Re-evaluation of Genetic Variants in Parkinson's Disease Using Targeted Panel and Next-Generation Sequencing.

Parkinson's disease (PD) is a complex disorder with a significant genetic component. Genetic variations associated with PD play a crucial role in the disease's inheritance and prognosis. Currently, 31 genes have been linked to PD in the OMIM database, and the number of genes and genetic variations identified is steadily increasing. To establish a robust correlation between phenotype and genotype, it is essential to compare research findings with existing literature. In this study, we aimed to identify genetic variants associated with PD using a targeted gene panel with next-generation sequencing (NGS) technology. Our objective was also to explore the idea of re-analyzing genetic variants of unknown significance (VUS). We screened 18 genes known to be related to PD using NGS in 43 patients who visited our outpatient clinic between 2018-2019. After 12-24 months, we re-evaluated the detected variants. We found 14 different heterozygous variants classified as pathogenic, likely pathogenic, or VUS in 14 individuals from nonconsanguineous families. We re-evaluated 15 variants and found changes in their interpretation. Targeted gene panel analysis with NGS can help identify genetic variants associated with PD with confidence. Re-analyzing certain variants at specific time intervals can be especially beneficial in selected situations. Our study aims to expand the clinical and genetic understanding of PD and emphasizes the importance of re-analysis.

Copy number variations in patients with idiopathic recurrent pregnancy loss: an arrayCGH approach.

BACKGROUND: It is not always possible to determine the causative basis of pregnancy losses and even today it has been reported that 50% of cases with recurrent pregnancy loss (RPL) have no reason to be detected. In our study, it is aimed to reveal the copy number variations (CNVs) of the genes which presumably have a potential effect in individuals with RPL and contribute to subsequent functional studies in the follow-up. METHODS: We retrospectively evaluated the array-comparative genomic hybridization (aCGH) data of cytogenetically 64 normal individuals (21 couples, 11 unrelated women, and 11 unrelated men) who had applied to our outpatient clinic from January 2016 to December 2017, for the history of idiopathic two or more RPL. RESULTS: A total of 83 CNVs were detected in 56 different chromosomal regions [36% (20/56) is deletion and 64% (36/56) is duplication] in 40/64 (62.5%) of the cases. Two detected deleterious CNVs encompassing 1p36.22-p36.21 and 10q11.22 chromosomal locus have been reported as pathogenic according to the Database of Genomic Variants (DGV). DISCUSSION: CNVs that may play a role in the genetic etiology of idiopathic RPL were revealed in our study and potential chromosomal loci were introduced to the literature for further analysis. The detection of CNVs and their association with reproduction such as RPL, infertility, and even other diseases will allow us to have more information about the clinical consequences and will make it possible to provide more accurate and comprehensive genetic counseling.

A New Mutation, Hb A2-Canakkale [δ10(A7)Ala→Val; HBD: c.32C>T], and Other Well-Known δ Variants Identified in a Selected Cohort with Low Hb A2 Levels.

Hemoglobinopathies are the most common single-gene disorders, and ß-thalassemia (ß-thal) imposes a tremendous health burden on Turkey. Thus, premarital carrier screening is obligatory in Turkey, as it is in some other countries. As a result of this mandatory procedure, at routine clinical checkups, many individuals who had undergone premarital screening but did not have any clinical symptoms and/or hematological findings, have compulsorily been required to undergo further evaluation due to abnormal levels of hemoglobin (Hb) fractions (Hb A, Hb A2 and Hb F). Many consequences, such as mutations in unrelated gene(s) or someone's nutritional status, have been reported to affect the Hb fractions levels. In the present study, we aimed to determine whether HBD has a molecular causative role in patients with low Hb A2 levels (below 1.8%). The study was conducted with 20 individuals with low Hb A2 levels who had applied to our outpatient clinic. All DNA samples were analyzed for the HBD gene. Nineteen of the 20 subjects were diagnosed to carry a mutation with one of four different δ-globin variants. Three of them had been described previously [Hb A2-Yialousa (HBD: c.82G>T), Hb A2-Bornova (HBD: c.350G>C) and Hb A2-Yokoshima (HBD: c.77G>A)]. The novel [δ10(A7)Ala→Val, HBD: c.32C>T] mutation was defined as a new δ variant and reported to the HbVar database as Hb A2-Canakkale. In conclusion, the molecular characterization of Hb A2 low levels has been suggested to be significant for a definite diagnosis and counseling.

