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Gunsel AS, Ergoren MC, Kemal H, Kafshboran HR, Cerit L, Turgay A, Duygu H. Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population. Genes (Basel) 2023; 14:1967. [PMID: 37895316 PMCID: PMC10606490 DOI: 10.3390/genes14101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions.
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Affiliation(s)
- Aziz Suat Gunsel
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus;
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hatice Kemal
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | | | - Levent Cerit
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
| | - Ayla Turgay
- Laboratory of Medical Genetics, Near East University Hospital, Near East University, Nicosia 99138, Cyprus;
| | - Hamza Duygu
- Department of Cardiology, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus; (A.S.G.); (H.K.); (L.C.); (H.D.)
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Daghagh H, Rahbar Kafshboran H, Daneshmandpour Y, Nasiri Aghdam M, Talebian S, Nouri Nojadeh J, Hamzeiy H, Biskup S, Sakhinia E. Homozygous mutation in CSF1R causes brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS). Bioimpacts 2022. [DOI: 10.34172/bi.2022.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Introduction: The CSF1R gene encodes the receptor for colony-stimulating factor-1, the macrophage, and monocyte-specific growth factor. Mutations in this gene cause hereditary diffuse leukoencephalopathy with spheroids (HDLS) with autosomal dominant inheritance and BANDDOS (Brain Abnormalities, Neurodegeneration, and Dysosteosclerosis) with autosomal recessive inheritance. Methods: Targeted gene sequencing was performed on the genomic DNA samples of the deceased patient and a fetus along with ten healthy members of his family to identify the disease-causing mutation. Bioinformatics tools were used to study the mutation effect on protein function and structure. To predict the effect of the mutation on the protein, various bioinformatics tools were applied. Results: A novel homozygous variant was identified in the gene CSF1R, c.2498C>T; p.T833M in exon 19, in the index patient and the fetus. Furthermore, some family members were heterozygous for this variant, while they had not any symptoms of the disease. In silico analysis indicated this variant has a detrimental effect on CSF1R. It is conserved among humans and other similar species. The variant is located within the functionally essential PTK domain of the receptor. However, no structural damage was introduced by this substitution. Conclusion: In conclusion, regarding the inheritance pattern in the family and clinical manifestations in the index patient, we propose that the mentioned variant in the CSF1R gene may cause BANDDOS.
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Affiliation(s)
- Hossein Daghagh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Nasiri Aghdam
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahrzad Talebian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Nouri Nojadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Hamzeiy
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
- Connective Tissue Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Khabbazi A, Rahbar Kafshboran H, Nasiri Aghdam M, Nouri Nojadeh J, Daghagh H, Daneshmandpour Y, Kazemzadeh M, Hamzeiy H, Sakhinia E. A new report of autoinflammation and PLCG2-associated antibody deficiency and immune dysregulation (APLAID) with a homozygous pattern from Iran. Immunol Lett 2020; 221:27-32. [PMID: 32014489 DOI: 10.1016/j.imlet.2020.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 11/26/2022]
Abstract
Autoinflammation and PLCG2-associated antibody deficiency and immune dysregulation (APLAID) is an autosomal dominant autoinflammatory disease characterized by episodic skin, musculoskeletal, ophthalmic and gastrointestinal tract symptoms. Here we report an 11-year-old girl with a history of repeated episodes of fever, myalgia, arthralgia, abdominal pain, and urticarial rash in the trunk and limbs. Chest and pelvic X-Ray, sacroiliac joints MRI, brain MRI and abdominal CT scan were normal. Anti-nuclear antibody, Rheumatoid factor, cryoglobulin, ANCA/PR3, p-ANCA/MPO, anti-smooth muscle antibody and anti-mitochondrial antibody were negative. Serology for cytomegalovirus, Epstein-Barr, hepatitis B, hepatitis C, and HIV viruses was negative. Serum immunoglobulins were in the normal range. Genetic analysis for familial Mediterranean fever syndrome was negative. Whole exome sequencing was carried out to identify the genetic cause of our patient. We identified a homozygous missense variant (c.579C > G, p. His193Gln) in exon 7 of the PLCG2 gene. Bioinformatic analysis and clinical symptoms suggests this variant to be pathogenic in the homozygous state for APLAID and thus probably acting in an autosomal recessive manner. Our bioinformatic analysis also showed this novel mutation to have detrimental effects on the 3D structure of the PLCG2 protein, which is well conserved among many other similar species.
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Affiliation(s)
- Alireza Khabbazi
- Connective Tissue Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Maryam Nasiri Aghdam
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Nouri Nojadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Daghagh
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Kazemzadeh
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Hamzeiy
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Genomize Inc., Istanbul, Turkey
| | - Ebrahim Sakhinia
- Connective Tissue Diseases Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Rahbar Kafshboran H, Bonyadi M, Miri H, Haghi M, Nikravesh A, Abdolmohammadi R, Hossein Somi M, Khoshbaten M. Association of TNF-α -857 Polymorphism with Inflammatory Bowel Disease in a Group of Iranian Azeri Individuals. Middle East J Dig Dis 2014; 6:28-31. [PMID: 24829702 PMCID: PMC4005480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/26/2013] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic, relapsing, inflammatory disorder of the gastrointestinal tract that includes two entities, Crohn's disease (CD) and ulcerative colitis (UC). As with other complex diseases, both genetic susceptibility and environmental factors play role in the pathogenesis of these diseases. The tumor necrosis factor α (TNF-α) gene is located in the IBD3 region on chromosome 6p21 which is a good functional candidate for involvement in susceptibility to IBD. In addition, the promoter region of TNF-α contains various polymorphisms that have shown a significant association with IBD. METHODS In this case control study we investigated the TNF-α -857 polymorphism in 109 patients (89 UC and 16 CD) who suffered from IBD and 100 healthy age, sex and ethnicity matched adults selected from the same population, as the control group. The polymorphism was checked by amplification refractory system (ARMS) and polymerase chain reaction (PCR). RESULTS Investigation of the association of TNF-α -857 gene promoter polymorphism with both types of IBD showed no significant difference in genotype and allele frequencies of this polymorphism between UC patients and controls. However, a possible association of TNF-α -857 polymorphism (p=0.03) was identified with CD. CONCLUSION TNF-α -857 polymorphism may have a role in the development of CD in the Iranian Azeri Turkish population.
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Affiliation(s)
- Haniyeh Rahbar Kafshboran
- 1Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran
,3Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Bonyadi
- 2Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
,3Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
,Corresponding Author: Mortaza Bonyadi, PhD Center of Excellence for Biodiversity, Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran Tel: +98 411 3357622 Fax:+98 411 3357622
| | - Hamidreza Miri
- 1Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran
| | - Mehdi Haghi
- 2Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Abbas Nikravesh
- 1Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran
| | - Reza Abdolmohammadi
- 3Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- 3Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manouchehr Khoshbaten
- 3Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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