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    Mediterranean Journal of Hematology and Infectious Diseases
    (Mattioli 1885, 2023) Qipa, Egzona; Acar, Muradiye; Bozkurt, Sureyya; Buyukdogan, Murat; Sonmez, Hazal B.; Sayitoglu, Muge; Erbilgin, Yucel
    Acute lymphoblastic leukemia (ALL) is a malignant disease of hematopoietic stem cells. B cell ALL (B-ALL) is characterized by highly proliferative and poorly differentiated progenitor B cells in the bone marrow. Chromosomal rearrangements, aberrant cell signaling, and mutations lead to dysregulated cell cycle and clonal proliferation of abnormal B cell progenitors. In this study, we aimed to examine hot spot genetic variations in the RUNX1, IDH2, and IL2RA genes in a group of (n=52) pediatric B-ALL. Sanger sequencing results revealed a rare RUNX1 variant p.Leu148Gln in one B-ALL patient with disease recurrence. Additionally, common intronic variations rs12358961 and rs11256369 of IL2RA were determined in two patients. None of the patients had the IDH2 variant.RUNX1, IDH2, and IL2RA variations were rare events in ALL. This study detected a novel pathogenic RUNX1 variation in a patient with a poor prognosis. Examining prognostically important genetic anomalies of childhood lymphoblastic leukemia patients and the signaling pathway components will pilot more accurate prognosis estimations.
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    Mutational landscape of severe combined immunodeficiency patients from Turkey
    (Wiley, 2020) Fırtına, Sinem; Ng, Yuk Yin; Ng, Özden Hatırnaz; Kıykım, Ayça; Aydıner, Elif; Nepesov, Serdar; Camcıoğlu, Yıldız; Sayar, Esra H.; Reisli, İsmail; Torun, Selda H.; Çöğürlü, Tuba; Uygun, Dilara; Şimşek, Işıl E.; Kaya, Ayşenur; Erol Cipe, Funda; Çağdaş, Deniz; Yücel, Esra; Çekiç, Şükrü; Uygun, Vedat; Barış, Safa; Özen, Ahmet; Özbek, Ugur; Sayitoglu, Muge
    Severe combined immunodeficiency (SCID) has a diverse genetic aetiology, where a clinical phenotype, caused by single and/or multiple gene variants, can give rise to multiple presentations. The advent of next-generation sequencing (NGS) has recently enabled rapid identification of the molecular aetiology of SCID, which is crucial for prognosis and treatment strategies. We sought to identify the genetic aetiology of various phenotypes of SCIDs and assessed both clinical and immunologic characteristics associated with gene variants. An amplicon-based targeted NGS panel, which contained 18 most common SCID-related genes, was contumely made to screen the patients (n = 38) with typical SCID, atypical SCID or OMENN syndrome. Allelic segregations were confirmed for the detected gene variants within the families. In total, 24 disease-causing variants (17 known and 7 novel) were identified in 23 patients in 9 different SCID genes: RAG1 (n = 5), RAG2 (n = 2), ADA (n = 3), DCLRE1C (n = 2), NHEJ1 (n = 2), CD3E (n = 2), IL2RG (n = 3), JAK3 (n = 4) and IL7R (n = 1). The overall success rate of our custom-made NGS panel was 60% (39.3% for NK+ SCID and 100% for NK- SCID). Incidence of autosomal-recessive inherited genes is more frequently found in our cohort than the previously reported populations probably due to the high consanguineous marriages in Turkey. In conclusion, the custom-made sequencing panel was able to identify and confirm the previously known and novel disease-causing variants with high accuracy.
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    PTEN and AKT1 variations in childhood T-Cell acute lymphoblastic leukemia
    (Galenos Yayincilik, 2020) Küçükcankurt, Fulya; Erbilgin, Yücel; Fırtına, Sinem; Ng, Özden Hatırnaz; Karakaş, Zeynep; Celkan, Tülin Tiraje; Ünüvar, Ayşegül; Özbek, Uğur; Sayitoglu, Muge
    Objective: PTEN/AKT pathway deregulations have been reported to be associated with treatment response in acute leukemia. This study examined pediatric T-cell acute lymphoblastic leukemia (T-ALL) samples for PTEN and AKT1 gene variations and evaluated the clinical findings. Materials and Methods: Fifty diagnostic bone marrow samples of childhood T-ALL cases were investigated for the hotspot regions of the PTEN and AKT1 genes by targeted next-generation sequencing. Results: A total of five PTEN variations were found in three of the 50 T-ALL cases (6%). Three of the PTEN variations were first reported in this study. Furthermore, one patient clearly had two different mutant clones for PTEN. Two intronic single-nucleotide variations were found in AKT1 and none of the patients carried pathogenic AKT1 variations. Conclusion: Targeted deep sequencing allowed us to detect both low-level variations and clonal diversity. Low-level PTEN/AKT1 variation frequency makes it harder to investigate the clinical associations of the variants. On the other hand, characterization of the PTEN/AKT signaling members is important for improving case-specific therapeutic strategies.
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    Somatic hypermutation defects in two adult hyper immunoglobulin M patients
    (Springer, 2022) Yılmaz, Hülya; Fırtına, Sinem; Saritas, Merve; Sayitoglu, Muge; Ar, Muslum Cem
    Hyper immunoglobulin M (HIGM) syndrome is a rare disorder of the immune system with impaired antibody functions. The clinical picture of the patients varies according to the underlying genetic variation. In this study, we identifed two novel variants in AID and UNG genes, which are associated with autosomal recessive type HIGM, by targeted next-generation sequencing (NGS) panel. A biallelic 11 base pair deletion (c.278_288delATGTGGCCGAC) in the coding sequence of activation-induced cytidine deaminase (AID) gene was identifed in a 36-year-old patient. Biallelic two base pair insertion in exon 7 of uracil nucleoside glycosylase (UNG) gene (c.924_925insGG) was identifed in a 40-year-old patient. Both variants were confrmed by Sanger sequencing. HIGM, like many of the other primary immunodefciencies, is a rare and difcultto-diagnose entity with heterogeneous clinical phenotypes. It should be suspected in patients with a history of early-onset recurrent respiratory infections, enlarged lymph nodes, and autoimmune disorders. There might be a delay in diagnosis until adulthood especially in subtle cases or if HIGM is not included in the diferential diagnosis due lacking of awareness. In this regard, genetic testing with NGS-based diagnostic panels provide a rapid and reasonable tool for the molecular diagnosis of patients with immunodefciencies and hence, decrease the time to diagnose and prevent infection-related complications associated with increased morbidity and mortality.