Recurrent symptomatic urolithiasis in a patient with cystic fibrosis.

A 6-month-old girl, previously diagnosed with cystic fibrosis (CF), was admitted to hospital for nephrolithiasis. Her parents were first-degree cousins. The patient underwent endoscopic stone management. Despite no family history of stones and medical treatment with potassium citrate, the patient developed recurrent renal stones and atypical urinary tract infections during follow-up. Basic investigations were all normal. Due to consanguinity and early presentation of nephrolithiasis, metabolic causes such as cystinuria and hyperoxaluria were considered. Cystinuria was excluded due to normal cystine levels. High urinary oxalate excretion was found as expected due to absorptive (secondary) hyperoxaluria in CF patients. An early stone burden in the patient with a history of medical treatment and consanguinity led us to perform a genetic testing. Genetic testing revealed a missense homozygous variant in exon 1 of the AGXT gene. The patient was diagnosed with primary hyperoxaluria type 1. Two rare life-threatening genetic diseases were found together in the same child.

Evaluation of chromosomal abnormalities in the postnatal cohort: A single-center study on 14,242 patients.

BACKGROUND AND AIM: Chromosomal analysis is a laboratory technique used to examine the chromosomes of an individual, offering insights into chromosome numbers, structures, and arrangements to diagnose and comprehend genetic diseases. This retrospective study provides a comprehensive understanding of the distribution by indications in a large cohort of 14,242 patients and the frequency of chromosomal abnormalities in different clinical populations. METHOD: The study examined various indications for karyotype evaluation, with recurrent pregnancy loss being the most common indication, followed by intellectual disability, dysmorphic features, congenital anomalies, and developmental delay. RESULTS: The overall chromosomal abnormality rate was found to be 5.4%, with numerical abnormalities accounting for the majority of cases (61.7%). Trisomies, particularly trisomy 21, were the most frequent numerical abnormalities. In terms of structural abnormalities, inversions and translocations were the most commonly identified. The rates of chromosomal anomalies varied in specific indications such as amenorrhea, disorders of sex development, and Turner syndrome. The study also highlighted significant differences between males and females in the presence of chromosomal abnormalities across certain indications. Males exhibited a higher incidence of chromosomal abnormalities in cases of Down syndrome and infertility, whereas females showed higher abnormalities in terms of recurrent pregnancy loss. CONCLUSION: While this study provides valuable insights into the frequency and distribution of chromosomal abnormalities, it has limitations, including its retrospective design and reliance on data from a single medical genetics department. Nevertheless, the findings emphasize the importance of karyotype analysis in diagnosing chromosomal disorders and providing appropriate management, while also pointing to potential gender-related variations in chromosomal abnormalities that warrant further investigation.

A Case Series of Three Patients with Cleidocranial Dysplasia: Clinical Presentation and Diagnostic Considerations.

Cleidocranial dysplasia (CCD) is a rare genetic condition that affects the bones and teeth. In our study, we presented three cases of CCD, including one with a new mutation and two with a family history. Case 1 had a unique heterozygous frameshift mutation (NM_001015051,c.762del, p.(Ser256Valfs*2)), while Case 2 and her brother (Case 3) had a common pathogenic missense mutation (NM_001015051,c.674G, p.Arg225Gln), which was also found in their father. The mutation in Case 1 was not reported before. Interestingly, the symptoms in Case 1, with the new mutation, were less severe than the other cases and the previous reports.

Contribution of genotypes in Prothrombin and Factor V Leiden to COVID-19 and disease severity in patients at high risk for hereditary thrombophilia.

Thrombotic and microangiopathic effects have been reported in COVID-19 patients. This study examined the contribution of the hereditary thrombophilia factors Prothrombin (FII) and Factor V Leiden (FVL) genotypes to the severity of COVID-19 disease and the development of thrombosis. This study investigated FII and FVL alleles in a cohort of 9508 patients (2606 male and 6902 female) with thrombophilia. It was observed that 930 of these patients had been infected by SARS-CoV-2 causing COVID-19. The demographic characteristics of the patients and their COVID-19 medical history were recorded. Detailed clinical manifestations were analyzed in a group of cases (n = 4092). This subgroup was age and gender-matched. FII and FVL frequency data of healthy populations without thrombophilia risk were obtained from Bursa Uludag University Medical Genetic Department's Exome Databank. The ratio of males (31.08%; 27.01%) and the mean age (36.85 ± 15.20; 33.89 ± 14.14) were higher among COVID-19 patients compared to non-COVID-19 patients. The prevalence of FVL and computerized tomography (CT) positivity in COVID-19 patients was statistically significant in the thrombotic subgroup (p < 0.05). FVL prevalence, CT positivity rate, history of thrombosis, and pulmonary thromboembolism complication were found to be higher in deceased COVID-19 patients (p < 0.05). Disease severity was mainly affected by FVL and not related to genotypes at the Prothrombin mutations. Overall, disease severity and development of thrombosis in COVID-19 are mainly affected by the variation within the FVL gene. Possible FVL mutation should be investigated in COVID-19 patients and appropriate treatment should be started earlier in FVL-positive patients.

Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS-CoV-2 from 946 whole-exome sequencing data in the Turkish population.

Heterogeneity in symptoms associated with COVID-19 in infected patients remains unclear. ACE2 and TMPRSS2 gene variants are considered possible risk factors for COVID-19. In this study, a retrospective comparative genome analysis of the ACE2 and TMPRSS2 variants from 946 whole-exome sequencing data was conducted. Allele frequencies of all variants were calculated and filtered to remove variants with allele frequencies lower than 0.003 and to prioritize functional coding variants. The majority of detected variants were intronic, only two ACE2 and three TMPRSS2 nonsynonymous variants were detected in the analyzed cohort. The main ACE2 variants that putatively have a protective or susceptibility effect on SARS-CoV-2 have not yet been determined in the Turkish population. The Turkish genetic makeup likely lacks any ACE2 variant that increases susceptibility to SARS-CoV-2 infection. TMPRSS2 rs75603675 and rs12329760 variants that were previously defined as common variants that have different allele frequencies among populations and may have a role in SARS-CoV-2 attachment to host cells were determined in the population. Overall, these data will contribute to the formation of a national variation database and may also contribute to further studies of ACE2 and TMPRSS2 in the Turkish population and differences in SARS-CoV-2 infection among other populations.

A truncating variant in the THOC6 gene with new findings in a patient with Beaulieu-Boycott-Innes syndrome.

Beaulieu-Boycott-Innes syndrome (BBIS; MIM#613680) is a rare, autosomal recessive neurodevelopmental genetic disorder associated with pathogenic variants in the THOC6 gene (*615403). Intellectual disability, dysmorphic facial features, developmental delay, structural cardiac and genitourinary anomalies, and dental caries are suggestive findings of the syndrome. Exome sequencing (ES) may facilitate the diagnosis of this syndrome, whose clinical features can be nonspecific. Here we report a BBIS patient with a homozygous truncating variant (NM_024339.5:c.299G>A; p.Trp100Ter) in the THOC6 gene, diagnosed by ES analysis. The patient's variant is novel and some features such as clivus dysplasia, occult spina bifida, tapered fingers, and upturned fleshy earlobes have not been reported in the literature before. This new case report will expand the knowledge of BBIS and provide more information about the genetic variants and phenotypic spectrum. Also, new cases with THOC6 variants will define the core clinical features and common phenotypes of the BBIS over time.

A comprehensive molecular analysis and genotype-phenotype correlation in patients with familial mediterranean fever.

Familial Mediterranean fever is an auto inflammatory genetic disease involving especially Turks, Armenians, Arabs and non-Ashkenazi Jews and caused by variants in the MEFV gene. In this study, we aimed to evaluate the distribution and frequency of clinical, MEFV gene variants in FMF patients and the relationship between mutations in different exons and phenotype-genotype and clinical findings. 1028 patients diagnosed as FMF were included. The most common genotypes were M694V / R202Q heterozygous (10.4%), M694V homozygous (7.5%), M694V / E148Q / R202Q heterozygous (4.6%), V726A heterozygous (4.5%), M680I heterozygous (4.2%). c.1611-1 G > C, G152R, S104C, R116S, E336K, R461Q mutations were detected in the literature for the first time in FMF patients. We also divided the patients into 4 groups according to whether the MEFV mutations were exon 10 or non-exon 10. The first group consisted of non-exon 10 homozygous or compound heterozygous (n = 180) patients, Group 2 consisted of exon 10- non-exon 10 compound heterozygous (n = 318) patients, Group 3 consisted of exon 10 homozygous or compound heterozygous (n = 256) patients, while Group 4 consisted of heterozygous (n = 227) patients at any exon. There was no significant difference between the groups in terms of abdominal pain, arthritis, arthralgia, vomiting diarrhea, erysipelas like rash, amyloidosis, renal failure family history. There was no difference in fever between Group 1 (55.6%) and 2 (62.3%); however, these two groups were different from Group 3 (75.8%) and 4 (76.7%). Group 3 (18.8%) had the highest rate of appendectomy. In addition, allele frequencies of all mutations detected in the analyses were compared with allele frequencies of healthy people in the gnomad database. It is useful to analyse all exons in the MEFV gene with the next generation sequence analysis in the detection of FMF disease. S104C, R116S, G152R, E336K, R461Q, L508Q and c.1611-1 G > C mutations are also new variants in literature. c.1611-1 G > C is a possible pathogenic variant.

