Browsing by Author "Nepesov, Serdar"

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Mutational landscape of severe combined immunodeficiency patients from Turkey
(Wiley, 2020-06-02) Fırtına, Sinem; Ng, Yuk Yin; Ng, Özden Hatırnaz; Kıykım, Ayça; Aydiner, Elif; Nepesov, Serdar; Camcıoğlu, Yıldız; Sayar, Esra H.; Reisli, Ismail; Torun, Selda H.; Çöğürlü, Tuba; Uygun, Dilara; Şimşek, Işıl E.; Kaya, Ayşenur; Çipe, Funda; Çağdaş, Deniz; Yücel, Esra; Uygun, Vedat; Barış, Safa; Özen, Ahmet; Özbek, Uğur; Sayitoğlu, Müge; Çekiç, Şükrü; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Çocuk İmmünoloji Anabilim Dalı.; 0000-0002-9574-1842; L-1933-2017; 56117061000
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.
Primary antibody deficiencies in Turkey: Molecular and clinical aspects
(Humana Press, 2021-09-30) Fırtına, Sinem; Ng, Yuk Yin; Ng, Özden H.; Kıykım, Ayça; Özek, Esra Yücel; Kara, Manolya; Aydıner, Elif; Nepesov, Serdar; Camcıoğlu, Yıldız; Sayar, Esra H.; Güngören, Ezgi Yalçın; Reisli, İsmail; Torun, Selda H.; Haskoloğlu, Şüle; Çoğurlu, Tuba; Kaya, Ayşenur; Çekiç, Şükrü; Barış, Safa; Özbek, Uğur; Özen, Ahmet; Sayitoğlu, Müge; ÇEKİÇ, ŞÜKRÜ; Bursa Uludağ Üniversitesi/Tıp Fakültesi/Pediatrik İmmünoloji Anabilim Dalı.; 0000-0002-9574-1842; L-1933-2017
Primary antibody deficiencies (PAD) are the most common subtype of primary immunodeficiencies, characterized by increased susceptibility to infections and autoimmunity, allergy, or malignancy predisposition. PAD syndromes comprise of immune system genes highlighted the key role of B cell activation, proliferation, migration, somatic hypermutation, or isotype switching have a wide spectrum from agammaglobulinemia to selective Ig deficiency. In this study, we describe the molecular and the clinical aspects of fifty-two PAD patients. The most common symptoms of our cohort were upper and lower respiratory infections, bronchiectasis, diarrhea, and recurrent fever. Almost all patients (98%) had at least one of the symptoms like autoimmunity, lymphoproliferation, allergy, or gastrointestinal disease. A custom-made next-generation sequencing (NGS) panel, which contains 24 genes, was designed to identify well-known disease-causing variants in our cohort. We identified eight variants (15.4%) among 52 PAD patients. The variants mapped to BTK (n = 4), CD40L (n = 1), ICOS (n = 1), IGHM (n = 1), and TCF3 (n = 1) genes. Three novel variants were described in the BTK (p.G414W), ICOS (p.G60*), and IGHM (p.S19*) genes. We performed Sanger sequencing to validate pathogenic variants and check for allelic segregation in the family. Targeted NGS panel sequencing can be beneficial as a suitable diagnostic modality for diagnosing well-known monogenic PAD diseases (only 2-10% of PADs); however, screening only the coding regions of the genome may not be adequately powered to solve the pathogenesis of PAD in all cases. Deciphering the regulatory regions of the genome and better understanding the epigenetic modifications will elucidate the molecular basis of complex PADs.
Primary antibody deficiencies in Turkey: Molecular and clinical aspects (oct, 10.1007/s12026-021-09242-z, 2021)
(Springer, 2021-10-19) Fırtına, Sinem; Ng, Yuk Yin; Ng, Ozden H.; Kiykim, Ayca; Ozek, Esra Yucel; Kara, Manolya; Aydiner, Elif; Nepesov, Serdar; Camcioglu, Yildiz; Sayar, Esra H.; Gungoren, Ezgi Yalcin; Reisli, Ismail; Torun, Selda H.; Haskologlu, Sule; Cogurlu, Tuba; Kaya, Aysenur; Baris, Safa; Ozbek, Ugur; Ozen, Ahmet; Sayitoglu, Muge; Çekiç, Şükrü; ÇEKİÇ, ŞÜKRÜ; Bursa Uludağ Üniversitesi/Tıp Fakültesi.; 0000-0002-9574-1842; L-1933-2017
The original published version of this article contained a mistake in one of the afliations. The correct afliation of author Manolya Kara (7) should read: Istinye University Faculty of Medicine, VM MedicalPark Pendik Hospital, Pediatric Infectious Diseases Clinic, Istanbul, Turkey The original article has been corrected.