, Renato; Sekerel, Bülent E.To dissect the role of immunogenetics in allergy and asthma, we performed a phenome-wide association study in 974 Turkish children selected from a cross-sectional study conducted using ISAAC (International Study of Asthma and Allergies in Children) Phase II tools. We investigated 9 loci involved in different immune functions (ADAM33, ADRB2, CD14, IL13, IL4, IL4R, MS4A2, SERPINE1, and TNF) with respect to 116 traits assessed through blood tests, hypertonic saline challenge tests, questionnaires, and skin prick tests. Multiple associations were observed for ADAM33: rs2280090 was associated with reduced MEF240% (i.e., the ratio of Mean Expiratory Flow after 240s of hypertonic saline inhalation with respect to the age-and ancestry-matched reference value) and with an increased risk of allergic bronchitis (p = 1.77*10(-4) and p = 7.94*10(-4), respectively); rs3918396 was associated with wheezing and eczema comorbidity (p = 3.41*10(-4)). IL4 rs2243250 was associated with increased FEV240 (Forced Expiratory Flow Volume after 240s of hypertonic saline inhalation; p = 4.81*10(-4)) and CD14 rs2569190 was associated with asthma diagnosis (p = 1.36*10(-3)). ADAM33 and IL4 appeared to play a role in the processes linked to allergic airway inflammation and lung function. Due to its association with wheezing and eczema comorbidity, ADAM33 may also be involved in the atopic march.Öğe Bronşial hiperreaktivite (Bhr) ve astımda genotip-fenotip ilişkisi(Tübitak, 2016) Karaca, Şefayet; Kocabaç, Can; Özgül, R. Köksal; Şekerel, E. Bülent; Kalaycı, C. Ömer; Karaca, Mehmet; Civelek, Ersoy; Şahiner, MuratAstım ve allerjik hastalıklara yatkınlıklar risk allelleri ve çevresel faktörlerin karmaşık etkileşiminin bir sonucudur. Bu yatkınlıklar poligenik ve kalıtılır özelliklerle ilişkilidir. Bugün, astım ve allerjik hastalıkların patogenezinde önemli olan çok sayıda lokus ve risk alleli bilinmektedir. Bu çalışmada, immun fonksiyonda önemli olan bazı genlerin BHR, allerji ve astım bağlantılı fenotiplerde rolünün belirlenmesi amacıyla, kan analizleri, bronş provakasyon testi, deri testleri ve ISSAC anketi ile elde edilen, solunum sistemi hastalıkları ile ilişkili 116 özellik analiz edilmiştir. İmmun fonksiyonda önemli olan 9 farklı gen (ADAM33, ADRB2, IL13, IL4, IL4R, MS4A2, CD14, SERPINE1 ve TNF) allerji-astım fenotipi ile süreklilik arz eden bağlantıları nedeniyle seçilmiştir. Bu genlere ait 21 polimorfik variant, ISSAC Faz II yöntemi kullanılarak sağlanmış olan 960 katılımcıya ait DNA örneklerinde Kompetatif Allel Spesifik PCR (KASP) tekniği kullanılarak genotiplenmiştir. Veriler, bilinen lokuslarda yeni fenotipik ilişkilerin belirlenmesinde etkin olduğu vurgulanan Phenome-wide association studies (PheWAS) kullanılarak analiz edilmiştir. Bunun yanısıra bakılan genetik özellikler için haplotip grupları belirlenerek populasyon içi ve populasyonlar arası benzerlik ve farklılıklar araştırılmıştır. İmmunogenetik farklılıkların belirlenmesi için 480 sağlıklı bireyde haplotip analizi sonuçları 1000 Genom Projesi Faz 3 kapsamındaki 5 atasal gruptan 26 farklı populasyonla karşılaştırılmıştır. Son olarak Türk ve Avrupa populasyonlarında farklı dağılım sergileyen ve immunogenetik lokuslar üzerine fonksiyonel etkileri olan haplotipler belirlenmiştir.Öğe Genetic diversity of disease-associated loci in Turkish population(Nature Publishing Group, 2015) Karaca, Şefayet; Cesuroğlu, Tomris; Karaca, Mehmet; Erge, Sema; Polimanti, RenatoMany consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.Öğe GSTM1, GSTP1, and GSTT1 genetic variability in Turkish and worldwide populations(Wiley-Blackwell, 2015) Karaca, Şefayet; Karaca, Mehmet; Cesuroğlu, Tomris; Erge, Sema; Polimanti, RenatoObjective: Glutathione S-transferase (GST) variants have been widely investigated to better understand their role in several pathologic conditions. To our knowledge, no data about these genetic polymorphisms within the Turkish population are currently available. The aim of this study was to analyze GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V (rs1695), and GSTP1*A114V (rs1138272) variants in the general Turkish population, to provide information about its genetic diversity, and predisposition to GST-related diseases. Methods: Genotyping was performed in 500 Turkish individuals using the Sequenom MassARRAY platform. A comparative analysis was executed using the data from the HapMap and Human Genome Diversity Projects (HGDP). Sequence variation was deeply explored using the Phase 1 data of the 1,000 Genomes Project. ResultsThe variability of GSTM1, GSTT1, and GSTP1 polymorphisms in the Turkish population was similar to that observed in Central Asian, European, and Middle Eastern populations. The high linkage disequilibrium between GSTP1*I105V and GSTP1*A114V in these populations may have a confounding effect on GSTP1 genetic association studies. In analyzing GSTM1, GSTT1, and GSTP1 sequence variation, we observed other common functional variants that may be candidates for associated studies of diseases related to GST genes (e.g., cancer, cardiovascular disease, and allergy). Conclusions: This study provides novel data about GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V, and GSTP1*A114V variants in the Turkish population, and other functional variants that may affect GSTM1, GSTT1, and GSTP1 functions among worldwide populations. This information can assist in the design of future genetic association studies investigating oxidative stress-related diseases. Am. J. Hum. Biol. 27:310-316, 2015. (c) 2014 Wiley Periodicals, Inc.