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Alhuthali HM, Ataya EF, Alsalmi A, Elmissbah TE, Alsharif KF, Alzahrani HA, Alsaiari AA, Allahyani M, Gharib AF, Qanash H, Elmasry HM, Hassanein DE. Molecular patterns of alpha-thalassemia in the kingdom of Saudi Arabia: identification of prevalent genotypes and regions with high incidence. Thromb J 2023; 21:115. [PMID: 37950286 PMCID: PMC10636822 DOI: 10.1186/s12959-023-00560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Alpha-thalassemia (α-thalassemia) is one of the most common monogenic diseases in Saudi Arabia and is associated with significant morbidity. Premarital testing programs in Saudi Arabia reduce the burden of hemoglobinopathy disorders, and ongoing monitoring is required. We aimed to explore the molecular nature of α-globin genes and identify the most common genotypes and regions with a high risk of α-thalassemia in Saudi Arabia. METHODS This retrospective study was conducted between January 2021 and December 2022. Six hundred twenty-five samples from patients with microcytic hypochromic anemia in Saudi Arabia were analyzed using reverse dot blot hybridization (RDBH)-based multiplex-PCR, which screens for the known 21 mutations of α-globin genes. RESULTS Seven mutations in the α-globin gene were identified in 88.96% (556) patients. The most frequent abnormality of a-globin genes was -α3.7 (62.3%), followed by α2IVS1(-5nt) (20.7%) and α2 polyA-1 (α2T.Saudi) (14.1%). Interestingly, α2 polyA-2 (α2T.Turkish) was identified in Saudi and presented with -MED, causing Haemoglobin H disease. The incidence of α-thalassemia in Saudi Arabia's cities showed significant differences (P = 0.004). Jeddah City had the highest percentage of cases (25%), followed by Makkah (23%), Taif (13.3%), and Al-Ahassa (12.4%). CONCLUSION The study provides current knowledge about the molecular nature of α- thalassemia, highlights the common genotypes that could contribute to disease occurrence in the Saudi population, and sheds light on Saudi regions with a high incidence. It also recommends further studies in a larger population and with differently composed molecular assays to verify these findings.
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Affiliation(s)
- Hayaa M Alhuthali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia.
| | - Eman F Ataya
- Basic sciences, College of Applied Medical Sciences, Albaha University, Albaha, 4781, Saudi Arabia
- Lecturer of Public Health and Community Medicine, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Alaa Alsalmi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Triq E Elmissbah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Hind A Alzahrani
- Basic sciences, College of Applied Medical Sciences, Albaha University, Albaha, 4781, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Mamdouh Allahyani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Amal F Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, PO Box 11099, Taif, 21944, Saudi Arabia
| | - Husam Qanash
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Hail, 55476, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, Hail, 55473, Saudi Arabia
| | - Heba M Elmasry
- Al Borg Medical laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut, Egypt
| | - Doha Elsayed Hassanein
- Al Borg Medical laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
- Misr University for Sciences and Technology, Clinical and Chemical Pathology Department, Cairo, Egypt
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Xie X, Gan J, Liu Z, Zhou Y, Yuan K, Chen Z, Chen S, Zhou R, Liu L, Huang X, Zhang Y, Liu Q, Zhang W, Huang J, Chen J. Prevalence and genetic analysis of triplicated α-globin gene in Ganzhou region using high-throughput sequencing. Front Genet 2023; 14:1267892. [PMID: 37928241 PMCID: PMC10620506 DOI: 10.3389/fgene.2023.1267892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
α-globin gene triplication carriers were not anemic in general, while some studies found that α-globin gene triplication coinherited with heterozygous β-thalassemia may cause adverse clinical symptoms, which yet lacks sufficient evidence in large populations. In this study, we investigated the prevalence and distribution of α-globin gene triplication as well as the phenotypic characteristics of α-globin gene triplication coinherited with heterozygous β-thalassemia in Ganzhou city, southern China. During 2021-2022, a total of 73,967 random individuals who received routine health examinations before marriage were genotyped for globin gene mutations by high-throughput sequencing. Among them, 1,443 were α-globin gene triplication carriers, with a carrier rate of 1.95%. The most prevalent mutation was αααanti3.7/αα (43.10%), followed by αααanti4.2/αα (38.12%). 42 individuals had coinherited α-globin gene triplication and heterozygous β-thalassemia. However, they did not differ from the individuals with heterozygous β-thalassemia and normal α-globin (αα/αα) in terms of mean corpuscular volume (MCV) and mean corpuscular hemoglobin (MCH) levels. In addition, heterogenous clinical phenotypes were found in two individuals with the same genotype. Our study established a database of Ganzhou α-globin gene triplication and provided practical advice for the clinical diagnosis of α-globin gene triplication.