A New Case of Rare Microdeletion 10q22.3q23 along with Mosaic Klinefelter Syndrome Associated with Facial Dysmorphic Finding, Atrial Ventricular Septal Defect, and Motor Retardation.

The chromosome 10q22.3q23.2 deletion syndrome is characterized by craniofacial dysmorphic features, developmental delay, congenital heart defect, and hand/foot abnormalities. In this study, we report a patient carrying a microdeletion of 7.5 Mb at 10q22.3q23.2 and in addition a mosaicism mos 47,XXY[47]/46,XY[23]. This male patient was 3 years and 3 months years old at the time of genetic evaluation. Atrial ventricular septal defect (AVSD), mild hypotonia, torticollis, and left-sided club foot were noticed after birth. The boy had surgical correction of the AVSD and the club foot. His dysmorphic features were frontal bossing, overfolded ear helix, hypertelorism, epicanthal folds, broad base of nose, flat nasal bridge, full cheeks, thick lips, micrognathia, and joint hyperextensibility. His speech/language development was delayed. Klinefelter syndrome is one of the most common congenital chromosomal abnormalities, but usually it is detected in puberty or in adulthood when reproductive failure occurs. Deletions in the 10q22.3q23.2 region are rare, and previously only a few numbers of cases were described with this microdeletion, but none of them together with Klinefelter syndrome and it could be associated with our case clinical features. The new case described will improve understanding the phenotype associated with 10q22.3q23.2 microdeletions. By presenting this case, we aimed to improve the understanding of the phenotype caused by the rare 10q22.3q23.2 deletion and to show the rare coexistence of this deletion with Klinefelter syndrome.

Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium.

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

Prognostic Prediction of BRCA Mutations by 18F-FDG PET/CT SUVmax in Breast Cancer

Objectives: This study aimed to investigate the prognostic prediction of germline BRCA1 and BRCA2 mutations by comparing the maximum standardized uptake value (SUVmax) obtained from 18fluoride-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT), which is considered a prognostic factor in breast cancer (BC). Methods: Retrospective interdisciplinary laboratory results of 92 patients with BC who had germline BRCA1 or BRCA2 mutation profiles and underwent 18F-FDG PET/CT were compared. Genotyping was made by next-generation sequencing, and PET/CT scans were re-evaluated. The histopathological data, genetic results, and clinical demographics of all patients were recorded. Patients were divided into two groups in accordance with the presence of germline BRCA1 and/or BRCA2 mutations. Between-group statistical comparison was performed. Results: In PET/CT performed for primary staging, patients with BRCA-positive BC had significantly higher SUVmax (p=0.039), larger tumor size (p=0.025), and presence of axillary nodal metastases (p=0.023) than patients with BRCA-negative BC. Although the Ki-67 index was higher in the BRCA-positive group than BRCA-negative group, this difference was not significant (p=0.157). Moreover, in the BRCA-positive and negative groups, SUVmax, Ki-67 index, and tumor size, grade, and stage were significantly correlated with each other. Conclusion: The results of this study showed a strong association between BRCA mutations and SUVmax, which indicates the poor prognosis of BC.

The high frequency of chromosomal copy number variations and candidate genes in epilepsy patients.

