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    Lymphoma predisposing gene in an extended family: CD70 signaling defect
    (Springer/Plenum Publishers, 2020) Khodzhaev, Khusan; Bay, Sema Buyukkapu; Kebudi, Rejin; Altındirek, Didem; Kaya, Ayşenur; Erbilgin, Yücel; Ng, Özden Hatırnaz; Kıykım, Ayça; Erol Çipe, Funda; Şen Zengin, Feride; Fırtına, Sinem; Ng, Yuk Yin; Aksoy, Başak Adaklı; Sayitoğlu, Müge
    Genome-wide sequencing studies in pediatric cancer cohorts indicate that about 10% of patients have germline mutations within cancer predisposition genes. Within this group, primary immune deficiencies take the priority regarding the vulnerability of the patients to infectious agents and the difficulties of cancer management. On the other hand, early recognition of these diseases may offer specific targeted therapies and hematopoietic stem cell transplantation as an option. Besides therapeutic benefits, early diagnosis will provide genetic counseling for the family members. Within this context, an extended family with multiple consanguineous marriages and affected individuals, who presented with combined immune deficiency (CID) and/or Hodgkin lymphoma phenotype, were examined by exome sequencing. A pathogenic homozygous missenseCD70variation was detected (NM_001252.5:c332C>T) in concordance withCD70phenotype and familial segregation was confirmed.CD70variations in patients with CID and malignancy have very rarely been reported. This paper reports extended family with multiple affected members with CID and malignancy carrying a missenseCD70variation, and reviews the rare cases reported in the literature. Primary immune deficiencies appear to be a potential cause for pediatric cancers. Better focusing on these inborn disorders to prevent or make an early diagnosis of malignant transformation and reduce mortalities is important.
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    A novel candidate gene for predisposition of hodgkin lymphoma; Pregnan x receptor (PXR)
    (AMER SOC HEMATOLOGY, 2021) Kebudi, Rejin; Erbilgin, Yücel; Khodzhaev, Khusan; Sarıtaş, Merve; Bozkurt, Ceyhun; Sayitoğlu, Müge
    No Abstract Available
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    Prognostic gene alterations and clonal changes in childhood B-ALL
    (Pergamon-Elsevier Science Ltd, 2019) Erbilgin, Yücel; Fırtına, Sinem; Mercan, Sevcan; Ng, Özden Hatırnaz; Karaman, Serap; Taşar, Orçun; Karakaş Zeybek, Didem; Celkan, Tulin Tiraje; Zengin, Emine; Sarper, Nazan; Yildirmak, Zeynep Yildiz; Şişko, Sinem; Özbek, Uğur; Sayitoğlu, Müge
    Genomic profiles of leukemia patients lead to characterization of variations that provide the molecular classification of risk groups, prediction of clinical outcome and therapeutic decisions. In this study, we examined the diagnostic (n = 77) and relapsed (n = 31) pediatric B-cell acute lymphoblastic leukemia (B-ALL) samples for the most common leukemia-associated gene variations CRLF2, JAK2, PAX5 and IL7R using deep sequencing and copy number alterations (CNAs) (CDKN2A/2B, PAX5, RB1, BTG1, ETV6, CSF2RA, IL3RA and CRLF2) by multiplex ligation proximity assay (MLPA), and evaluated for the clonal changes through relapse. Single nucleotide variations SNVs were detected in 19% of diagnostic 15.3% of relapse samples. The CNAs were detected in 55% of diagnosed patients; most common affected genes were CDKN2A/2B, PAX5, and CRLF2. Relapse samples did not accumulate a greater number of CNAs or SNVs than the cohort of diagnostic samples, but the clonal dynamics showed the accumulation/disappearance of specific gene variations explained the course of relapse. The CDKN2A/2B were most frequently altered in relapse samples and 32% of relapse samples carried at least one CNA. Moreover, CDKN2A/2B alterations and/or JAK2 variations were associated with decreased relapse-free survival. On the other hand, CRLF2 copy number alterations predicted a better survival rate in B-ALL. These findings contribute to the knowledge of CDKN2A/2B and CRLF2 alterations and their prognostic value in B-ALL. The integration of genomic data in clinical practice will enable better stratification of ALL patients and allow deeper understanding of the nature of relapse.
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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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    Zinc finger protein 384 ( ZNF384) impact on childhood mixed phenotype acute leukemia and B-cell precursor acute lymphoblastic leukemia
    (Taylor and Francis, 2022) Sudutan, Tuğce; Erbilgin, Yücel; Hatırnaz, Özden; Karaman, Serap; Karakaş, Zeynep; Küçükcankurt, Fulya; Celkan, Tülin Tiraje; Timur, Çetin; Özdemir, Gül Nihal; Hacısalihoglu, Sadan; Aylan Gelen, Sema; Sayitoğlu, Müge
    B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a heterogeneous malignancy and consists of several genetic abnormalities. Some of these abnormalities are used in clinics for risk calculation and treatment decisions. Patients with ZNF384 rearrangements had a distinct expression profile regardless of their diagnosis, BCP-ALL or mixed phenotype acute leukemia (MPAL) and defined as a new subtype of ALL. In this study, we screened 42 MPAL and 91 BCP-ALL patients for the most common ZNF384 fusions; ZNF384::TCF3, ZNF384::EP300 and ZNF384::TAF15 by using PCR. We identified ZNF384 fusions in 9.5% of MPAL and 7.6% of BCP-ALL. A novel breakpoint was identified in ZNF384::TCF3 fusion in one BCP-ALL patient. T-myeloid MPAL patients showed significantly lower ZNF384 expression compared to lymphoid groups. Patients with ZNF384r had intermediate survival rates based on other subtypes. Prognostic and patient-specific treatment evaluation of ZNF384 fusions in both ALL and MPAL might help to improve risk characterization of patients.