1
|
Tolba A, Mandour I, Musa N, Elmougy F, Hafez M, Abdelatty S, Ibrahim A, Soliman H, Labib B, Elshiwy Y, Ramzy T, Elsharkawy M. Copy Number Variations in Genetic Diagnosis of Congenital Adrenal Hyperplasia Children. Front Genet 2022; 13:785570. [PMID: 35309130 PMCID: PMC8924405 DOI: 10.3389/fgene.2022.785570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Congenital adrenal hyperplasia (CAH) is a monogenic disorder caused by genetic diversity in the CYP21A2 gene, with 21-hydroxylase deficiency (21-OHD) as the most common type. Early sex assignment and early diagnosis of different genetic variations with a proper technique are important to reduce mortality and morbidity. Proper early sex identification reduces emotional, social, and psychological stress. Aim: Detection of a spectrum of aberrations in the CYP21A2 gene, including copy number variations, gene conversion, chimeric genes, and point variations. Methods: The CYP21A2 gene was screened using MLPA assay in 112 unrelated Egyptian children with 21-OHD CAH (33 males and 79 females). Results: In the studied group, 79.5% were diagnosed within the first month of life. 46.8% of the genetic females were misdiagnosed as males. Among the copy number variation results, large deletions in 15.4% and three types of chimeric genes in 9% (CH-1, CH-7, and CAH-X CH-1) were detected. Regarding gene dosage, one copy of CYP21A2 was found in 5 cases (4.5%), three copies were detected in 7 cases (6.3%), and one case (0.9%) showed four copies. Eight common genetic variants were identified, I2G, large deletions, large gene conversion (LGC), I172N, F306 + T, -113 SNP, 8bp Del, and exon 6 cluster (V237E and M239K) with an allelic frequency of 32.62%, 15.45%, 7.30%, 3.00%, 2.58%, 2.15%, 0.86%, and 0.86%, respectively. Conclusion: High prevalence of copy number variations highlights the added value of using MLPA in routine laboratory diagnosis of CAH patients.
Collapse
Affiliation(s)
- Aisha Tolba
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Iman Mandour
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Noha Musa
- Diabetes, Endocrine and Metabolism Pediatric Unit, Cairo University, Giza, Egypt
| | - Fatma Elmougy
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Mona Hafez
- Diabetes, Endocrine and Metabolism Pediatric Unit, Cairo University, Giza, Egypt
| | - Sahar Abdelatty
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Amany Ibrahim
- Diabetes, Endocrine and Metabolism Pediatric Unit, Cairo University, Giza, Egypt
| | - Hend Soliman
- Diabetes, Endocrine and Metabolism Pediatric Unit, Cairo University, Giza, Egypt
| | - Bahaaeldin Labib
- Royal College of Surgeons in Ireland, Medical University of Bahrain, Giza, Egypt
| | - Yasmine Elshiwy
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Tarek Ramzy
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
| | - Marwa Elsharkawy
- Clinical and Chemical Pathology Department, Cairo University, Giza, Egypt
- *Correspondence: Marwa Elsharkawy,
| |
Collapse
|
2
|
Ponomarenko M, Rasskazov D, Arkova O, Ponomarenko P, Suslov V, Savinkova L, Kolchanov N. How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter. BIOMED RESEARCH INTERNATIONAL 2015; 2015:359835. [PMID: 26516624 PMCID: PMC4609514 DOI: 10.1155/2015/359835] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/24/2015] [Indexed: 01/11/2023]
Abstract
The use of biomedical SNP markers of diseases can improve effectiveness of treatment. Genotyping of patients with subsequent searching for SNPs more frequent than in norm is the only commonly accepted method for identification of SNP markers within the framework of translational research. The bioinformatics applications aimed at millions of unannotated SNPs of the "1000 Genomes" can make this search for SNP markers more focused and less expensive. We used our Web service involving Fisher's Z-score for candidate SNP markers to find a significant change in a gene's expression. Here we analyzed the change caused by SNPs in the gene's promoter via a change in affinity of the TATA-binding protein for this promoter. We provide examples and discuss how to use this bioinformatics application in the course of practical analysis of unannotated SNPs from the "1000 Genomes" project. Using known biomedical SNP markers, we identified 17 novel candidate SNP markers nearby: rs549858786 (rheumatoid arthritis); rs72661131 (cardiovascular events in rheumatoid arthritis); rs562962093 (stroke); rs563558831 (cyclophosphamide bioactivation); rs55878706 (malaria resistance, leukopenia), rs572527200 (asthma, systemic sclerosis, and psoriasis), rs371045754 (hemophilia B), rs587745372 (cardiovascular events); rs372329931, rs200209906, rs367732974, and rs549591993 (all four: cancer); rs17231520 and rs569033466 (both: atherosclerosis); rs63750953, rs281864525, and rs34166473 (all three: malaria resistance, thalassemia).
