Molecular Genetic Diagnosis with Targeted Next Generation Sequencing in a Cohort of Turkish Osteogenesis Imperfecta Patients and Their Genotype-phenotype Correlation.

Introduction: Osteogenesis imperfecta (OI) is a group of phenotypically and genetically heterogeneous connective tissue disorders that share similar skeletal anomalies causing bone fragility and deformation. This study aimed to investigate the molecular genetic etiology and determine the relationship between genotype and phenotype in OI patients with targeted next-generation sequencing (NGS). Method: In patients with OI, a targeted NGS analysis panel (Illumina TruSight One) containing genes involved in collagen/bone synthesis was performed on the Illumina Nextseq550 platform. Results: Fifty-six patients (female/male: 25/31) from 46 different families were enrolled in the study. Consanguinity between parents was noted in 15 (32.6%) families. Clinically according to Sillence classification; 18(33.1%) patients were considered to type I, 1(1.7%) type II, 26(46.4%) type III and 11(19.6%) type IV. Median body weight was -1.1 (-6.8, - 2.5) SDS, and height was -2.3 (-7.6, - 1.2) SDS. Bone deformity was detected in 30 (53.5%) of the patients, while 31 (55.4%) were evaluated as mobile. Thirty-six (60.7%) patients had blue sclera, 13 (23.2%) had scoliosis, 12 (21.4%) had dentinogenesis imperfecta (DI), and 2 (3.6%) had hearing loss. Disease-causing variants in COL1A1 and COL1A2 genes were found in 24 (52.1%) and 6 (13%) families, respectively. In 8 (17.3%) of the remaining 16 (34.7%) families, the NGS panel revealed disease-causing variants in three different genes (FKBP10, SERPINF1, and P3H1). Nine (23.6%) of the variants detected in all investigated genes were not previously reported in the literature and were classified to be pathogenic according to ACMG guidelines pathogenity scores. In ten (21.7%) families, a disease-related variant was not found in a total of 13 OI genes included in the panel. Conclusion: Genetic etiology was found in 38 (82.6%) of 46 families by targeted NGS analysis. In addition, 9 new variants were assessed in known OI genes which is a significant contribution to the literature.

Dicentric Recombinant Chromosome 18 due to Maternal Paracentric Inversion Analyzed by Array CGH.

Introduction: Chromosomal abnormalities are mostly found in 0.5-0.8% of live-born infants with developmental and morphological defects. Paracentric inversions are structural intrachromosomal rearrangements resulting in a risk of chromosomally unbalanced gametes in carriers. Case Presentation: Herein, we report a patient with dicentric rearrangement of chromosome 18 due to maternal paracentric inversion of chromosome 18. The patient was a girl, aged 3 years and 11 months. She was referred due to multiple congenital abnormalities, severe intellectual disability, and motor retardation. She had microcephaly, prominent metopic suture, synophrys, epicanthic folds, telecanthus, wide-set alae nasi, wide columella, bilateral cleft lip and palate, pectus carinatum, umbilical hernia, pes planus, and anteriorly displaced anus. She had bilateral external auditory canal stenosis and mild right-sided and moderate left-sided sensorineural hearing loss. Echocardiography showed secundum-type atrial septal defect and mild tricuspid failure. Brain magnetic resonance imaging showed only thinning of posterior areas of the corpus callosum. Chromosome analysis showed 46,XX,dic rec(18) by GTG and C banding. Dicentric chromosome was confirmed by fluorescence in situ hybridization analysis. Paternal karyotype was normal 46,XY but maternal chromosome analysis showed a paracentric inversion in chromosome 18 with 46,XX,inv(18)(q11.2?q21.3?) karyotype. Array CGH was performed on a peripheral blood sample from the patient and showed duplication at 18p11.32p11.21 and 18q11.1q11.2, and deletion at 18q21.33q23. The patient's final karyotype is arr 18p11.32p11.21(64,847_15,102,598)×3,18q11.1q11.2(18,542,074_22,666,470)×3,18q21.33q23(59,784,364_78,010,032)×1. Discussion: To the best of our knowledge, this is the first report of a patient with dicentric chromosome 18 due to a parental paracentric inversion of chromosome 18. We present the genotype-phenotype correlation with literature review.