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Affiliation(s)
- Xinxing Xie
- Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi, China
| | - Jinhui Gan
- Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi, China
| | - Zezhang Liu
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Yulian Zhou
- Dayu Maternal and Child Health Hospital, Ganzhou, Jiangxi, China
| | - Kun Yuan
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Zhigang Chen
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | | | - Rui Zhou
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Lipei Liu
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Tianjin, China
| | | | - Yan Zhang
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Qian Liu
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Wenqian Zhang
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Jungao Huang
- Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi, China
| | - Junkun Chen
- Ganzhou Maternal and Child Health Hospital, Ganzhou, Jiangxi, China
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Ejaz S, Abdullah I, Usman M, Iqbal MA, Munawar S, Khan MI, Imtiaz N, Tahir H, Bari MI, Rasool T, Fatima A, Anwar R, Durrani A, Hameed Y. Mutational analysis of hemoglobin genes and functional characterization of detected variants, through in-silico analysis, in Pakistani beta-thalassemia major patients. Sci Rep 2023; 13:13236. [PMID: 37580329 PMCID: PMC10425424 DOI: 10.1038/s41598-023-35481-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/18/2023] [Indexed: 08/16/2023] Open
Abstract
Thalassemia is one of the most prevalent genetic disorders worldwide. The present study aimed to explore the mutational spectrum of all hemoglobin (HB) encoding genes and to identify the potentially damaging and pathogenic variants in the beta (β)-thalassemia major patients and thalassemia minor carriers of Southern Punjab, Pakistan. A total of 49 β-thalassemia major patients and 49 carrier samples were screened for the identification of HBA1, HBA2, HBB, HBD, HBE1, HBG1 and HBG2 variants by NGS. PCR was performed for the amplification of HB encoding genes and the amplified product of 13 patients and 7 carrier samples were processed for the Sanger sequencing. Various bioinformatics tools and databases were employed to reveal the functional impact and pathogenicity potential of the observed variants. Results depicted a total of 20 variants of HB-related genes by NGS and 5 by Sanger sequencing in thalassemia patients. While 20 variants by NGS and 3 by Sanger were detected in carriers. Few known genetic variants of HB-encoding genes are being reported for the first time in Pakistani thalassemia patients and carriers. However, two novel HBB variants c.375A>C (p.P125P) and c.*61T>G and a novel variant of HBE1 (c.37A>T (p.T13S)) were also documented. Pathogenicity analysis predicted the pathogenic potential of HBB variants (c.47G>A (p.W16*), c.27-28insG (p. S10fs), and c.92+5G>C) for β thalassemia. The study of functional impact indicated that these HBB variants result in the premature termination of translation leading to the loss of functional β-globin protein. It is therefore suggested that the pathogenic HBB variants, identified during present study, can be employed for the diagnosis, carrier screening, and planning therapy of thalassemia.