OBJECTIVE: Epilepsy is a chronic brain disease and is estimated to affect more than 50 million people worldwide.Epilepsy is a polygenic and multifactorial disease.Genetic causes play a major role in 40-60 % of all epilepsies.Copy number variations(CNVs) have been reported in approximately 5-12 % of patients with different types of epilepsy.Here we aimed to determine the diagnostic yield of the aCGH in epilepsy and to reveal new candidate genes and CNVs by analyzing aCGH data retrospectively. METHODS: The clinical data of 80 patients with the diagnosis of epilepsy were examined retrospectively and the raw data of aCGH of these patients were reanalyzed in the light of current literature. RESULTS: Pathogenic/likely pathogenic CNVs were detected in 14 of 80 patients and 12 of these CNVs (15 %) were associated with epilepsy phenotype. In addition, 18 CNVs in 16 different chromosomal loci that were evaluated as the variant of unknown clinical significance(VOUS). In four cases (5%), CNVs associated with epilepsy were less than 100 kb and these accounted for 13.3 % of all epilepsy associated CNVs. CONCLUSION: The diagnostic yield of aCGH in epilepsy patients was found to be higher than most studies in the literature. MACROD2,ADGRB3(BAI3),SOX8,HIP1,PARK2 and TAFA2 genes were evaluated as potential epilepsy-related genes and NEDD9,RASAL2 and TNR genes thought to be the candidate genes for epilepsy. Our study showed that the diagnostic efficiency of aCGH in epilepsy is high and with more comprehensive studies, it will contribute to the elucidation of genes involved in genetic etiology in epilepsy patients.

Prevalence of MEFV gene mutations in a large cohort of patients with suspected familial Mediterranean fever in Central Anatolia.

BACKGROUND: Familial Mediterranean fever (FMF), an autosomal recessive, autoinflammatory disease that is common in Arabs, Jews, Armenians and Turks, is caused by mutations in the MEFV gene, which encodes a protein called pyrin. The disease is characterised by recurrent fever, peritonitis, pleuritis, abdominal pain and arthralgia. OBJECTIVE: Determine the distributions of MEFV mutations and their relationship with clinical manifestations. DESIGN: Retrospective, descriptive. SETTING: Turkish community. SUBJECTS AND METHODS: The study included patients with complaints related to FMF who were admitted to the research hospital of Cumhuriyet University between 2005 and 2017. FMF was diagnosed by physical examination using the Tel-Hashomer criteria. MEFV mutations were detected by reverse hybridization strip assay and pyrosequencing. MAIN OUTCOME MEASURE: The prevalence of specific MEFV gene mutations in a large cohort of Middle Anatolia. SAMPLE SIZE: 10 033 patients admitted, 1223 with confirmed mutations. RESULTS: Of 1684 patients diagnosed by Tel-Hashomer criteria, mutation screening confirmed that 1223 patients (72.6%) had FMF. Male/female ratio of the FMF patients was 1.3:1. One or more FMF mutations were found in 4497 patients (44.8%). 3262 had heterozygous or carrier mutations, 821 had compound heterozygous mutation, 381 had homozygous mutations, and 21 had triple mutations. Sixty-six percent had a family history of the disease and 13.7% of the patients had parental consanguinity. Main symptoms found in the patients were abdominal pain (85.2%), fever (84%), chest pain (30.2%), arthralgia (28.6%), rash or erysipelas-like erythema (8.2%). The most common mutation in this population was M694V (39%) of 5753 alleles. CONCLUSION: M694V was the most frequent mutation in our population (Middle Anatolia, Turkey) and cause severe forms of the disease. Patients with E148Q, V726A and R761H mutations may have milder FMF symptoms. There was a high rate of carriers in our study group. LIMITATIONS: Amyloidosis, an important complication of the disease, needs to be analyzed. CONFLICT OF INTEREST: None.

The Analysis of GJB2, GJB3, and GJB6 Gene Mutations in Patients with Hereditary Non-Syndromic Hearing Loss Living in Sivas.

OBJECTIVES: The aim of the present study was to investigate the presence of GJB2, GJB3, and GJB6 gene mutations in non-syndromic sensorineural hearing loss (NSHL) cases living in Sivas region, to provide appropriate genetic counseling for cases who were found to have mutation, and to contribute to decrease the frequency of mutant allele in the next generation and plan treatment and rehabilitation with early diagnosis. MATERIALS AND METHODS: The study included 53 unrelated cases that were diagnosed with congenital NSHL between June 2009 and March 2010. Multiplex ligation-dependent probe amplification method was used for genotyping of GJB2, GJB3, and GJB6 gene mutations. RESULTS: Heterozygous 35delG variant was determined in 1.9% (n=1) of cases, homozygous 35delG in 15.1% (n=8), heterozygous IVS1+1G>A mutation in 1.9% (n=1), compound heterozygous in 3.8% (n=2), and homozygous IVS1+1G>A variant in 3.8% (n=2). None of the cases had mutation in GJB3 and GJB6 genes. Mutated allele frequencies in the present study were found to be 17.9% for 35delG and 6.6% for IVS1+1G>A. CONCLUSION: The present study showed that 35delG mutation is the most common variant in the Sivas region, and that IVS1+1G>A mutation should be investigated in hearing loss. Another result of the present study was that genetic analyzes would allow early diagnosis of hearing impairments particularly when infants whose parents have consanguinity do not pass the newborn hearing screening.