Fatal Pulmonary Embolism Due to Inherited Thrombophilia Factors in a Child With Wolfram Syndrome.

Wolfram syndrome-1 is a rare and severe autosomal recessive neurodegenerative disease characterized by diabetes mellitus (DM), optic atrophy, diabetes insipidus, and deafness. Poorly controlled type 1 DM increases the risk for thrombosis. However, coexistence of DM and hereditary thrombosis factors is rarely observed. Here we present the case of a 13.5-year-old, nonfollowed girl newly diagnosed with poorly controlled Wolfram syndrome on the basis of the results of clinical and laboratory examinations. On the eighth day after diabetic ketoacidosis treatment, pulmonary embolism developed in the subject. Thrombus identified in the right atrium using echocardiography was treated by emergency thrombectomy. Homozygous mutation in the methylenetetrahydrofolate reductase gene C677T, heterozygous factor-V Leiden mutation, and active protein C resistance were identified in the patient. The patient was lost because of a recurring episode of pulmonary embolism on the 86th day of hospitalization. We present this case to highlight the need for investigating hereditary thrombosis risk factors in diabetic patients in whom thromboembolism develops.

A Newborn with Congenital Mixed Phenotype Acute Leukemia After In Vitro Fertilization.

Congenital leukemia is a rare disease. The majority of cases of this disease are acute myelogenous leukemia (AML). Congenital acute lymphoblastic leukemia (ALL) is rare and most often is of B cell lineage. Rarely, some cases have been designated biphenotypic or mixed phenotype acute leukemia (MPAL). Herein, we report a preterm newborn referred to us as a result of the appearance of blue-violaceous dermal nodules on her body at birth. She was a twin and the product of an in vitro fertilization (IVF) pregnancy. Physical examination showed jaundice, hepatosplenomegaly, and peripheral facial nerve palsy in addition to dermal nodules. Bone marrow aspiration showed 40% blasts of lymphoid lineage; skin biopsy and its immunohistochemistry revealed myeloblastic infiltration of the dermis. Cytogenetic analysis (46,XX), fluorescence in situ hybridization (FISH) analysis, and cranial magnetic resonance were normal. The patient was diagnosed with congenital MPAL, and an association between IVF and congenital leukemia was suggested.

Expression of ERCC1 and its clinicopathological correlations in non-small cell lung cancer.

Excision Repair Cross-Complementing Group 1 (ERCC1) is an important DNA repair gene, playing critical role in nucleotide excision repair pathway and having a significant influence on genomic instability. Some studies support that ERCC1 might be a potential predictive and prognostic marker in non-small cell lung cancer (NSCLC). ERCC1 has also been shown to be a promising biomarker in NSCLC treated with a cisplatin-based regimen. Therefore, the determination of ERCC1 expression at DNA, mRNA and protein level in different stages of NSCLC is still an important topic in the cancer. Ninety-one formalin-fixed paraffin-embedded tumor samples histopathologically diagnosed as NSCLC were examined in this study. ERCC1 expression at protein level were scored by immunohistochemistry. The gene amplification and mRNA expression levels for ERCC1 were determined by real-time quantitative PCR. There was complete concordance among the three methods in 39 tumor samples (42.9%). A strong correlation was found between DNA amplification and mRNA expression (r=0.662) while there was no correlation between mRNA and protein assessment for ERCC1 expression (r=-0.013). ERCC1 expression at mRNA and DNA level (63.1 and 84.2%, respectively) in tumors at stage III was higher than at the other stages. In contrast, the protein expression at stage II and III (56.6 and 52.6%, respectively) of NSCLC was lower than that of tumors with stage I NSCLC. These results show that the mechanism by which ERCC1 expression might play a role in tumor behavior. This study was also confirmed that the appropriate validation and qualification in methods used for ERCC1 status were needed before its clinical application and implementation.

