Investigation of (Epi)genetic causes in syndromic short children born small for gestational age.

Intrauterine onset syndromic short stature constitutes a group of diseases that pose challenges in differential diagnosis due to their rarity and clinical as well as molecular heterogeneity. The aim of this study was to investigate the presence of (epi)genetic causes in children born small for gestational age (SGA) and manifesting clinically undiagnosed syndromic short stature. The study group comprised twenty-nine cases selected from the syndromic SGA cohort. Various analyses were performed, including chromosomal microarray (CMA), methylation-specific-multiple ligation probe amplification for chromosomes 6,14 and 20, and whole exome sequencing (WES). Pathogenic copy number variants (CNVs) on chromosomes 2q13, 22q11.3, Xp22.33, 17q21.31, 19p13.13 and 4p16.31 causing syndromic growth disturbance were detected in six patients. Maternal uniparental disomy 14 was identified in a patient. WES was performed in the remaining 22 patients, revealing pathogenic variants in nine cases; six were monoallelic (ACAN, ARID2, NIPBL, PIK3R1, SMAD4, BRIP1), two were biallelic (BRCA2, RFWD3) and one was hemizygous (HUWE1). Seven of these were novel. Craniofacial dysmorphism, which is an important clue for the diagnosis of syndromes, was very mild in all patients. This study unveiled, for the first time, that ARID2 mutatios can cause syndromic SGA. In conclusion, a high (55.2%) diagnosis rate was achieved through the utilization of CMA, epigenetic and WES analyzes; 15 rare syndromes were defined, who were born with SGA and had atypical and/or mild dysmorphic findings. This study not only drew attention to the association of some rare syndromes with SGA, but also introduced novel genes and CNVs as potential contributors to syndromic SGA.

Association of polymorphisms in the sex hormone genes with the presence and severity of coronary artery disease.

OBJECTIVE: Coronary artery disease (CAD) is an important public health problem worldwide. Therefore, it is important to identify the molecular mechanisms and the candidate gene polymorphisms involved in the development of CAD. In this study, we focused on 2 polymorphisms of the atherosclerosis-related genes, ESR1 and CYP19A1. METHODS: Unselected 339 individuals who underwent coronary angiography were divided into 2 groups: those with normal coronary arteries (≤30% stenosis) and those with critical disease (≥50% stenosis). Individuals were genotyped for CYP19A1 rs10046 C/T and ESR1 rs2175898 A/G polymorphisms using hybridization probes in real-time PCR. In addition, Gensini and SYNTAX scores were assessed. RESULTS: ESR1 polymorphism was significantly associated with CAD in men (p=0.036) via G allele carriage. Multiple logistic regression analyses showed that ESR1 rare allele carriage was associated with CAD presence (Odds ratio=2.12, 95% confidence interval 1.01-4.1, p=0.025), adjusted for age, HDL-C, LDL-C and smoking status in the male group. CYP19A1 rs10046 T allele carriers had a 2.84-fold increased risk for complex CAD in multiple logistic regression analysis (p=0.016). Furthermore, the univariate analysis of variance indicated that T allele carriage of rs10046 polymorphism was associated with increased SYNTAX and Gensini scores (p<0.05). Female patients who were ESR1 G allele carriers with CAD had higher adiponectin levels (p=0.005), whereas HbA1c levels were associated with T allele of CYP19A1 in the CAD group (p=0.004) and male CAD group (p=0.018). CONCLUSION: The CYP19A1 and ESR1 polymorphisms were associated with the presence and severity of CAD. These gene polymorphisms warrant further studies for the elucidation of their contribution to CAD development.

Seven patients with Smith-McCort dysplasia 2: Four novel nonsense variants in RAB33B and follow-up findings.