Blau syndrome with a rare mutation in exon 9 of NOD2 gene.

Blau syndrome is an autosomal dominant rare disease caused by mutations in NOD2 gene. Less than 200 patients published with Blau Syndrome Worldwide. We reported a 41-year old female Turkish patient diagnosed as Blau syndrome. Granulomatous dermatitis and severe headache, as well as recurrent chest and pelvic pain have been present since she was 8 years old. Arthritis started when she was teenage, hypertension diagnosed when she was 20 and other symptoms also occurred during the lifetime (severe preeclampsia, ischemic stroke, recurrent hemiparesis, recurrent-transient-vision-loss and renal-artery-stenosis). Genomic DNA was isolated from peripheral blood and 12 genes sequenced in Autoinflammatory panel on IonTorrent-S5-NGS platform with Parseq-VariFind™AIPassay. NGS analysis showed 107 variants in in the index case, mainly benign with no strong association with Blau syndrome. Additionally, we identified one very rare missense mutation in NOD2 gene (c2803G>A, p.Val935Met) and in silico assessment of the mutation indicated possible pathogenic significance and strong association with Blau syndrome. In addition, we analyzed family members of the index case and identified the same mutation in NOD2 gene. The segregation analysis shows the presence of the same mutant allele in NOD2 gene in the index case affected sister, as well as in her son with arthralgia, while in her non affecter brother we didn't detect the Val935Met mutation in NOD2 gene. Blau Syndrome is known as a very rare disease, mainly caused by mutations in NOD2 gene. Missense mutation diagnosed in our case could be responsible for the phenotype of the index case. Our results indicate the importance of NGS testing and its major role in the detection of rare mutations that may responsible for the onset of autoinflammatory disorders.

The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance.

Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members.

Evaluation of the physical and biological dosimetry methods in iodine-131-treated patients.

The aim of the study was to compare physical and biological dosimetry methods in iodine-131 (I-131)-receiving patients. The present study comprised of 47 patients (mean age: 47.9 ± 15.8 years), treated with I-131. Group I consisted of 17 patients with hyperthyroidism and mean administered activity of this group was 432.9 ± 111 MBq. There were 15 follow-up patients of differentiated thyroid cancer (DTC) in Group II with mean administered activity of 185 ± 22.2 MBq, who were administered scanning dose of I-131. Group III comprised of 15 patients with DTC, ablated with high-dose of I-131, and this group's mean administered activity was 4347.5 ± 695.6 MBq. The whole-body absorbed doses were calculated in all patients both with the Medical Internal Radiation Dosimetry (MIRD) method using MIRDOSE3 software and cytokinesis-block micronucleus (MN) assay-based MN analysis and were compared. The whole-body absorbed dose, calculated by MIRD method, showed very good correlation with the administered I-131 activity (r = 0.89, P < 0.001), but it was moderate in the MN method (r = 0.52, P < 0.01). Absorbed dose estimations with MIRD method were 49.2 ± 20.8 mGy in Group I, 6.5 ± 1.6 mGy in Group II, and 154.3 ± 47.8 mGy in Group III; the differences were statistically significant (P < 0.001), as expected. Pre- and posttreatment MN frequencies differed significantly in all groups (P < 0.05). The whole-body absorbed doses, based on MN method, were 68.2 ± 17.5, 46.0 ± 11.4, and 90.5 ± 26.9 mGy in Groups I-III, respectively. The difference was significant between Group II and Group III (P < 0.01). The mean absorbed dose was 74.6 ± 27.9 mGy with MN versus 68.0 ± 67.1 mGy in MIRD method (P = 0.087) in the entire study population and the correlation was moderate (r = 0.73, P < 0.001). The whole-body absorbed doses, estimated by MN method, showed moderate correlation with administered radioiodine activities in low radioiodine doses and had significantly different and fluctuating values as compared to MIRD method in patients treated with I-131.