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Affiliation(s)
- Samina Ejaz
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Iqra Abdullah
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Usman
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | | | - Sidra Munawar
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Irfan Khan
- Department of Hematological Diseases, Thalassemia and Bone Marrow Transplantation, Bahawal Victoria Hospital, Bahawalpur, 63100, Pakistan
| | - Nagina Imtiaz
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Hanniah Tahir
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Muhammad Ihsan Bari
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Tayyaba Rasool
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Aneeza Fatima
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Ramsha Anwar
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Ayman Durrani
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Yasir Hameed
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
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Forouzesh Pour F, Karimi K, Ghaderi Z, Tavakoli Koudehi A, Najmabadi H. Heterozygosity for the Novel HBA2: c.*91_*92delTA Polyadenylation Site Variant on the α2-Globin Gene Expanding the Genetic Spectrum of α-Thalassemia in Iran. Hemoglobin 2020; 44:423-426. [PMID: 33054440 DOI: 10.1080/03630269.2020.1831529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
There are four copy numbers of α-globin genes (16p13.3) in the human genome and the number of defective α-globin genes dictates the severity of α-thalassemia (α-thal). Mutations that occur in the 3' untranslated region (3'UTR), and especially at the polyadenylation (polyA) sites, affect the translation, stability and export of mRNA. A patient with hypochromic microcytic anemia was referred to the Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran by the health network. Molecular analysis of genomic DNA for the evaluation of mutations on the α- and β-globin genes was performed. Direct sequencing of the hemoglobin (Hb) subunit α2 (HBA2) gene revealed a two nucleotide deletion between +816 and +817 in the 3'UTR, located at the polyA site, which seems to be a novel pathogenic variant. This novel variant expands the genetic spectrum of α-thal in the 3'UTR of the HBA2 gene.
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Affiliation(s)
| | - Keyvan Karimi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zhila Ghaderi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Amjad F, Fatima T, Fayyaz T, Khan MA, Qadeer MI. Novel genetic therapeutic approaches for modulating the severity of β-thalassemia (Review). Biomed Rep 2020; 13:48. [PMID: 32953110 PMCID: PMC7484974 DOI: 10.3892/br.2020.1355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/13/2020] [Indexed: 12/13/2022] Open
Abstract
Thalassemia is a genetic haematological disorder that arises due to defects in the α and β-globin genes. Worldwide, 0.3-0.4 million children are born with haemoglobinopathies per year. Thalassemic patients, as well as their families, face various serious clinical, socio-economic, and psychosocial challenges throughout their life. Different therapies are available in clinical practice to minimize the suffering of thalassemic patients to some extent and potentially cure the disease. Predominantly, patients undergo transfusion therapy to maintain their haemoglobin levels. Due to multiple transfusions, the iron levels in their bodies are elevated. Iron overload results in damage to body organs, resulting in heart failure, liver function failure or endocrine failure, all of which are commonly observed. Certain drugs have been developed to enhance the expression of the γ-gene, which ultimately results in augmentation of fetal haemoglobin (HbF) levels and total haemoglobin levels in the body. However, its effectiveness is dependent on the genetic makeup of the individual patient. At present, allogeneic haematopoietic Stem Cell Transplantation (HSCT) is the only practically available option with a high curative rate. However, the outcome of HSCT is strongly influenced by factors such as age at transplantation, irregular iron chelation history before transplantation, histocompatibility, and source of stem cells. Gene therapy using the lentiglobin vector is the most recent method for cure without any mortality, graft rejection and clonal dominance issues. However, delayed platelet engraftment is being reported in some patients. Genome editing is a novel approach which may be used to treat patients with thalassemia; it makes use of targeted nucleases to correct the mutations in specific DNA sequences and modify the sequence to the normal wild-type sequence. To edit the genome at the required sites, CRISPR/Cas9 is an efficient and accurate tool that is used in various genetic engineering programs. Genome editing mediated by CRISPR/Cas9 has the ability to restore the normal β-globin function with minimal side effects. Using CRISPR/Cas9, expression of BCL11A can be downregulated along with increased production of HbF. However, these genome editing tools are still under in-vitro trials. CRISPR/Cas9 has can be used for precise transcriptional regulation, genome modification and epigenetic editing. Additional research is required in this regard, as CRISPR/Cas9 may potentially exhibit off-target activity and there are legal and ethical considerations regarding its use.