Öğe Haplotype analysis of non-HLA immunogenetic loci in Turkish and worldwide populations(Elsevier Science Bv, 2016) Karaca, Şefayet; Karaca, Mehmet; Civelek, Ersoy; Özgül, Rıza Köksal; Şekerel, Bülent Enis; Polimanti, RenatoImmunogenes (i.e., genes related to the immune system and its functions) are involved in the predisposition to numerous traits and their variation contributes to the phenotypic variability observed among human groups. Turkish population presents particular genetic features since its genetic pool is an admixture of European, Middle-Eastern, and Central Asian ancestries. Here, we analyzed the haplotype structure of four immunogenetic loci (i.e., ADAM33; IL13-IL4; IL4R; MS4A2) in 482 subjects from five different regions of Turkey. Genotyping was performed using KASP technology. Turkish data were compared with the haplotype information available from the 1000 Genomes Project Phase 3 (26 human populations from 5 ancestry groups). We did not observe significant differences among Turkish groups. Comparing other ancestries, we identified haplotype similarity of Turkish subjects with European populations in IL13-1L4, IL4R, and ADAM33 loci; and with central Asians in MS4A2 region. Considering loci displaying Turkish-European haplotype similarity (i.e., IL13-1L4, IL4R, and ADAM33), we observed differences between Turkish subjects and northern/western Europeans. Conversely, no significant difference was determined in MS4A2 between Turkish and central Asian populations. Finally, we assessed the haplotypes responsible for the differences between Turkish and European samples and the potential functional effects on the immunogenetic loci investigated. (C) 2016 Elsevier B.V. All rights reserved.Öğe Haplotypic similarity in immunogenes of Turkish population with Europeans and Central Asians(Wiley-Blackwell, 2016) Karaca, Şefayet; Karaca, Mehmet; Civelek, Ersoy; Şekerel, Bülent Enis; Polimanti, Renato[Abstract Not Available]Öğe High prevalence of cerebral venous sinus thrombosis (CVST) as presentation of cystathionine beta-synthase deficiency in childhood: Molecular and clinical findings of Turkish probands(Elsevier Science Bv, 2014) Karaca, Mehmet; Hismi, Burcu; Özgul, Riza Koksal; Karaca, Şefayet; Yılmaz, Didem Yücel; Coşkun, Turgay; Sivri, Hatice Serap; Tokatlı, Ayşegül; Dursun, AliClassical homocystinuria is the most commonly inherited disorder of sulfur metabolism, caused by the genetic alterations in human cystathionine beta-synthase (CBS) gene. In this study, we present comprehensive clinical findings and the genetic basis of homocystinuria in a cohort of Turkish patients. Excluding some CBS mutations, detailed genotype-phenotype correlation for different CBS mutations has not been established in literature. We aimed to make clinical subgroups according to main clinical symptoms and discussed these data together with mutational analysis results from our patients. Totally, 16 different mutations were identified; twelve of which had already been reported, and four are novel (p.N93Y, p.L251P, p.D281V and c.829-2A>T). The probands were classified into three major groups according to the clinical symptoms caused by these mutations. A psychomotor delay was the most common diagnostic symptom (n = 12, 46.2% neurological presentation), followed by thromboembolic events (n = 6, 23.1% vascular presentation) and lens ectopia, myopia or marfanoid features (n = 5, 19.2% connective tissue presentation). Pyridoxine responsiveness was 7.7%; however, with partial responsive probands, the ratio was 53.9%. In addition, five thrombophilic nucleotide changes including MTHFR c.677 C>T and c.1298 A>C, Factor V c.1691 G>A, Factor II c.20210 G>A, and SERPINE1 4G/5G were investigated to assess their contributions to the clinical spectrum. We suggest that the effect of these polymorphisms on clinical phenotype of CBS is not very clear since the distribution of thrombophilic polymorphisms does not differ among specific groups. This study provides molecular findings of 26 Turkish probands with homocystinuria and discusses the clinical presentations and putative effects of the CBS mutations. Crown Copyright (C) 2013 Published by Elsevier B.V. All rights reserved.