[Evaluation of the Association between Lithium Treatment and GSK3ß Polymorphism in Bipolar Disorder Patients]. / Iki Uçlu Bozukluk Hastalarinda Lityuma Yanit ile GSK-3ß Polimorfizmi Iliskisinin Degerlendirilmesi.

OBJECTIVE: There is a lack of evidence regarding clinical predictors for the treatment response to lithium, which is the main stay treatment option for bipolar disorder. Studies that examined the mechanistic action of lithium revealed that glycogen synthase kinase 3ß (GSK-3ß) enzymeinhibition was important in regard to treatment responses. Based on this background, we aimed to investigate the association between responses to lithium treatment and five different polymorphisms of GSK-3ß. METHOD: Lithium treatment response scale (LTRS) scores for 100 patients diagnosed with bipolar disorders type I were calculated according to the hospital records. Blood samples were collected and genomic DNA was obtained using the MagNA Pure Compact automatic isolation method. The GSK-3ß: rs17183904, rs17183897, rs34009575, rs34002644, and rs17183890 polymorphisms were analyzed by real time PCR. RESULTS: In this cohort, the mean age of patients was 41.1±10.3 years, the mean age of disease onset was 24.5±8.2, and the mean LTRS score was 4.9±1.8. There was no statistically significant difference for LTRS scores between groups in terms of gender, marital status, level of education, and the type of first episode. LTRS was significantly higher in only the patients harbouring GSK-3ß rs17183890 AG genotype (p=0.008, t:2.71). Interestingly, no differences were found for the remaining polymorphisms. CONCLUSION: The specific GSK-3ß polymorphism that associated with lithium-response in our study may help to predict lithium responses and to develop individualized treatment. We presume that our pharmacogenomic findings may also provide important contributions to the clinical practice in regard to future evaluation of the treatment adherence and side effects. To obtain these goals, further genome-wide scanning studies conducted on larger sample cohorts are required.

The prevelance of human papillomavirus (HPV) genotypes detected by PCR in women with normal and abnormal cervico-vaginal cytology.

OBJECTIVES: Cervical cancer is the second most common type of cancer for women worldwide with a great proportion proved to be related to human papillomavirus (HPV) infection. As infection with HPV is the strongest risk factor for cervical neoplasia, detection of HPV genotypes in cervical and vaginal specimens of women with normal and abnormal cytology seems to be of paramount importance in cervical cancer screening. The objective of the study is to evaluate the prevalence and HPV genotypes among women with normal or abnormal Pap smear tests. MATERIAL AND METHODS: This retrospective study was conducted in a tertiary care university hospital in western Turkey. A total of 201 patients in whom both HPV typing and Pap test was performed between 2012 and 2016 in our obstetrics and gynecology department were enrolled in this study. Clinical and laboratory data were obtained for all participants. Cervical smears of the patients were classified by the Bethesda system and HPV analyses were done using the polymerase chain reaction (PCR) method. RESULTS: This study included 201 women, 72 of whom had normal and 129 of whom had abnormal Pap smear results. HPV DNA was detected in 91 (45.2%) of the 201 investigated women. Out of 72 patients with normal cervico-vaginal cytology, HPV positivity was detected in 35 (49%) patients, whereas 33 (35%) patients out of 94 with ASCUS , 18 (62%) patients out of 29 with LSIL and 5 (83%) patients out of 6 with HSIL had HPV positivity. Out of 35 HPV positive women that had normal pap test results, 25 (75%) were found to have high risk HPV (HR-HPV) genotypes. In women with ASCUS, LSIL and HSIL, HR-HPV genotype rates were found to be 94%, 89% and 100% respectively. The most common identified HPV types were HPV58, HPV16, HPV31, HPV33, HPV11 and HPV35. CONCLUSIONS: The frequency of HPV infection was found to be higher in our study compared to previous reports. Moreover, although HR-HPV genotypes were also detected in patients with normal cervical cytology, a majority of patients with HR-HPV genotypes were associated with abnormal cervical smear cytology including high rates of atypical squamous cells of undetermined significance, low-grade squamous intraepithelial lesion, and high-grade squamous intraepithelial lesion.