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Affiliation(s)
- Fareeha Amjad
- Department of Microbiology and Molecular Genetics, University of The Punjab, Lahore, Punjab 54590, Pakistan
| | - Tamseel Fatima
- Department of Microbiology and Molecular Genetics, University of The Punjab, Lahore, Punjab 54590, Pakistan
| | - Tuba Fayyaz
- Department of Microbiology and Molecular Genetics, University of The Punjab, Lahore, Punjab 54590, Pakistan
| | - Muhammad Aslam Khan
- Sundas Molecular Analysis Centre (SUNMAC), Sundas Foundation, Lahore, Punjab 54000, Pakistan
| | - Muhammad Imran Qadeer
- Department of Microbiology and Molecular Genetics, University of The Punjab, Lahore, Punjab 54590, Pakistan.,Sundas Molecular Analysis Centre (SUNMAC), Sundas Foundation, Lahore, Punjab 54000, Pakistan
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6
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Luo SQ, Chen XY, Tang N, Huang J, Zhong QY, Cai R, Yan TZ. Pedigree Analysis of Nonhomologous Sequence Recombination of HBA1 and HBA2 Genes. Hemoglobin 2020; 44:329-333. [PMID: 32811243 DOI: 10.1080/03630269.2020.1807355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this study was to investigate a family with nonhomologous sequence recombination of HBA1 and HBA2 genes and provide a favorable basis for genetic counseling and eugenics. Peripheral blood of family members was collected. Hematological parameters were determined by an automated cell counter and hemoglobin (Hb) analysis was performed using high performance liquid chromatography (HPLC). Villus samples were taken for prenatal diagnosis (PND). Gap-polymerase chain reaction (gap-PCR) and reverse dot-blot were used for thalassemia genotyping. DNA sequencing was used to analyze the gene sequence of HBA1 (α1-globin) and HBA2 (α2-globin). The nonhomologous sequence recombination allelic variant of HBA1 and HBA2 genes were identified, namely, a gene conversion on the HBA2 gene called α12 (HBA12). The α12 allele consists primarily of the HBA2 gene sequence except for a segment of the IVS-II in which HBA2-specific sequences have been replaced by HBA1-specific sequences. The following genotypes were observed: - -SEA/αα12 (Southeast Asian deletion), αα/αα12 and αQSα/αα12 (Hb Quong Sze or Hb QS; HBA2: c.377T>C), and all manifested as small cell hypochromic anemia. To find the α12 allele in the Chinese population and clarify the influence of the α12 allele and its common inheritance with abnormal Hb and α-thalassemia (α-thal) on α-globin gene expression can help guide clinical diagnosis and genetic counseling.
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Affiliation(s)
- Shi-Qiang Luo
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xing-Yuan Chen
- Department of Laboratory Medicine, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ning Tang
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jun Huang
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Qing-Yan Zhong
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Ti-Zhen Yan
- Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China.,Institute of Reproduction and Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi Zhuang Autonomous Region, People's Republic of China
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Aldakeel SA, Ghanem NZ, Al-Amodi AM, Osman AK, Al Asoom LI, Ahmed NR, Almandil NB, Akhtar MS, Azeez SA, Borgio JF. Identification of seven novel variants in the β-globin gene in transfusion-dependent and normal patients. Arch Med Sci 2020; 16:453-459. [PMID: 32190157 PMCID: PMC7069418 DOI: 10.5114/aoms.2019.84825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/20/2018] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Abnormality in HBB results in an inherited recessive blood disorder, which can be caused by variants at the transcriptional or translational level affecting the stability and the production of the HBB chain. The severity of the disease relies on the variant's characteristics. This study aimed to identify the common β-globin HBB variants in the population of the Eastern Province, which has the highest prevalence of blood diseases in Saudi Arabia. MATERIAL AND METHODS Direct sequence of β-globin HBB gene, and alpha-globin HBA1 and HBA2 genes was performed on a total of 545 blood samples (transfusion-dependent: 215, 106 men and 109 women; normal healthy subjects: 330, 197 men and 133 women) collected from Saudi Arabian participants in the Eastern region. RESULTS A total of 36 variants in HBB gene were revealed with 11 variants that have been reported for the first time in Saudi Arabia, including 7 novel variants that have been identified for the first time in HBB gene. The novel variants consisted of two exonic (HBB:c.252C>T; HBB:c.281G>T) and five intronic variants (c.316-183_316-168del; c.315+241T>A; c.315+376T>C; c.316-114C>G; c.315+208T>G) at HBB gene. The novel exonic variants and three (c.316-183_316-168del; c.315+241T>A; c.315+376T>C) intronic variants were co-inherited with α deletion. CONCLUSIONS This current study updated the HBB gene variations with newly identified variants of HBB gene and co-inheritance with α-globin deletions. The identified β-globin mutations will strengthen the genetic reference that could aid in characterizing mutations that are associated with phenotype of thalassemia in a specific region.