A Rare Cause of Neonatal Hemolytic Anemia: Glutathione Synthetase Deficiency.

BACKGROUND: Isolated hemolysis or hemolytic anemia and 5-oxoprolinuria are 2 distinct medical conditions in the clinical spectrum associated with glutathione synthetase deficiency. CLINICAL OBSERVATION: A 1-day-old female baby presented with anemia and respiratory distress. Her hemoglobin level was 9.5 g/dL and the total serum bilirubin level was 5.6 mg/dL. Metabolic acidosis was detected in her blood gas analysis. Metabolic acidosis recurred despite treatment and further investigation was required. Her 5-oxoproline level was 3815 mmol/mol creatinine in urine organic acid analysis, and a homozygous mutation [p.R125H (c.374G>A)] was found in the glutathione synthetase gene. CONCLUSIONS: GSD has been observed in very few patients and is rarely considered in the differential diagnosis of hemolytic anemia in newborns.

Does thiol-disulphide balance show oxidative stress in different MEFV mutations?

Many studies have shown that oxidative stress levels increase in patients with Familial Mediterranean Fever (FMF). Thiols are a class of compounds that include a sulfhydryl group (-SH) and can react with free oxygen radicals to protect tissues. We aimed to investigate thiol-disulphide homeostatic status in FMF patients and examined the effect of different mutations in the MEFV gene on the thiol-disulphide balance. We investigated thiol-disulphide parameters in patients with FMF and healthy controls. To determine the differential effect of MEFV gene mutations on thiol-disulphide balance, subjects were divided into five groups based on homozygous or compound heterozygous exon 10 and nonexon 10 mutations. Tests of thiol-disulphide homeostasis were conducted using the automated spectrophotometric method. Patients with FMF had significantly lower native thiol [433.8 µmol/l (243.3-536.4) vs. 484.1 µmol/L (340.2-612.3), p  < 0.001], total thiol levels [459.7 µmol/L (281.3-575.4) vs. 529.9 µmol/L (363-669.5), p < 0.001], and disulphide levels [14.0 µmol/l (2.7-33.3) vs. 24.4 µmol/l (7.2-36.6), p < 0.001] compared to the control group. Moreover, disulphide/native thiol (3.4 ± 1.7 vs. 4.7 ± 1.3, p < 0.001) and disulphide/total thiol (3.1 ± 1.4 vs. 4.3 ± 1.0 p < 0.001) were also detected lower in the FMF group compared to the control group. But the native thiol/total thiol ratios (93.6 ± 2.9 vs. 91.3 ± 2.1, p < 0.001) were higher in the FMF group. There was no significant difference between the native thiol, total thiol, and disulphide levels of individuals with nonexon 10 homozygous or compound heterozygous (Group 1), nonexon 10-exon 10 compound heterozygous (Group 2), exon 10 homozygous or compound heterozygous (Group 3), and heterozygous (Group 4) mutations. However, these parameters significantly differed from those of the healthy control group. Since no differences were found in our study between thiol and disulfide levels of Groups 1, 2 and 3, we believe that this rate cannot be shown as an indicator of oxidative damage in different mutations of FMFs. To the best of our knowledge, this study is the first study that demonstrates the effect of different FMF mutations on the thiol-disulphide balance.

Combination of two different homozygote mutations in Pompe disease.

Pompe disease (OMIM no 232300) is an autosomal recessive inherited metabolic disorder, caused by glycogen accumulation in the lysosome due to deficiency of the lysosomal acid 03B1-glucosidase enzyme. Here we report the case of an 8-month-old girl of consanguineous Turkish parents, who was diagnosed with the infantile form of Pompe disease. Two different uncommon homozygote mutations (c.32-13 T > G homozygote and c.1856G > A homozygote) were detected. The patient had a more progressive clinical course than expected. We emphasize the rare combination of genetic mutations in this Turkish family with Pompe disease.

Micronucleus testing as a cancer detector: endometrial hyperplasia to carcinoma.