Expression and amplification of Topoisomerase-2α in type 1 and type 2 papillary renal cell carcinomas and its correlation with HER2/neu amplification.

The current study was undertaken to investigate chromosomal and genetical aberrations leading to overexpression of Topoisomerase-2α (TOP2α) and to reveal the possible association of these aberrations with HER2/neu overexpression and gene amplification, and to search for the relationship between TOP2α and HER2/neu status with prognostical biomarkers in papillary renal cell carcinoma (RCC), a group of tumors with diverse molecular, chromosomal and clinical features. Archival cases of papillary RCC obtained from Departments of Pathology of Pamukkale, Ege and Dokuz Eylul Universities were studied in two groups (type 1 and type 2) each containing 20 cases. The level of TOP2α and HER2/neu expression by tumor cells were determined immunohistochemically. A multicolor FISH probe was used to define both amplification of HER2/neu and TOP2α genes, and polysomy 17. The ratio of cells expressing TOP2α in type 1 and type 2 papillary RCC were 24.29% and 6.89%, respectively. The difference was statistically significant comparing the average or median values of groups separately (p = 0.002). The expression levels of TOP2α and HER2/neu were also correlated. TOP2α and HER2/neu were co-amplified in both groups. Immunohistochemical expression was not observed in 15 of 23 cases with HER2/neu amplification. The most frequent finding detected by FISH method was polysomy of chromosome 17. We had contradictory results compared with the findings reported in the limited numbers of literature. It shows us that papillary RCC constitute a heterogenous group of tumors with various cytogenetic features and morphological classification of these tumors may not be compatible with their molecular characteristics.

Determination of apoptosis, proliferation status and O6-methylguanine DNA methyltransferase methylation profiles in different immunophenotypic profiles of diffuse large B-cell lymphoma.

OBJECTIVE: Our aim was to investigate the expression of apoptosis-associated proteins (bcl-2, bcl-xl, bax, bak, bid), apoptotic index (AI) and proliferation index (PI) in germinal center B-cell-like immunophenotypic profile (GCB) and non-GCB of diffuse large B-cell lymphoma (DLBCL). METHODS: The methylation status of the promoter region of O6-methylguanine-DNA yerine O6-methylguanine-DNA methyltransferase (MGMT) gene and its relation with immunophenotypic differentiation of DLBCLs were also investigated. 101 cases were classified as GCB (29 cases) or non-GCB (72 cases). Apoptosis-associated proteins and PI were determined by IHC, and TUNEL method was used to determine AI. MGMT methylation analysis was performed by real-time PCR. RESULTS: The PI was significantly higher in GCB compared with non-GCB (p=0.011). Percentage of cells stained with bcl-6 was positively correlated with the percentage of cells expressing bcl-2 (p=0.023), AI (p=0.006) and PI (p<0.001), while a significant negative correlation was observed with the percentage of cells expressing bax (p=0.027). The percentage of cells stained with MUM1 showed a significantly positive correlation with the percentage of cells expressing bcl-xl (p=0.003), bid (p=0.002), AI (p<0.001), and PI (p=0.001). MGMT methylation analysis was performed in 95 samples, and methylated profile was found in 31 cases (32.6%). GCB was found in 6 cases (22.2%) and non-GCB was determined in 25 cases (36.8%) out of 31 with MGMT methylated samples. There was no significant association between MGMT methylation status and immunophenotypic profiles (p=0.173). CONCLUSION: These results suggest that bcl-6 protein expression may be responsible for the high PI in GCB. Additionally, we found that apoptosis-associated proteins were not significantly associated with immunophenotypic profiles.