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Affiliation(s)
- Sumayh A. Aldakeel
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Neda Z. Ghanem
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Amani M. Al-Amodi
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahoud Khalid Osman
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Nazish Rafique Ahmed
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mohammed Shakil Akhtar
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed Abdul Azeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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8
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AbdulAzeez S, Almandil NB, Naserullah ZA, Al-Jarrash S, Al-Suliman AM, ElFakharay HI, Borgio JF. Co-inheritance of alpha globin gene deletion lowering serum iron level in female beta thalassemia patients. Mol Biol Rep 2020; 47:603-606. [PMID: 31705350 DOI: 10.1007/s11033-019-05168-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/30/2019] [Indexed: 12/21/2022]
Abstract
In the Eastern province of Saudi Arabia, thalassemia is highly common. Data on the effect of alpha globin gene variation on the concentration of iron on transfusion dependent Saudis are scanty. A total of 166 transfusions dependent β-thalassemia were included in this study to understand association between the alpha globin gene variation and concentration of iron. Using multiplex PCR, the alpha globin gene deletions were identified. Also, HBA1 and HBA2 genes were sequenced by Sanger sequencing. Saudi transfusion dependent female β-thalassemia patients with wild alpha globin genotype (αα/αα) were observed with iron level beyond the normal range. However, normal range of iron was observed in transfusion dependent Saudi female beta thalassemia patients co-inherited with double (-α3.7/-α3.7, or --Fil/αα or --MED/αα or - (α) 20.5/αα) or double heterozygosity (- -/-α3.7) alpha globin gene deletions, which is significantly (p < 0.0001) less compared to the Saudi transfused female with wild alpha globin genotype (αα/αα). The co-inheritance alpha globin gene deletions in female beta thalassemia patients were significantly lowering serum iron. Detailed studies can be taken forward to identify the molecular pathways involved in globin gene deletion as modulator.
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Affiliation(s)
- Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | | | | | | | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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9
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Al-Amodi AM, Ghanem NZ, Aldakeel SA, Ibrahim Al Asoom L, Rafique Ahmed N, Almandil NB, Naserullah ZA, Al-Jarrash S, Shakil Akhtar M, AbdulAzeez S, Al-Ali AK, Borgio JF. Hemoglobin A 2 (HbA 2) has a measure of unreliability in diagnosing β-thalassemia trait (β-TT). Curr Med Res Opin 2018; 34:945-951. [PMID: 29383950 DOI: 10.1080/03007995.2018.1435520] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Detection of β-thalassemia trait or carriers (β-TT) depends significantly on an increase in Hemoglobin A2 (HbA2) levels, which is found at low levels (<3%) in normal healthy individuals and elevated levels (≥3.5%) in β-TT individuals. The study was designed to evaluate the reliability of the diagnostic parameter HbA2 in the differentiation of β-TT and non-β-TT in Saudis. METHODS The widely used high performance liquid chromatography (Variant II Bio-Rad) was used to measure HbA2 levels in blood. Sanger sequencing was used to screen the variation in globin genes (HBB, HBD, HBA1, and HBA2). All the study subjects were divided into βTT and non-βTT (wild) categories based on the presence or absence of HBB variations and further sub-divided into false positive, true positive, false negative, and true negative, based on HbA2 values. RESULTS Out of 288 samples, 96 had HBB gene mutations. Of the 96 β-TT samples, sickle cell trait (SCT) samples (n = 58) were excluded, while the remaining (38 β-TT) were included in the detailed analysis: seven subjects with the HBB mutation had normal HbA2 (<3%), and three were borderline (3.1-3.9%). The remainder (n = 28) had an elevated HbA2 level (>4%). Based on HbA2 analysis alone, both these groups would be incorrectly diagnosed as normal. Similarly, of the 189 non-β-TT samples, 179 had normal HbA2, eight had borderline HbA2, and two had a HbA2 level above 4%. Based on HbA2 analysis alone, borderline and >4% HbA2 individuals, negative for β-TT, can be incorrectly diagnosed as carriers. CONCLUSION Given the percentage of samples falling in the HbA2 "borderline" and "normal" categories, it can be concluded that HbA2 has a measure of unreliability in the diagnosis of β-thalassemia carriers.