Collapse
Affiliation(s)
- Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga Arkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr Ponomarenko
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA
| | - Valentin Suslov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
3
|
Brønstad I, Skinningsrud B, Bratland E, Løvås K, Undlien D, Sverre Husebye E, Wolff ASB. CYP21A2 polymorphisms in patients with autoimmune Addison's disease, and linkage disequilibrium to HLA risk alleles. Eur J Endocrinol 2014; 171:743-50. [PMID: 25249698 DOI: 10.1530/eje-14-0432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Steroid 21-hydroxylase, encoded by CYP21A2, is the major autoantigen in autoimmune Addison's disease (AAD). CYP21A2 is located in the region of the HLA complex on chromosome 6p21.3, which harbours several risk alleles for AAD. The objective was to investigate whether CYP21A2 gene variants confer risk of AAD independently of other risk alleles in the HLA loci. DESIGN DNA samples from 381 Norwegian patients with AAD and 340 healthy controls (HC) previously genotyped for the HLA-A, -B, -DRB1, and -DQB1 and MICA loci were used for genotyping of CYP21A2. METHODS Genotyping of CYP21A2 was carried out by direct sequencing. Linkage of CYP21A2 to the HLA loci was assessed using UNPHASED version 3.0.10 and PHASE version 2.1. RESULTS Heterozygotes of the single-nucleotide polymorphisms (SNPs) rs397515394, rs6467, rs6474, rs76565726 and rs6473 were detected significantly more frequently in AAD patients compared with HC (P<0.005), but all SNPs were in a linkage disequilibrium (LD) with high-risk HLA-DRB1 haplotypes. rs6472C protected against AAD (odds ratio=0.15, 95% CI (0.08-0.30), P=3.8×10(-10)). This SNP was not in an LD with HLA loci (P=0.02), but did not increase protection when considering the effect of HLA-DRB1 alleles. Mutations causing congenital adrenal hyperplasia were found in heterozygosity in <1.5% of the cases in both groups. CONCLUSION Genetic variants of CYP21A2 associated to AAD are in LD with the main AAD risk locus HLA-DRB1, and CYP21A2 does not constitute an independent susceptibility locus.
Collapse
Affiliation(s)
- Ingeborg Brønstad
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Beate Skinningsrud
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Eirik Bratland
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Kristian Løvås
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Dag Undlien
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Eystein Sverre Husebye
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| | - Anette Susanne Bøe Wolff
- Department of Clinical ScienceUniversity of Bergen, Laboratory building, 8th floor, Bergen 5021, NorwayDepartment of Medical GeneticsOslo University Hospital, Oslo 0407, NorwayDepartment of MedicineHaukeland University Hospital, Bergen 5021, NorwayInstitute of Medical GeneticsUniversity of Oslo, Oslo 0315, Norway
| |
Collapse
|
4
|
Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013; 5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.
Collapse
Affiliation(s)
- Zsófia Bánlaki
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | |
Collapse
|
5
|
Bay JT, Schejbel L, Madsen HO, Sørensen SS, Hansen JM, Garred P. Low C4 gene copy numbers are associated with superior graft survival in patients transplanted with a deceased donor kidney. Kidney Int 2013; 84:562-9. [PMID: 23715124 DOI: 10.1038/ki.2013.195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/01/2013] [Accepted: 03/08/2013] [Indexed: 11/09/2022]
Abstract
Complement C4 is a central component of the classical and the lectin pathways of the complement system. The C4 protein exists as two isotypes C4A and C4B encoded by the C4A and C4B genes, both of which are found with varying copy numbers. Deposition of C4 has been implicated in kidney graft rejection, but a relationship between graft survival and serum C4 concentration as well as C4 genetic variation has not been established. We evaluated this using a prospective study design of 676 kidney transplant patients and 211 healthy individuals as controls. Increasing C4 gene copy numbers significantly correlated with the C4 serum concentration in both patients and controls. Patients with less than four total copies of C4 genes transplanted with a deceased donor kidney experienced a superior 5-year graft survival (hazard ratio 0.46, 95% confidence interval: 0.25-0.84). No significant association was observed in patients transplanted with a living donor. Thus, low C4 copy numbers are associated with increased kidney graft survival in patients receiving a kidney from a deceased donor. Hence, the degree of ischemia may influence the clinical impact of complement.
Collapse
Affiliation(s)
- Jakob T Bay
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | | | | |
Collapse
|
6
|
Current Opinion in Endocrinology, Diabetes & Obesity. Current world literature. Curr Opin Endocrinol Diabetes Obes 2010; 17:293-312. [PMID: 20418721 DOI: 10.1097/med.0b013e328339f31e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|