Smith-McCort dysplasia 2 (SMC2) is a rare spondylo-epiphyseal-metaphyseal dysplasia caused by biallelic RAB33B variants. Short trunk dwarfism and radiological findings including the lacy ilia appearance and double bumps of the vertebral bodies are typical features. To date, only eight patients with SMC2 had been reported. The aim of this study is to evaluate the follow-up findings of seven patients from five families with SMC2 and to present four novel variants in RAB33B. The age of diagnosis of the patients was between 4 and 18 years. All patients had variable degrees of short trunk dwarfism with barrel chest, waddling gait, hyperlordosis, genu valgum, elbow and finger joint stiffness, which became more evident with growth. Lacy iliac crest, short ilia with basilar hypoplasia, platyspondyly, dysplastic acetabulum with small and/or laterally displaced femoral heads, and small, irregular carpal bones were detected on skeletal radiographies of all patients. Typical double hump appearance of vertebral bodies was present in patients under 12 years of age, which disappeared after puberty and development of elongated vertebral bodies was also observed. At the time of diagnosis, six patients were able to walk independently; patients who were followed for five to nine years, developed severe hip pain, hip and knee joints stiffness and difficultly of walking after 10 years of age. Only two patients could walk independently during final examination. We detected four novel nonsense variants (p.Gln85Ter, p. Cys48Ter, p. Arg94Ter and p. Gln134Ter) in RAB33B. This study provides important data on long-term skeletal findings of the patients with SMC2.

Neurofibromatosis type 1: Expanded variant spectrum with multiplex ligation-dependent probe amplification and genotype-phenotype correlation in 138 Turkish patients.

OBJECTIVE: To investigate the variant spectrum and genotype-phenotype correlations in a Turkish cohort with Neurofibromatosis Type-1 (NF1). MATERIALS AND METHODS: We retrospectively investigated the clinical and molecular data of 138 NF1 patients from 129 families who had been followed-up for a median of 3.9 (1.25-18.5) years. RESULTS: NF1 sequencing revealed 73 different intragenic variants, 19 of which were novel. Seven large deletions were detected by multiplex ligation-dependent probe amplification (MLPA) analyses. The total detection rate of pathogenic NF1 variants was found to be 87.1%. Comparing age groups, cutaneous neurofibromas, freckling, and Lisch nodules were more prevalent in patients older than 12 years (p > .05). Optic glioma detected in 17.3% of the patients and was significantly more common before the age of 6 (p > .001). Other solid tumors developed in 5% of the patients. There was no genotype-phenotype correlation between patients with truncating and nontruncating variants. However, six out of seven patients with large deletions had significant developmental delay, one patient with the c.2970_2972delAAT (p.Met992del) variant had only typical pigmentary features, and another patient with the c.4267A > G (p.Lys1423Glu) variant had CALMs, freckling, neurofibromas, and Noonan-like phenotype. CONCLUSIONS: We described 19 novel variants and seven large deletions in NF1. Applying MLPA assay in NF1 is useful in expanding the molecular diagnosis. Although very limited genotype-phenotype correlation has been reported in NF1, the fact that specific phenotypic findings were observed in our patients with large deletions and two intragenic variants supports the studies published recently.

Investigation of (epi)genotype causes and follow-up manifestations in the patients with classical and atypical phenotype of Beckwith-Wiedemann spectrum.

Beckwith-Wiedemann syndrome (BWS) is a genomic imprinting disorder, characterized by macroglossia, abdominal wall defects, lateralized overgrowth, and predisposition to embryonal tumors. It is caused by the defect of imprinted genes on chromosome 11p15.5, regulated by imprinting control (IC) domains, IC1, and IC2. Rarely, CDKN1C and chromosomal changes can be detected. The aim of this study is to retrospectively evaluate 55 patients with BWS using the new diagnostic criteria developed by the BWS consensus, and to investigate (epi)genetic changes and follow-up findings in classic and atypical phenotypes. Loss of methylation in IC2 region (IC2-LoM), 11p15.5 paternal uniparental disomy (pUPD11), and methylation gain in IC1 region (IC1-GoM) are detected in 31, eight, and five patients, respectively. Eleven patients have had no molecular defects. Thirty-five patients are classified as classical and 20 as atypical phenotype. Patients with classical phenotype are more frequent in the IC2-LoM (25/31), while patients with atypical phenotype are common in the pUPD11 group (5/8). Malignant tumors have developed in six patients (10.9%); three of these patients have IC1-GoM, two pUPD11, one IC2-LoM genotype, and four an atypical phenotype. We observed that the face was round in the infantile period and elongated as the child grew-up, developing prognathism and becoming asymmetrical if hemi-macroglossia was present in the classical phenotype. These findings were mild in the atypical phenotype. These results support the importance of using the new diagnostic criteria to facilitate the diagnosis of patients with atypical phenotype who have higher tumors risk. This study also provides important information about facial gestalt.

The rs2175898 Polymorphism in the ESR1 Gene has a Significant Sex-Specific Effect on Obesity.

