PURPOSE: Despite advances in genetic diagnostics, the molecular cause of a significant proportion of DSDs remains unknown. The aim of this study was to identify copy number variations (CNVs) using chromosomal microarray analysis (CMA) technology in DSD patients with previously undetected molecular genetic etiology and to investigate their phenotypic associations with these variations. METHODS: This study included DSD cases without chromosomal abnormalities and without any variants detected by sequence analysis methods, including whole-exome sequencing analysis. We evaluated variant pathogenicity according to the American College of Medical Genetics and Genomics guidelines and recorded the phenotypic findings of the cases. All pathogenic variants were subjected to segregation analysis. RESULTS: Of the 20 patients included in the study, 16 (80%) were classified as 46,XY DSD and 4 (20%) as 46,XX DSD. Initial clinical diagnoses in this 46,XX DSD group included gonadal dysgenesis in two patients (50%) and androgen excess in the remaining two (50%). Among the 46,XY DSD patients, five patients (31.25%) were presumed to be androgen insensitive, nine (56.25%) were diagnosed with defects in androgen biosynthesis, and two (12.5%) had gonadal dysgenesis. CMA detected 38 CNVs in 16 patients (80%), comprising 12 deletions (31.6%) and 26 duplications (68.4%). Three pathogenic CNVs were detected in 3 patients (15%), whereas 27 variants of uncertain significance were identified in 13 patients (65%). CONCLUSION: In selected cases, the diagnostic approach should incorporate CMA to elucidate the molecular etiology of DSD. Furthermore, CMA may prove to be an invaluable tool in the search for new genes responsible for DSD.

Lhermitte-Duclos disease (LDD) is a rare dysplastic gangliocytoma of the cerebellum, typically manifesting as a hamartomatous lesion in the posterior fossa. Currently, LDD has been only linked to PTEN pathogenic variants, with the PI3K/AKT/mTOR pathway acting as the primary signaling cascade responsible for its pathogenesis. We present a case of LDD in which a novel germline heterozygous splice site variant (c.183–2 A > G) in the SUFU gene and a somatic heterozygous missense variant (c.389 G > A) in the PTEN gene, identified from tumor tissue were detected by targeted next-generation sequencing (NGS). SUFU, a tumor suppressor gene, primarily inhibits the hedgehog (Hh) signaling pathway and furthermore influences the AKT/mTOR pathway. Pathogenic variants in SUFU have been linked to medulloblastoma, and their potential role in LDD remains under investigation. Given that both conditions involve granule cell progenitors and are influenced by impaired Hh signaling, they may share a similar developmental path. This is the first research indicating that SUFU may play a role in the etiology of LDD, despite SUFU variants being associated with several central nervous system malignancies. The SUFU variant was shown to disrupt splicing via Sanger sequencing and gel electrophoresis of RNA extracted from blood. Analysis of DNA from tumor tissue using the TWIST Exome 2.0 Panel revealed de novo pathogenic SUFU (c.183–2 A > G) and PTEN (c.389G > A) variants. This paper establishes an initial link between LDD and germline SUFU along with somatic PTEN variants identified from tumor tissue, providing novel insights into the molecular pathogenesis of this rare condition.

Lhermitte-Duclos disease (LDD) is a rare dysplastic gangliocytoma of the cerebellum, typically presenting as a hamartomatous lesion in the posterior fossa. PTEN and the PI3K/AKT/mTOR pathway are involved in the pathogenesis of LDD. We present a case of a patient who incidentally was detected with LDD. A novel, pathogenic, heterozygous, de novo, splice site variant c.183-2A > G (NM_016169.4) in the SUFU gene was identified with targeted next-generation sequencing from genomic DNA. SUFU, a tumor suppressor gene, negatively regulates the hedgehog (Hh) signaling pathway. SUFU also influences WNT and PTEN/AKT/mTOR signaling pathways. While SUFU pathogenic variants are associated with various central nervous system (CNS) tumors, this is the first reported link between SUFU and LDD. The study delves into the role of SUFU in LDD development, establishing the novel SUFU variant as a potential genetic marker for the disease. Sanger sequencing and gel electrophoresis were applied to RNA isolated from blood to show that the variant disrupts splicing. DNA extracted from tumor tissue underwent NGS with the TWIST Exome 2.0 Panel. Results unveiled the de novo pathogenic SUFU (c.183-2A > G) and PTEN (c.389G > A) variants. In conclusion, this study establishes the first reported association between LDD and a germline, de novo SUFU variant, and sheds light on the crucial role of SUFU in LDD pathogenesis. It contributes to the broader understanding of genetic factors influencing this rare cerebellar disorder.