Öğe International warfarin genotype-guided dosing algorithms in the Turkish population and their preventive effects on major and life-threatening hemorrhagic events(Future Medicine LTD, 2015) Karaca, Şefayet; Bozkurt, Nujen Çolak; Cesuroğlu, Tomris; Karaca, Mehmet; Bozkurt, Mehmet; Eskioğlu, Erdal; Polimanti, RenatoTo determine the accuracy of international warfarin pharmacogenetic algorithms developed on large multiethnic cohorts (comprising more than 1000 subjects) to predict therapeutic warfarin doses in Turkish patients. Materials & methods: We investigated two Turkish warfarin-treated cohorts: patients with no history of hemorrhagic or thromboembolic event and patients with major and life-threatening hemorrhagic events. Results: International pharmacogenetic algorithms showed good performances in predicting the therapeutic dose of patients with no history of bleedings, but they did not significantly detect the incorrect warfarin dose of patients with major and life-threatening hemorrhagic events. Conclusion: Although genetic information can predict the therapeutic warfarin dose, the accuracy of the international pharmacogenetic algorithms is not sufficient to be used for warfarin screening in Turkish patients.Öğe Novel homogentisate dioxigenase (HGD) gene mutations in alkaptonuria patients(Springer, 2010) Hatipoglu, E.; Ozgul, R. K.; Sivri, H. S.; Coskun, T.; Tokatli, A.; Karaca, Şefayet; Kucuk, O.; Kilic, M.; Akcelik, M.; Dursun, A.[Abstract Not Available]Öğe Nutritional habits, lifestyle, and genetic predisposition in cardiovascular and metabolic traits in Turkish population(Elsevier Science Inc, 2016) Karaca, Şefayet; Erge, Sema; Cesuroğlu, Tomris; Polimanti, RenatoObjectives: Cardiovascular and metabolic traits (CMT) are influenced by complex interactive processes including diet, lifestyle, and genetic predisposition. The present study investigated the interactions of these risk factors in relation to CMTs in the Turkish population. Methods: We applied bootstrap agglomerative hierarchical clustering and Bayesian network learning algorithms to identify the causative relationships among genes involved in different biological mechanisms (i.e., lipid metabolism, hormone metabolism, cellular detoxification, aging, and energy metabolism), lifestyle (i.e., physical activity, smoking behavior, and metropolitan residency), anthropometric traits (i.e., body mass index, body fat ratio, and waist-to-hip ratio), and dietary habits (i.e., daily intakes of macro- and micronutrients) in relation to CMTs (i.e., health conditions and blood parameters). Results: We identified significant correlations between dietary habits (soybean and vitamin B12 intakes) and different cardiometabolic diseases that were confirmed by the Bayesian network learning algorithm. Genetic factors contributed to these disease risks also through the pleiotropy of some genetic variants (i.e., F5 rs6025 and MTR rs180508). However, we also observed that certain genetic associations are indirect since they are due to the causative relationships among the CMTs (e.g., APOC3 rs5128 is associated with low-density lipoproteins cholesterol and, by extension, total cholesterol). Conclusions: Our study applied a novel approach to integrate various sources of information and dissect the complex interactive processes related to CMTs. Our data indicated that complex causative networks are present: causative relationships exist among CMTs and are affected by genetic factors (with pleiotropic and non-pleiotropic effects) and dietary habits. (C) 2016 Elsevier Inc. All rights reserved.Öğe Phenotypic and molecular characterization of risk loci associated with asthma and lung function(Korean Academy of Asthma, Allergy and Clinical Immunology, 2020) Karaca, Mehmet; Atçeken, Nazente; Karaca, Şefayet; Civelek, Ersoy; Şekerel, Bülent Enİs; Polimanti, RenatoPurpose: Respiratory diseases have a highly multifactorial etiology where different mechanisms contribute to the individual's susceptibility. We conducted a deep characterization of loci associated with asthma and lung function by previous genome-wide association studies (GWAS). Methods: Sixteen variants were selected from previous GWAS of childhood/adult asthma and pulmonary function tests. We conducted a phenome-wide association study of these loci in 4,083 traits assessed in the UK Biobank (n = 361,194 participants). Data from the Genotype-Tissue Expression (GTEx) project were used to conduct a transcriptomic analysis with respect to tissues relevant for asthma pathogenesis. A pediatric cohort assessed with the International Study of Asthma and Allergies in Children (ISAAC) Phase II tools was used to further explore the association of these variants with 116 traits related to asthma comorbidities. Results: Our phenome-wide association studies (PheWAS) identified 206 phenotypic associations with respect to the 16 variants identified. In addition to the replication of the phenotypes tested in the discovery GWAS, we observed novel associations related to blood levels of immune cells (eosinophils, neutrophils, monocytes, and lymphocytes) for the asthma-related variants. Conversely, the lung-function variants were associated with phenotypes related to body fat mass. In the ISAAC-assessed cohort, we observed that risk alleles associated with increased fat mass can exacerbate allergic reactions in individuals affected by allergic respiratory diseases. The GTEx-based analysis showed that the variants tested affect the transcriptomic regulation of multiple surrounding genes across several tissues. Conclusions: This study generated novel data regarding the genetics of respiratory diseases and their comorbidities, providing a deep characterization of loci associated with asthma and lung function.