PURPOSE: Endometrium carcinoma (EC) is the fourth common cancer among women worldwide and the incidence is increasing. It is important to define the EC earlier for survival of the patients. METHODS: Women who had endometrial hyperplasia (EH) and EC in postmenopausal and premenopausal period were included to participate in this study. MN assay has been performed to participants for detection of the genetic damages and DNA instability. RESULTS: MN ratio was significantly higher in EC group compared to other two groups (EH and control groups) (p < 0.001). On the other hand, there was no significant difference among these groups with regard to number of gravidity and presence of a family history of cancer (p > 0.05). MN frequency and NDI were significantly correlated with the age in endometrial hyperplasia without atypia, endometrial cancer and control groups (r 0.546, p < 0.001; r 0.320, p 0.024; r 0.396, p 0.003, respectively). Similarly, MN frequency and NDI were significantly correlated with BMI in three groups (r 0.287, p 0.044; r 0.467, p 0.001; r 0.473, p 0.001, respectively). CONCLUSIONS: MN scoring in pre-neoplastic conditions of the endometrium can be used as adjunct in endometrium cancer screening. By using MN assay, discrimination may be possible among endometrial cancer, endometrial precancerous lesions and pathologically normal patients. This is an easy, simple, reliable, reproducible objective test and can be used in routine patient examination.

Three patients resembling Teebi-Shaltout syndrome.

Teebi-Shaltout syndrome (TSS) was first reported by Teebi and Shaltout in 1989. This entity is proposed to be inherited in autosomal recessive manner. The clinical features include characteristic facial features, ectodermal dysplasia, camptodactyly, and caudal appendage. Only one additional paper reporting four additional cases has been published since the first description. Clinical features common to all previously affected individuals diagnosed with TSS are craniofacial, orodental-ectodermal, and skeletal. This report summarizes and discusses the findings of three additional patients from two unrelated families with findings similar to TSS. These findings may be present in a genetically and phenotypically heterogeneous group of disorders similar to TSS. Presence of consanguinity and similarly affected siblings of both genders suggests autosomal recessive inheritance.

Asymmetric crying face in a newborn with isotretinoin embryopathy.

We report a newborn with asymmetric crying face and other anomalies whose mother had taken isotretinoin during the first month of pregnancy. We hypothesize that asymmetric crying face is a finding of retinoic acid embryopathy and results from the intrauterine effects of retinoic acid on the development of the depressor anguli oris muscle or the mandibular branch of the facial nerve.

The role of TNF-α and PAI-1 gene polymorphisms in familial Mediterranean fever.

OBJECTIVES: Familial Mediterranean fever (FMF) is one of the most serious inherited inflammatory disorders among Jewish, Armenian, Turkish and Arab populations. The imbalance between pro- and anti-inflammatory cytokines may play a role in its etiology. We have investigated whether tumor necrosis factor-alpha (TNF-α) and plasminogen activator inhibitor 1 (PAI-1) gene polymorphisms are associated with FMF and evaluated the relationship between these polymorphisms and genotypic manifestation of FMF. METHODS: We investigated single nucleotide polymorphisms of the TNF-α promoter at positions -308 G/A and the PAI-1 4G/5G gene polymorphism in peripheral blood leukocytes collected from 177 individuals with FMF with different genotype combinations. All of the polymorphisms of TNF-α and PAI-1 were detected by PCR and restriction fragment length polymorphism analysis. RESULTS: There were no association between the TNF-α/308 genotypes and mutations in FMF. In contrast, the PAI-1 4G/5G gene polymorphism may have a significant effect in FMF disease. CONCLUSIONS: Screening with PAI-1 gene polymorphism tests may be beneficial for tracing future FMF patients. However, further investigations are needed to reach a conclusion on the association between PAI-1 polymorphisms and FMF.

Are MUC5B and TERT mutations genetic risk factors for pulmonary fibrosis in individuals with severe COVID-19?

Introduction: The genetic risk factors for Coronavirus disease-2019 (COVID19)-associated pulmonary fibrosis (CAPF) are not clearly defined. Mutations in the genes encoding telomerase reverse transcriptase (TERT) and mucin 5B (MUC5B) are well-known genetic risk factors for pulmonary fibrosis. In this study, we aimed to show whether the most common proven mutations of pulmonary fibrosis affect the development of CAPF. Materials and Methods: Forty-eight patients who were matched for age, gender, COVID-19 disease severity, and respiratory support type and needed high flow nasal cannula, non-invasive mechanical ventilator, or invasive mechanical ventilator due to COVID-19 were followed up prospectively. Eighteen patients were excluded from the follow-up due to known structural lung disease, collagen tissue disease, and occupational exposure to fibrosis. The patients were called for follow-up three months after discharge, and CT was performed. Those with fibrosis (n= 15) in the third-month follow-up CT were included in the CAPF group, and those with complete resolution (n= 15) were included in the control group. Blood samples were taken for genetic analysis. Result: TERT gene study revealed that six (40%) of the fibrosis group was normal, while five were heterozygous (33.3%). MUC5B polymorphism was not detected in 10 (66.7%) of the fibrosis group. Conclusions: Individuals with TERT mutations may be at a higher risk for CAPF. Further studies are needed to clarify the genetic risk factors for CAPF.

