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    A novel homozygous six base pair deletion found in the NFATC2 gene in a patient with EBV-associated lymphoproliferation
    (2024) Erman, Baran; Köstel Bal, Sevgi; Aydoğmuş, Çiğdem; Ersoy, Gizem Zengin; Boztuğ, Kaan
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    Biallelic form of a known CD3E mutation in a patient with severe combined immunodeficiency
    (Springer/Plenum Publishers, 2020) Erman, Baran; Fırtına, Sinem; Fışgın, Tunç; Bozkurt, Ceyhun; Cipe, Funda Erol
    To the Editor: T cell receptor (TCR) complex consists of αβ or γδ TCR chains in combination with four CD3 subunits, CD3ε, CD3γ, CD3δ, and CDζ [1]. This complex is required for thymocyte development and the initiation of T cell-mediated adaptive immune responses. Although TCR chains bind antigenic peptides presented by MHC molecules, the CD3 subunits provide transduction of signals into the cytosol for the activation and differentiation of T lymphocytes [2]. CD3 deficiencies can cause a rare form of severe combined immunodeficiency (SCID). Although CD3ε, CD3δ, and CDζ mutations usually result in a T- B+ +NK+ SCID phenotype, CD3γ deficiency leads to a milder phenotype with autoimmunity [3]. Only 2% of patients with SCID have TCR defects [3]. The T cell antigen receptor epsilon subunit (CD3E) gene is located at 11q23.3 and has been associated with autosomal recessive SCID [4]. Only a few mutations of the CD3E gene have been identified so far [4–8]. Here, we identified the biallelic form of a known CD3E mutation in a patient with a severe T- B+ NK+ phenotype.
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    Correction to : Genetic evaluation of the patients with clinically diagnosed inborn errors of immunity by whole exome sequencing: results from a specialized research center for immunodeficiency in Türkiye
    (2024) Erman, Baran; Aba, Ümran; İpşir, Canberk; Pehlivan, Damla; Aytekin, Caner; Çildir, Gökhan; Çiçek, Begüm; Bozkurt, Ceren; Tekeoğlu, Sidem; Kaya, Melisa; Aydoğmuş, Çiğdem; Çipe, Funda; Sucak, Gülsan; Eltan, Sevgi Bilgiç; Özen, Ahmet; Barış, Safa; Karakoç-Aydıner, Elif; Kıykım, Ayça; Karaatmaca, Betül; Köse, Hülya; Kocacık Uygun, Dilara Fatma; Çelmeli, Fatih; Arıkoğlu, Tuğba; Özcan, Dilek; Keskin, Özlem; Arık, Elif; Soyak Aytekin, Elif; Cesur, Mahmut; Küçükosmanoğlu, Ercan; Kılıç, Mehmet; Yüksek, Mutlu; Bıçakçı, Zafer; Esenboğa, Saliha; Ayvaz, Deniz Çağdaş; Sefer, Asena Pınar; Güner, Şükrü Nail; Keleş, Sevgi; Reisli, İsmail; Muşabak, Uğur; Deveci Demirbaş, Nazlı; Haskoloğlu, Şule; Kılıç, Sara Şebnem; Metin, Ayşe; Doğu, Figen; İkincioğulları, Aydan; Tezcan, İlhan
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    Correction to: Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye (Journal of Clinical Immunology, (2024), 44, 7, (157), 10.1007/s10875-024-01759-w)
    (Springer, 2025) Erman, Baran; Aba, Ümran; İpşir, Canberk; Pehlivan, Damla; Aytekin, Caner; Çildir, Gökhan; Çiçek, Begüm; Bozkurt, Ceren; Tekeoğlu, Sidem; Kaya, Melisa; Aydoğmuş, Çiğdem; Çipe, Funda; Sucak, Gülsan; Eltan, Sevgi Bilgiç; Özen, Ahmet; Barış, Safa; Karakoç-Aydıner, Elif; Kıykım, Ayça; Karaatmaca, Betül; Köse, Hülya; Kocacık Uygun, Dilara Fatma; Çelmeli, Fatih; Arıkoğlu, Tuğba; Özcan, Dilek; Keskin, Özlem; Arık, Elif; Soyak Aytekin, Elif; Cesur, Mahmut; Küçükosmanoğlu, Ercan; Kılıç, Mehmet; Yüksek, Mutlu; Bıçakçı, Zafer; Esenboğa, Saliha; Ayvaz, Deniz Çağdaş; Sefer, Asena Pınar; Güner, Şükrü Nail; Keleş, Sevgi; Reisli, İsmail; Muşabak, Uğur; Deveci Demirbaş, Nazlı; Haskoloğlu, Şule; Kılıç, Sara Şebnem; Metin, Ayşe; Doğu, Figen; İkincioğulları, Aydan; Tezcan, İlhan
    Since the publication of this article we have noticed several errors within the main Table 1 of the manuscript. Four variants were given with different transcript IDs of the same gene. There are also 2 nomenclature errors in the variants of P58 and P117. The necessary corrections have been made in the table below. The errors do not affect the causality of the variants, the results or conclusions reported in the manuscript. The authors apologize for the error, and regret any inconvenience this may have caused. The original version has been corrected. (Table presented.) Patient no Clinical diagnosis (IUIS) Age Gender Consan Gene Variant Transcript ID Zygosity Consequence Novelty P18 CID 20 F + c.214G>A p.Gly72Ser NM_001199917.1 The true RefseqID should be NM_001199919.1 Hom Missense Novel P29 SCID 6 m F + c.551_555del p.Glu184Glyfs*2 c.241G>A p.Gly81Arg NM_000022.4 NM_000022.4 The true RefseqID should be NM_001322050 for these variants Comp. Het Out of frame/Deletion Missense Novel rs2065384316 P34 SCID 1 M + c.779A>G p.Glu260Gly NM_001322050 The true RefseqID should be NM_000022.4 for this variant Hom Missense rs1354071013 P58 SCID 2 M + c.1633delT p.Glu545AsnfsTer The correct nomenclature of this variant is c.1633del p.Glu545Asnfs*58 NM_001350965.2 Hom Out of frame/Deletion Novel P113 PAD/CVID 7 F + c.919C>T p.Arg307Trp NM_001372051.1 The true RefseqID should be NM_001080125.1 Hom Missense rs17860424 P117 SCID 1 F + c.2322G>A p.Arg737His The correct nomenclature of this variant is c.2210G>A p.Arg737His The nucleotide position 2322 refers an old transcript NM_000448.3 Hom Missense rs104894286