KRAS, BRAF oncogene mutations and tissue specific promoter hypermethylation of tumor suppressor SFRP2, DAPK1, MGMT, HIC1 and p16 genes in colorectal cancer patients.

BACKGROUND: Colorectal cancer is a serious disease that causes significant morbidity and mortality in developed countries. Genetic changes, such as mutations in proto-oncogenes and DNA repair genes, and loss of function in the tumor suppressor genes cause colorectal cancer development. Abnormal DNA methylation is also known to play a crucial role in colorectal carcinogenesis. OBJECTIVE: In this study, frequencies of KRAS and BRAF mutations, promoter hypermethylation profiles of SFRP2, DAPK1, MGMT, HIC1 and p16 genes, and possible associations between hypermethylation of these genes and KRAS and BRAF mutations were aimed to find out. METHODS: Ninety three colorectal cancer tissues and 14 normal colon mucosas were included in the study. Common twelve KRAS gene mutation were investigated with using reverse-hybridization strip assay method. BRAF V600E mutations were investigated with RFLP method. Hypermethylation status of five tumor suppressor genes were detected by using reverse-hybridization strip assay method after bisulfite modification of DNA. RESULTS: KRAS and BRAF mutation frequencies were determined as 54.84% and 12.9%, respectively. Promoter hypermethylation frequencies of tumor suppressor genes SFRP2, DAPK1, MGMT, HIC1 and p16 were determined as 66.7%, 45.2%, 40.9%, 40.9% and 15.1%, respectively. Statistically significant associations were found between BRAF mutation and SFRP2 and p16 tumor suppressor genes hypermethylation (SFRP2; p= 0.005, p16; p= 0.016). Compared to rectum, SFRP2 (p= 0.017) and MGMT (p= 0.013) genes have statistically significantly higher promoter hypermethylation in colon. CONCLUSIONS: Results of the current study have confirmed that KRAS mutations and SFRP2 hypermethylation can be used as genetic markers in colorectal cancer.

Micronucleus frequencies in groups receiving external or internal radiation.

OBJECTIVE: In the current study, we aimed to explore whether there is alteration between pre- and post-treatment micronucleus (MN) frequencies induced by internal and external ionizing radiation. MATERIALS AND METHODS: The study enrolled a total of 67 patients including patients admitted to our hospital for treatment of hyperthyroidism (n = 17), scanning with low-dose I-131 (n = 15), and ablative therapy with high-dose I-131 (n = 15) at Department of Nuclear Medicine as well as patients with different diagnoses receiving external radiotherapy with various doses and durations at Department of Radiation Oncology (n = 20). Thirty-two patients who received radioactive iodine and returned for a follow-up visit at 1 month. RESULTS: Considering both pre- and post-treatment MN frequencies of each group, lowest MN frequencies were detected for patients undergoing screening with low-dose I-131, and highest MN frequencies were found in radiotherapy patients. Comparison of pre- and post-treatment MN frequencies among hyperthyroidism, when pre- and post-treatment MN frequencies compared among hyperthyroidism, I-131 whole body scanning, ablation, and radiotherapy patient groups differences between MN frequencies were significant for each group (P < 0.05). CONCLUSION: Our study showed that MN analysis might be of value in determining chromosome damage that could potentially occur in patients exposed to internal and external radiation.

Associations of fractalkine receptor (CX3CR1) and CCR5 gene variants with hypertension, diabetes and atherosclerosis in chronic renal failure patients undergoing hemodialysis.