Osteopontin as an early predictor of atherosclerosis in attack-free Familial Mediterranean fever patients.

Familial Mediterranean fever (FMF) is an autoinflammatory disease that is associated with endothelial dysfunction and atherosclerosis. Osteopontin which is a multifunctional protein involved in the modulation of inflammatory processes may contribute to the development of atherosclerosis in FMF patients. Therefore, this cross-sectional study investigated the relationship of osteopontin with carotid intima media thickness (CIMT) and atherogenic indices in patients with FMF. Serum osteopontin levels, CIMT, Castelli risk index I and II, plasma atherogenic index (PAI), non - high-density lipoprotein cholesterol, and atherogenic coefficient (AC) in 64 attack-free FMF patients were compared with levels in 23 healthy control subjects. The serum osteopontin level, CIMT, Castelli risk index I, AC and PAI were significantly higher, and high-density lipoprotein cholesterol was significantly lower in FMF patients (P < .001, P < .001, P = .045, P = .016, P = .045, and P = .024; respectively). There were significant positive correlations between osteopontin and CIMT, PAI, AC, and Castelli risk index I (R = 0.580, R = 0.259, R = 0.233, R = 0.277; respectively) and there was significant negative correlation between osteopontin and high-density lipoprotein cholesterol (r= -0.309). Patients who had homozygote mutations had significantly higher osteopontin, PAI, Castelli risk index I and II level. The current study is the first to demonstrate significantly increased serum osteopontin levels in attack-free FMF patients compared with healthy controls. It was also associated with CIMT and many atherogenic indices. This finding provides a new experimental basis to understand the pathogenesis of inflammation-induced atherosclerosis in FMF patients. Furthermore, patients who had homozygote mutations had worse atherogenic indices than those with heterozygote mutations.

Wiedemann-Rautenstrauch syndrome: report of a variant case.

Wiedemann-Rautenstrauch syndrome (WRS) is a rare autosomal recessive disorder that includes premature aging phenotype at birth. The condition is also known as a neonatal progeroid syndrome. Up to now only a few published case reports have been documented. The syndrome is characterized by progeroid appearance, decreased subcutaneous fat, hypotrichosis, macrocephaly, and in some natal teeth. We describe a new patient with features of bilaterally pelvicalyceal ectasia and partial syndactyly on 2th and 3th toes, not previously described, to our knowledge.

TSHR is the main causative locus in autosomal recessively inherited thyroid dysgenesis.

Congenital hypothyroidism (CH) is the most common neonatal endocrine disorder and results in mental retardation if untreated. Eighty-five percent of CH cases are due to disruptions in thyroid organogenesis and are mostly sporadic, but about 2% of thyroid dysgenesis is familial, indicating the involvement of genetic factors in the aetiology of the disease. In this study, we aimed to investigate the Mendelian (single-gene) causes of non-syndromic and non-goitrous congenital hypothyroidism (CHNG) in consanguineous or multi-case families. Here we report the results of the second part (n=105) of our large cohort (n=244), representing the largest such cohort in the literature, and interpret the overall results of the whole cohort. Additionally, 50 sporadic cases with thyroid dysgenesis and 400 unaffected control subjects were included in the study. In familial cases, first, we performed potential linkage analysis of four known genes causing CHNG (TSHR, PAX8, TSHB, and NKX2-5) using microsatellite markers and then examined the presence of mutations in these genes by direct sequencing. In addition, in silico analyses of the predicted structural effects of TSHR mutations were performed and related to the mutation specific disease phenotype. We detected eight new TSHR mutations and a PAX8 mutation but no mutations in TSHB and NKX2-5. None of the biallelic TSHR mutations detected in familial cases were present in the cohort of 50 sporadic cases. Genotype/phenotype relationships were established between TSHR mutations and resulting clinical presentations. Here we conclude that TSHR mutations are the main detectable cause of autosomal recessively inherited thyroid dysgenesis. We also outline a new genetic testing strategy for the investigation of suspected autosomal recessive non-goitrous CH.