No strong association between HER-2/neu protein overexpression and gene amplification in high-grade invasive urothelial carcinomas.

The generation of urothelial carcinoma is caused by the accumulation of various molecular changes, as in most malignancies. There are conflicting data about the status of HER-2/neu oncogene in urothelial carcinomas. The aim of this study was to determine the status of HER-2/neu oncogene in high-grade invasive urothelial carcinoma of urinary bladder both in protein and DNA level. We evaluated HER-2/neu protein overexpression by immunohistochemistry (IHC) and gene amplification by fluorescent in situ hybridization (FISH) and real-time quantitative PCR in paraffin-embedded samples of high-grade invasive urothelial carcinoma obtained from 36 patients. Polysomy 17 was also assessed by FISH. Immunohistochemically, HER-2/neu protein overexpression was observed in 22 (61.1%) tumors (ten tumors with score 3+ and 12 with score 2+). Fourteen of 36 tumors (38.9%) were evaluated as negative (score 0 or 1+). Complete concordance between FISH and the PCR was seen in all of the samples scored as 0 and 1+ by IHC. HER-2/neu gene amplification was observed in three of 27 (11.1%) tumors by FISH (nine samples were non-informative) and in eight of 36 (22.2%) tumors by the PCR. The complete concordance between HER2-2/neu protein overexpression and gene amplification was seen only in three of 27 tumors. Polysomy 17 was seen in nine tumors (33.3%). The results indicated that, in contrast to breast cancer, there was no strong association between HER-2/neu overexpression and gene amplification in invasive urothelial carcinomas, and polysomy 17 was higher in tumors showing HER-2/neu overexpression.

Detection of Y chromosomal material in patients with a 45,X karyotype by PCR method.

A 45,X karyotype is one of the common chromosomal abnormalities characterized by short stature, lack of development of secondary sexual characteristics, webbed neck and cubitus valgus. This phenotype was described by Turner in 1938 and was called Turner syndrome (TS). About 40-60% of the patients with TS phenotype have a 45,X karyotype, the rest either have a structurally abnormal X or Y chromosome or mosaicism with a second cell line. Determination of Y chromosome derivatives in patients with a 45,X karyotype is important for the management of these patients due to increased risk of gonadoblastoma. Low level mosaicism of Y chromosome may be missed by cytogenetic methods. The aim of our study is to analyze cryptic Y chromosome derivatives using Y specific sequences in 40 Turkish patients with a pure 45,X karyotype. Fourteen different Y specific sequences along the Y chromosome were selected for the detection of cryptic Y chromosome material by PCR analysis. The present study demonstrated that 2 patients with a 45,X karyotype (5%) have Y specific sequences except sex related region Y (SRY). One of them had displayed enhanced virilisation whereas other showed no virilisation. In conclusion, it has been found by PCR analysis that 5% of patients with a 45,X karyotype have Y chromosome sequences in the absence of any marker chromosome by cytogenetic analysis. The data also suggest that the patients with a 45,X karyotype should be analyzed for the presence of Y chromosome derivatives by sensitive methods, such as PCR, in order to calculate the future risk of developing gonadoblastoma.

The role of RELN in lissencephaly and neuropsychiatric disease.

Reelin is an extracellular matrix-associated protein important in the regulation of neuronal migration during cerebral cortical development. Point mutations in the RELN gene have been shown to cause an autosomal recessive human brain malformation termed lissencephaly with cerebellar hypoplasia (LCH). Recent work has raised the possibility that reelin may also play a pathogenic role in other neuropsychiatric disorders. We sought, therefore, to define more precisely the phenotype of RELN gene disruption. To do this, we performed a clinical, radiological, and molecular study of a family in whom multiple individuals carry a chromosomal inversion that disrupts the RELN locus. A 6-year-old girl homozygous for the pericentric inversion 46,XX,inv7(p11.2q22) demonstrated the same clinical features that have been previously described in association with RELN point mutations. The girl's brain magnetic resonance imaging (MRI) findings, including pachygyria and severe cerebellar hypoplasia, were identical to those seen with RELN point mutations. Fluorescence in situ hybridization confirmed that one of the breakpoints of this inversion mapped to within the RELN gene, and Western blotting revealed an absence of detectable serum reelin protein. Several relatives who were heterozygous for this inversion were neurologically normal and had no signs of psychotic illness. Our findings demonstrate the distinctive phenotype of LCH, which is easily distinguishable from other forms of lissencephaly. Although RELN appears to be critical for normal cerebral and cerebellar development, its role, if any, in the pathogenesis of psychiatric disorders remains unclear.