Polymorphisms in the ESR1 gene have been associated with obesity and lipid metabolism. There are also important sex-related differences in the prevalence of obesity and related phenotypes. Therefore, we aimed to interrogate the association of the ESR1 rs2175898 gene polymorphism with obesity, obesity-related variables, and lipid levels in men and women as separate groups. Two thousand twenty-two randomly selected middle-aged and elderly Turks were genotyped for ESR1 rs2175898 polymorphism using real-time polymerase chain reaction with hybridization probes. We found sex-related differences of the ESR1 rs2175898 polymorphism in obesity. Logistic regression analysis after adjustment for age, smoking status, physical activity, diabetes mellitus, and the presence of menopause status in women demonstrated significantly decreased risk for obesity in female AG genotype carriers (OR 0.69; 95% CI 0.52-0.91; p = 0.010), and in male GG genotype carriers (OR 0.49; 95% CI 0.25-0.96; p = 0.039), Furthermore, carriers of the rs2175898 G allele exhibited a lower body mass index in both sexes and decreased waist circumference in women but not in men. Our findings also showed significantly higher serum total-C levels (p = 0.007) in the carriers of the AG+GG/AG genotype compared with the AA genotype in men. The AG genotype of the ESR1 rs2175898 polymorphism in women and GG genotype in men were found to have a decreased likelihood for obesity compared with the other rs2175898 genotypes.

Risk of obesity and metabolic syndrome associated with FTO gene variants discloses clinically relevant gender difference among Turks.

Gene variations in the fat mass- and obesity-associated gene (FTO) have shown controversial associations with obesity and metabolic syndrome (MetS) in several populations. We explored the association of FTO gene with obesity, MetS, and insulin-related parameters separately in men and women. Two SNPs in the FTO, gene rs9939609 and rs1421085, were genotyped by the Taqman System in 1967 adults (mean age of the whole group 50.1 ± 12.0; 48.4 % male). A random sample of the Turkish Adult Risk Factor cohort was cross-sectionally analyzed. Both SNPs exhibited strong linkage disequilibrium (r(2) = 0.85) and minor alleles were associated with risk of obesity in women and of MetS in men. Carriers of the rs1421085 C-allele exhibited higher body mass index (BMI) in each gender. Adjusted fasting insulin and HOMA index were significantly higher in C-allele carriers in men alone. Logistic regression analysis demonstrated significantly increased likelihood for obesity in female C-risk allele carriers (OR 1.61; 95 % CI 1.19-2.18), after adjustment for age, smoking status, alcohol usage, physical activity grade and presence of diabetes mellitus. Male C-allele carriers were at increased risk for MetS (OR 1.44; 95 % CI 1.07-1.95), adjusted for age, smoking status, alcohol consumption, and physical activity. Further adjustment for BMI attenuated the MetS risk, indicating interaction between C-allele, gender and BMI. The FTO gene in Turkish adults contributes independently to obesity in women and-by interacting with BMI-to MetS and insulin resistance in men.

Minor allele of the APOA4 gene T347S polymorphism predisposes to obesity in postmenopausal Turkish women.

The aim of this study was to examine the relationship between APOA4 gene T347S polymorphism with obesity measures and serum lipids in Turkish adults. Randomly selected sample of 1,554 adults (754 men, mean age 50.4 ± 11.9 years and 800 women, mean age 49.6 ± 11.8 years) were included in the study. 346 Women (43.2 %) were postmenopausal. Genotyping was performed by using hybridization probes in real-time PCR. Not men but postmenopausal women, carrying the S347 allele, were associated with 1.5 kg/m(2) higher BMI (P = 0.016) and 3.6 cm wider waist circumference (P = 0.005) than postmenopausal T347 homozygotes, controlled for covariates. Logistic regression analyses of this polymorphism, adjusted for age, fasting triglyceride, smoking status, alcohol consumption and physical activity disclosed the rare allele to be associated with obesity in postmenopausal women at an odds of 1.80 (95 % CI 1.09-2.97; P = 0.021). Serum apoB level was lower in S347 allele carriers (110.9 ± 2.9 mg/dL) than in T347 homozygotes (119.0 ± 2.4 mg/dL; P = 0.035) in men but not women. APOA4 T347S polymorphism was unrelated to lipids and other lipoproteins in either gender. The APOA4 S347 allele predisposes to obesity and high waist circumference in Turkish postmenopausal women. ApoB levels are lower only in men in S347 allele carriers.