BACKGROUND:PTEN is a tumour suppressor gene and well-known for being frequently mutated in several cancer types. Loss of immunogenicity can also be attributed to PTEN loss, because of its role in establishing the tumour microenvironment. Therefore, this study aimed to represent the link between PTEN and cGAS-STING activity, a key mediator of inflammation, in tumour samples of glioblastoma patients.METHODS:Tumour samples of 36 glioblastoma patients were collected. After DNA isolation, all coding regions of PTEN were sequenced and analysed. PTEN expression status was also evaluated by qRT-PCR, western blot, and immunohistochemical methods. Interferon-stimulated gene expressions, cGAMP activity, CD8 infiltration, and Granzyme B expression levels were determined especially for the evaluation of cGAS-STING activity and immunogenicity.RESULTS:Mutant PTEN patients had significantly lower PTEN expression, both at mRNA and protein levels. Decreased STING, IRF3, NF-KB1, and RELA mRNA expressions were also found in patients with mutant PTEN. Immunohistochemistry staining of PTEN displayed expressional loss in 38.1% of the patients. Besides, patients with PTEN loss had considerably lower amounts of IFNB and IFIT2 mRNA expressions. Furthermore, CD8 infiltration, cGAMP, and Granzyme B levels were reduced in the PTEN loss group.CONCLUSION:This study reveals the immunosuppressive effects of PTEN loss in glioblastoma tumours via the cGAS-STING pathway. Therefore, determining the PTEN status in tumours is of great importance, like in situations when considering the treatment of glioblastoma patients with immunotherapeutic agents.

INTRODUCTION:The luteinizing hormone/choriogonadotropin receptor (LHCGR) plays a critical role in sexual differentiation and reproductive functions in men and women. Inactivating mutations in this gene lead to Leydig cell hypoplasia (LCH), and cause disorders of sex development (DSD) in patients with 46,XY. In this study, it was aimed to discuss the clinical, laboratory and molecular genetic analysis results of nine patients with 46,XY karyotype who had mutations in the LHCGR gene.MATERIALS AND METHODS:The ages, complaints, anthropometric measurements and hormonal results (follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone) of the patients at the time of admission were recorded retrospectively from their medical records. The mutations in the LHCGR gene were investigated using the Sanger sequencing method.FINDINGS:In this study, LHCGR gene mutations were detected in a total of nine patients as a result of the analysis of the index patients presenting with primary amenorrhea from four different families and the examination of the families. In the first three families with no consanguinity between, the same mutation was detected in seven patients in total (Homozygous c.161 + 4A > G). A different mutation was detected in the fourth family (Homozygous p.A483D c.1448C > A).CONCLUSION:In this study, nine patients with karyotype 46,XY, most of whom presented with the complaint of delayed puberty/primary amenorrhea, were diagnosed with LCH. Especially in patients, in whom the elevation of LH is pronounced and there is no testosterone synthesis, LCH should be considered.