Sex chromosome aneuploidy rates in the somatic cells of infertile men.

OBJECTIVE: A large number of studies have shown that the prevalence of somatic chromosome abnormalities detectable with karyotyping is higher in infertile men. However, a normal somatic karyotype does not exclude the chance of having low level mosaicism. STUDY DESIGN: Eleven men with severe oligozoospermia and 10 healthy, fertile men were included in this study. All the patients had severe oligozoospermia with sperm counts < or =3,000,000/ mL. All participants had normal physical findings and testicular volume. The probe for dual-color fluorescence in situ hybridization consisted of an alpha satellite sequence in the centromeric region of chromosome X (DXZ1) and satellite III DNA at the Yq12 region of chromosome Y (DYZ1). RESULTS: The sex chromosome aneuploidy rate was significantly higher in subjects than in controls (p<0.001). The median incidence of sex chromosome aneuploidy in the oligozoospermic group was 4.5% (range, 0.8-7.3%), while in the control group it was 0.7% (range, 0.2-1.2%)., CONCLUSION: The incidence of aneuploidy in somatic cells is significantly greater in oligozoospermic men than in normal controls. That may suggest that chromosome instability is a result of altered genetic control during mitotic cell division. Our results demonstrate that men with oligozoospermia have an elevated risk for sex chromosome abnormalities in their somatic cells.

A case with proximal femoral focal deficiency (PFFD) and fibular A/hypoplasia (FA/H) associated with urogenital anomalies.

Malformations of the lower limbs are rare and heterogeneous anomalies. Some congenital anomalies involving face, gastrointestinal system, skeletal system, urogenital system, heart, lung and diaphragma associated with lower limb malformations have been described in the literature. Here, we report a case of left proximal femoral focal deficiency (PFFD) together with fibular aplasia associated with left undescended testis and hypospadias. The putative embryologic mechanisms of lower limb defects and their possible association with lower urogenital tract malformations are also discussed.

Femoral-facial syndrome with hemifacial microsomia and hypoglossia.

We present a boy diagnosed as femoral-facial syndrome with total agenesis of right lower limb, agenesis of femur and fibula of left lower limb and micrognathia, long philtrum as facial features. Some additional features were described as hemifacial microsomia, preauricular tags and hypoglossia.

[Family history, clinical features, and molecular characterization of a patient with autosomal recessive non-syndromic hearing loss]. / Otozomal resesif isitme kaybi olan bir olguda aile öyküsü, klinik ve moleküler incelemeler.

Autosomal recessive non-syndromic hearing loss is the most common form of inherited childhood deafness. Identification of the responsible gene in this type of hearing loss presents difficulties because of marked genetic heterogenicity and limited clinical presentation. A two-year-old girl was referred to our clinic because of congenital hearing loss. Family history showed that her brother and six relatives of her parents were also affected by unilateral or bilateral hearing loss. There was no consanguinity between the parents, though they were from close villages. Audiometric studies revealed severe bilateral sensorineural hearing loss. Molecular analysis of the index patient documented that autosomal recessive non-syndromic hearing loss resulted from the homozygous 35delG mutation in the connexin 26 gene.

Familial influence on parkinsonism in a rural area of Turkey (Kizilcaboluk-Denizli): a community-based case-control study.