  • Küçük Resim
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    Genetic evaluation of the patients with clinically diagnosed inborn errors of immunity by whole exome sequencing: results from a specialized research center for immunodeficiency in Türkiye
    (2024) Erman, Baran; Aba, Ümran; İpşir, Canberk; Pehlivan, Damla; Aytekin, Caner; Çildir, Gökhan; Çiçek, Begüm; Bozkurt, Ceren; Tekeoğlu, Sidem; Kaya, Melisa; Aydoğmuş, Çiğdem; Çipe, Funda; Sucak, Gülsan; Eltan, Sevgi Bilgiç; Özen, Ahmet; Barış, Safa; Karakoç-Aydıner, Elif; Kıykım, Ayça; Karaatmaca, Betül; Köse, Hülya; Kocacık Uygun, Dilara Fatma; Çelmeli, Fatih; Arıkoğlu, Tuğba; Özcan, Dilek; Keskin, Özlem; Arık, Elif; Soyak Aytekin, Elif; Cesur, Mahmut; Küçükosmanoğlu, Ercan; Kılıç, Mehmet; Yüksek, Mutlu; Bıçakçı, Zafer; Esenboğa, Saliha; Ayvaz, Deniz Çağdaş; Sefer, Asena Pınar; Güner, Şükrü Nail; Keleş, Sevgi; Reisli, İsmail; Muşabak, Uğur; Deveci Demirbaş, Nazlı; Haskoloğlu, Şule; Kılıç, Sara Şebnem; Metin, Ayşe; Doğu, Figen; İkincioğulları, Aydan; Tezcan, İlhan
    Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients' long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.
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    Immune reconstitution in the patients with talasemia major after hematopoietic stem cell transplantation
    (Turkish Soc Immunology, 2020) Erman, Baran; Adaklı Aksoy, Başak
    Introduction: Beta-thalaccemia (beta-TM) is one of the most common, autosomal recessive inherited hematologic disorder in the world. Since hematopoietic stem cell transplantation (HSCT) is the only curative treatment, determination of cellular immune reconstitution is crucial for understanding of a successful clinical outcome. Here, we evaluated lymphoid reconstitution in pediatric patients with thalassemia major after stem cell transplantation. Material and Methods: The study included 20 patients with beta-thalassemia major who underwent HSCT. We assessed the clinical and laboratory information of the patients retrospectively. Results: After one year from transplantation, all patients were alive and blood transfusion independent. CD4(+) T cell recovery was poor and CD4/CD8 ratio was impaired in the vast majority of the patients. Percentages and absolute counts of the other lymphoid cells generally reached the normal levels within 12 months. Seventeen patients had full donor chimerism while only 3 of 20 had low chimerism levels ranging between 55-86%. Conclusion: Although a successful clinical course and immune reconstitution were observed, the patients should be followed up carefully. Because, the poor engraftment of CD4(+) T lymphocytes may lead severe infections in the patients.
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    Invasive saprochaete capitata infection in a patient with autosomal recessive CARD9 deficiency and a review of the literature
    (Springer/Plenum Publishers, 2020) Erman, Baran; Fırtına, Sinem; Aksoy, Başak Adaklı; Aydoğdu, Selime; Genç, Gonca Erköse; Doğan, Öner; Cipe, Funda Erol; Fışgın, Tunç
    Purpose Autosomal recessive (AR) CARD9 deficiency is an inherited immune disorder which results in impaired innate immunity against various fungi. Superficial and invasive fungal infections, mainly caused by Candida or Trichophyton species, are the hallmark of CARD9 deficiency. Together with the increasing number of CARD9-deficient patients reported, different pathogenic fungal species have been described such as Phialophora, Exophiala, Corynespora, Aureobasidium, and Ochroconis. Saprochaete capitata is an opportunistic infectious agent in immunocompromised patients and is a common cause of invasive fungal disease in patients with hematological malignancies. In this study, we investigated the causative genetic defect in a patient with S. capitata fungal infection which disseminated to lymph nodes and common bile duct. Methods The identification of the isolated yeast strain was made by direct microscopic examination and confirmed by internal transcribed spacer (ITS) sequencing. We applied whole exome sequencing to search for the disease-causing mutation. Sanger sequencing was used to validate the mutation in the patient and his parents. Results S. capitata was isolated from the biopsy specimen as the causative microorganism responsible for the invasive fungal disease in the patient. Whole exome sequencing revealed a homozygous c.883C > T, (p.Q295*) mutation in CARD9, confirmed by Sanger sequencing. Conclusions This is the first report of invasive Saprochaete infection associated with autosomal recessive (AR) CARD9 deficiency in the literature and thereby further extends the spectrum of fungal diseases seen in these patients.