Aim: We conducted a retrospective study with the aim of determining the prevalence of lipoprotein lipase (LPL) mutation in patients with severe hypertriglyceridemia (HTG) and to study differences in characteristic features of HTG induced acute pancreatitis (AP). Materials and Methods: Seventy adults with a serum triglyceride (TG) level ≥500 mg/dL were included in the study. Baseline characteristics, LPL mutation and risk factors between those with and without HTG-AP were compared. Results: The mean age was 43 ± 12 years, and males accounted for 55.7%. Of the patients 35 had TG level <2000 mg/dL, and 35 patients had TG ≥2000 mg/dL. LPL mutation was found in 19 (27.1%) of the cases. The prevalence of AP was 67.1% (47 patients). Younger age, TG level, hemoglobin A1c (HbA1c) were significantly independent risk factors for the development of HTG-AP. When patients were divided into groups based on TG levels (group 1 with TG <2000 mg/dL, group 2 TG ≥2000 mg/dL) the prevalence of AP was significantly higher in group 2 (51.4% vs. 82.9%). Age and HbA1c lost their significance for development of AP. When the relationship between the frequency of AP and TG value was evaluated, the specificity of TG threshold value for developing AP was found to be 2235 mg/dL. There was no difference in prevalence of AP and TG level between mutation detected and undetected groups. Conclusion: There was no difference in prevalence of AP and TG level between variant detected and undetected groups. In contrast to the literature, higher levels of TG cut-off points to develop AP was determined.

Background/aim: Although cutting edge procedures such as cell-free fetal DNA isolation from maternal blood are now available, invasive prenatal tests are still being used extensively for prenatal diagnosis. The study aims to evaluate the demographic data, indications, and cytogenetic results of 9297 results of patients who underwent prenatal invasive testing for genetic analysis that were referred for the last 20 years in a University Medical Genetics Center. Materials and methods: The records of 8363 amniocenteses, 626 chorionic villus, and 308 cordocenteses samples were retrospectively evaluated and analyzed regarding referral reasons, indications and their cytogenetic results. The total numbers and the percentages of each group were recorded; Chi-square and logistic regression analyses were performed to give the statistical likelihood of different events. Results: The number of referrals decreased significantly after 2009. Risk of having trisomy 21 as well as trisomy 13 and 18 significantly increased in parallel with advanced maternal age. When the 21-25 age group was compared to the older age groups in terms of having a trisomy 21 pregnancy, the risk doubled in the 36-40, 5 times higher in 41-45 and 10-fold in 46-50 age groups. No significant linear correlation between maternal serum screening test results and trisomy 21 was found, however the difference between the pregnancies whom cut-off value above and below 1/250 in maternal serum screening test were significant. Conclusion: These data have provided useful information on the frequency of referrals to the reference genetics department, and the feasibility of genetic services. By reviewing the indications and their corresponding results, we can offer invaluable insights that will be useful in genetic counseling and also in the development of more effective genetic strategies.

Objective: Neurofibromatosis type 1 is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Wide spectrum of NF1-related clinical manifestations and mutation distribution makes genetic counselling difficult. Methods: The study enrolled 58 unrelated Turkish patients with clinically suspected NF1 referred to the Department of Medical Genetics. Individuals were eligible if they 1) met at least two of the main National Institutes of Health criteria or 2) had multiple cafe acute accent -au-lait macules as a child. Results: Fourty-one different disease-causing variants were identified in 42 (72.4%) individuals, including 17 novel variants. Twenty-four (58.2%) of the NF1 patients had de novo variants. Cafe acute accent -au-lait macules were observed in all patients (100%). Intracranial hamartoma was the second most common phenotype, found in 52.3% (22/42) of the patients. Other common manifestations were neurofibromas (35.7%), axillary or inguinal freckling (28.5%), and Lisch nodules (28.5%). Additionally, one patient had intra-abdominal malignant peripheral nerve sheath tumours and another patient underwent surgery for serous papillary ovarian cancer. Conclusion: In conclusion, this study is one of the largest studies from Turkey to investigate the NF1 mutation spectrum and genotype-phenotype correlations.