PURPOSE: We aimed to investigate the associations of fractalkine receptor (CX3CR1) V249I, T280M and CCR5-59029 A/G gene polymorphisms in chronic renal failure (CRF) subjects undergoing hemodialysis and to evaluate possible associations of these polymorphisms with hypertension (HT), diabetes mellitus (DM) and atherosclerosis (AS). METHODS: A total of 225 CRF subjects undergoing hemodialysis and 201 healthy controls were enrolled in the study. CRF subjects were divided into three major subgroups according to comorbidities including HT (n = 127), DM (n = 65) and AS (n = 33). Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism method. RESULTS: The II genotype and I allele frequencies of CX3CR1 V249I polymorphism were found significantly more frequent in CRF subjects, CRF subjects with DM and CRF subjects with AS compared with controls (p < 0.05 for all comparisons). G allele frequency of CCR5 polymorphism was found significantly more prevalent in CRF subjects with DM than that of controls. Further, GG genotype and G allele frequencies of CCR5 polymorphism were significantly more prevalent in CRF subjects with AS compared with controls (p < 0.05). We also explored these polymorphisms among CRF subjects with and without following comorbidities: HT, DM, AS. We found significant association between CRF subjects with HT and without HT in terms of genotype and allele frequencies of V249I polymorphism (p < 0.05). CX3CR1 T280M polymorphism was not found significantly different in none of the comparisons. CONCLUSION: These data demonstrate possible associations between CX3CR1 V249I and CCR5-59029 A/G polymorphisms and/or HT, DM and AS in CRF subjects.

The relationship between C-reactive protein rs3091244 polymorphism and ankylosing spondylitis.

AIMS: Previous studies have shown that C-reactive protein (CRP) gene polymorphism can be related to inflammatory changes. The present study aimed to examine the association between CRP gene polymorphism and clinical and laboratory findings in ankylosing spondylitis (AS) patients. MATERIALS AND METHODS: A total of 80 patients, 40 with AS and 40 controls, were included in the study. Diagnosis of AS was made according to Assessment in AS International Working Group criteria. Bath Ankylosing Spondylitis Disease Activity Index, Bath Ankylosing Spondylitis Functional Index, Bath Ankylosing Spondylitis Metrology Index and Bath Ankylosing Spondylitis Radiology Index scores were evaluated. CRP gene C, A and T alleles were evaluated and were determined using the analysis of melting curves after real time polymerase chain reaction. The odds ratios were calculated for all alleles and haploids of the CRP gene. We investigated the relationship between the CRP polymorphism and clinical and laboratory findings. RESULTS: A, C, T allele frequencies in the control group were 15%, 57.5% and 27.5%. The allele frequencies in the AS group were 38%, 68.8% and 26.2%. While C and T allele frequencies were shown to be similar in the two groups, A allele frequency was higher in the AS group compared to the control group. The CC wild allele was 42.5% in the control group and 47.5% in the AS group (P = 1.0). Odds ratios for the C allele were 1.6, for the CC haploid 1.2 and for the CT haploid 3.7. Chest expansion and finger-to-ground distance was better in the CRP gene polymorphism group compared to the no polymorphism group. CONCLUSION: The presence of the CRP gene CC wild haploid and C allele in patients may indicate an increased risk for AS.

The CYP4502D6 *4 and *6 alleles are the molecular genetic markers for drug response: implications in colchicine non-responder FMF patients.

The cytochrome P450 2D6 (CYP2D6) is a cytochrome P450 enzyme involved in the oxidative biotransformation of the xenobiotics, carcinogens and various clinically important drugs. Patients are evaluated in three sub-groups of extensive (EM), intermediate (IM) and poor metabolizer (PM) phenotypes due to their drug-metabolising ability for the target CYP2D6 gene. Colchicine non-responsive FMF patients were prospectively genotyped for the major CYP2D6 alleles in the current study. Major CYP2D6 alleles of *1, *3, *4, *5, and *6 were genotyped for 30 responsive and 60 non-responsive FMF patients by multiplex PCR-based reverse-hybridization StripAssay and real-time PCR methods. DNA banks isolated from blood-EDTA were retrospectively used in the current patients and results were compared statistically. Increased CYP2D6 *4 and *6 allele frequencies were highly detected in the colchicine non-responsive FMF patients when compared to the responsive group. Results showed the frequencies of major CYP2D6 *1(wild), *3(2637A > delA), *4(G1934A), *5(total gene deletion) and *6(1707T del) alleles in 0.550, 0.042, 0.158, 0.025 and 0.225 for non-responder and 0.880 and 0.120 (CYP2D6*1 and *4) for the responder groups, respectively. Despite small sample size, this study suggests that there is an association between CYP2D6*4 and CYP2D6*6 alleles and drug intoxicants in colchicine non-responder FMF patients.