This population-based study on parkinsonism in a genetically isolated community from a rural area of Turkey aimed to provide a selective evaluation of environmental and heritable risk factors. An increased prevalence of parkinsonism (4.1%) was detected in the village of Kizilcaboluk for people 65 years of age and older. This study included 36 patients with parkinsonism living in Kizilcaboluk and three times that number of age- and sex-matched people serving as controls. A questionnaire including demographic data, family history, education, occupation, data on exposures to pesticides, smoking, alcohol intake, and head trauma was administered. We found a significant association of parkinsonism cases with a positive family history in first-degree relatives (odds ratio [OR], 7.48; 95% confidence interval [CI], 2.52-22.17; P < 0.0001) and with pesticide exposure (OR, 2.96; 95% CI, 1.31-6.69; P = 0.015) compared to the control subjects. The value of genetically isolated populations for the identification of genetic risk factors for common and complex disorders has gained much attention recently because the genetic make-up of these populations is likely to be less complex than that of the general population and our findings should prompt investigations to the nature of a familial aggregation of parkinsonism in this population.

Cytogenetic studies in patients with reproductive failure.

BACKGROUND: Cytogenetic studies in patients with reproductive failure AIM: To investigate the contribution of chromosomal abnormalities in sub fertility and in couples with repeated abortions. METHODS: Hundred and 13 couples who had at least two or more spontaneous abortions and 65 women and 63 men with infertility were analyzed cytogenetically. RESULTS: Major chromosomal rearrangements were found in 8% and minor variants in 6% in the study population. Major chromosomal aberrations were judged to explain 4.9% of recurrent abortions and 13% of infertility. Chromosomal abnormalities in infertile men occurred in 5% and in infertile women in 21.5%. The chromosomal abnormalities were structural (57%), numerical (18%) or mosaics (25%). CONCLUSIONS: Chromosomal aberrations in recurrent abortions are mostly structural ones and those in female infertility mosaicism of sex chromosomes. Turner's syndrome, Turner variants and XY females are detected as a cause of female infertility. The structural and numerical aberrations of either sex or autosomal chromosomes were found in infertile men.

Laurence-Moon-Biedl syndrome with vaginal atresia.

A 15-year-old girl presented with the rare Laurence-Moon-Biedl syndrome, accompanied by vaginal atresia, and cervical dysgenesis. She was treated by hysterectomy and construction of a neovagina with bilateral pudendal thigh flaps. Two brothers and a sister (one of twins) were unaffected but the remaining brother also had the disease.

Progressive autosomal dominant optic atrophy and sensorineural hearing loss in a Turkish family.

PURPOSE: To describe the clinical features, mode of inheritance, and linkage analysis of ten affected members of a three-generation family with progressive optic atrophy and progressive hearing loss. MATERIALS AND METHODS: The proband, a 10-year-old boy, presented with progressive visual failure. Ten other members in his family, including his mother, half-sister, aunt, two uncles, grandfather, and some of the cousins, also had progressive visual loss and hearing loss. Six affected and four unaffected cases were examined in detail. Blood samples were drawn from 16 members for DNA extraction. Two loci previously described for optic atrophy were tested for linkage in the present family. RESULTS: The mode of inheritance was clearly autosomal dominant. Six members of the family were found to have progressive optic atrophy and hearing loss, both starting in the first decade of life. Total or red-green color blindness was detected in some patients. None of the members of this family showed evidence of other systemic disorders; however, four had blepharochalasis. No other cause could be found for the hearing or the visual loss. Linkage analysis excluded OPA1 and OPA2. CONCLUSION: The present Turkish family belongs to the group of individuals with autosomal dominantly inherited optic atrophies with hearing loss. Linkage analysis excluded OPA1 and OPA2, indicating that a novel gene defect underlies the disease in this family. Further genome-wide linkage analysis and identification of the disease-associated gene will help define the pathophysiology of this syndrome.