Amac: Gorlin Sendromu (OMIM #109400), bazal hucreli karsinomalar (BHK), iskelet anomalileri ve cenede gozlenen cok sayidaki kistlerle karakterize otozomal dominant kalitimli nadir bir hastaliktir. Gorlin Sendromunun %50-85’inden PTCH1 genindeki mutasyonlar sorumludur. Bu calismada klinik olarak Gorlin Sendromu tanisi dusunulen hastalarda yapilmis PTCH1 gen dizi analizlerinin retrospektif olarak degerlendirilmesi ve varyant saptanan hastalarda fenotip-genotip korelasyonu yapilmasi amaclanmistir. Gerec ve Yontem: Ege Universitesi Tip Fakultesi Hastanesi Tibbi Genetik Anabilim Dali’na basvuran Gorlin Sendromu dusunulen dort hastanin PTCH1 genindeki varyantlar ile klinik ve laboratuvar bulgulari geriye donuk olarak incelenmistir. Bulgular: PTCH1 gen dizi analizi yapilan dort hastada ucu yeni olmak uzere dort farkli varyant saptanmistir. Hastalardaki klinik bulgularin sikliklari ve dagilimi degerlendirildi. Sonuc: Bu calisma Turkiye’de yapilan Gorlin Sendromlu olgularda PTCH1 gen varyantlarinin dagilimi ile ilgili ilk calisma olup uc yeni varyant saptanmistir. Saptanan varyantlar ve klinik bulgular ile fenotip-genotip korelasyonu degerlendirilmistir.

BACKGROUND:Breast cancer is the most common malignancy in women and thought to be hereditary in 10% of patients. Recent next-generation sequencing studies have increased the detection of pathogenic or likely pathogenic (P/LP) variants in genes other than BRCA1/2 in patients with breast cancer. This study evaluated pathogenic variants, likely pathogenic variants, and variants of unknown significance in 18 hereditary cancer susceptibility genes in patients with BRCA1/2-negative breast cancer.PATIENTS AND METHODS:This retrospective study included 188 high-risk BRCA1/2-negative patients with breast cancer tested with a multigene cancer panel using next-generation sequencing.RESULTS:Among 188 proband cases, 18 variants in 21 patients (11.1%) were classified as P/LP in PALB2 (n = 6), CHEK2 (n = 5), MUTYH (n = 4), ATM (n = 3), TP53 (n = 2), BRIP1 (n = 1), and MSH2 (n = 1). Three novel P/LP variants were identified. An additional 28 variants were classified as variants of unknown significance and detected in 30 different patients (15.9%).CONCLUSION:This is one of the largest study from Turkey to investigate the mutation spectrum in non-BRCA hereditary breast cancer susceptibility genes. A multigene panel test increased the likelihood of identifying a molecular diagnosis in patients with BRCA 1/2-negative breast cancer at risk for a hereditary breast cancer syndrome. More studies are needed to enable the clinical interpretation of these P/LP variants in hereditary patients with breast cancer.

Amaç: Gorlin Sendromu (OMIM #109400), bazal hücreli karsinomalar (BHK), iskelet anomalileri ve çenede gözlenen çok sayıdaki kistlerle karakterize otozomal dominant kalıtımlı nadir bir hastalıktır. Gorlin Sendromunun %50-85’inden PTCH1 genindeki mutasyonlar sorumludur. Bu çalışmada klinik olarak Gorlin Sendromu tanısı düşünülen hastalarda yapılmış PTCH1 gen dizi analizlerinin retrospektif olarak değerlendirilmesi ve varyant saptanan hastalarda fenotip-genotip korelasyonu yapılması amaçlanmıştır. Gereç ve Yöntem: Ege Üniversitesi Tıp Fakültesi Hastanesi Tıbbi Genetik Anabilim Dalı’na başvuran Gorlin Sendromu düşünülen dört hastanın PTCH1 genindeki varyantlar ile klinik ve laboratuvar bulguları geriye dönük olarak incelenmiştir. Bulgular: PTCH1 gen dizi analizi yapılan dört hastada üçü yeni olmak üzere dört farklı varyant saptanmıştır. Hastalardaki klinik bulguların sıklıkları ve dağılımı değerlendirildi. Sonuç: Bu çalışma Türkiye’de yapılan Gorlin Sendromlu olgularda PTCH1 gen varyantlarının dağılımı ile ilgili ilk çalışma olup üç yeni varyant saptanmıştır. Saptanan varyantlar ve klinik bulgular ile fenotip-genotip korelasyonu değerlendirilmiştir.