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Affiliation(s)
- Amani M Al-Amodi
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Neda Z Ghanem
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Sumayh A Aldakeel
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- b Department of Physiology, College of Medicine , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Nazish Rafique Ahmed
- b Department of Physiology, College of Medicine , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Noor B Almandil
- c Department of Clinical Pharmacy Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | | | - Sana Al-Jarrash
- d Dammam Maternity and Child Hospital , Dammam , Saudi Arabia
| | - Mohammed Shakil Akhtar
- e Department of Biochemistry , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Sayed AbdulAzeez
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Amein K Al-Ali
- e Department of Biochemistry , Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - J Francis Borgio
- a Department of Genetic Research , Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
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Alaithan MA, AbdulAzeez S, Borgio JF. A comprehensive review of the prevalence of beta globin gene variations and the co-inheritance of related gene variants in Saudi Arabians with beta-thalassemia. Saudi Med J 2018; 39:329-335. [PMID: 29619482 PMCID: PMC5938644 DOI: 10.15537/smj.2018.4.21360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Beta-thalassemia is a genetic disorder that is caused by variations in the beta-hemoglobin (HBB) gene. Saudi Arabia is among the countries most affected bybeta-thalassemia, and this is particularly problematic in the Eastern regions. This review article is an attempt to compile all the reported mutations to facilitate further national-level studies to prepare a Saudi repository of HBB gene variations. In Saudi Arabians, IVSI-5 (G greater than C) and Cd 39 (C greater than T) are the most prevalent HBB gene variations out of 42 variations. The coinheritance of HBB gene variations with ATRX, HBA1, HBA2, HBA12, AHSP, and KLF1 gene variations were observed to be common in the Saudi population. National surveys on the molecular nature of hemoglobinopathies should be set up through collaborations between research centers from various regions to create a well-documented molecular data bank. This data bank can be used to develop a premarital screening program and lead to the best treatment and prevention strategies for beta-thalassemia.
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Affiliation(s)
- Mousa A Alaithan
- Department of Genetic Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia. E-mail.
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Borgio JF, AbdulAzeez S, Al-Muslami AM, Naserullah ZA, Al-Jarrash S, Al-Suliman AM, Al-Madan MS, Al-Ali AK. KLF1 gene and borderline hemoglobin A 2 in Saudi population. Arch Med Sci 2018; 14:230-236. [PMID: 29379553 PMCID: PMC5778434 DOI: 10.5114/aoms.2018.72245] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/29/2017] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION Elevated HbA2 (hemoglobin A2) level is considered the most reliable hematological parameter for the detection of β-thalassemia carriers. However, some carriers are difficult to recognize because the level of HbA2 is not in the distinctive carrier range, i.e. 4.0-6.0%; instead, some carriers have HbA2 levels between normal and carrier levels, i.e. borderline HbA2 (HbA2 = 3.1-3.9%). Studies have shown that variations in the erythroid Krüppel-like factor (KLF1) gene lead to borderline HbA2 in β-thalassemia carriers from various populations. The incidence of borderline HbA2 in Saudis is high. MATERIAL AND METHODS To confirm the influence of variations in KLF1, HBA1, HBA2 and HBB genes for the reduction of the level of HbA2 in Saudi β-thalassemia carriers, we performed a direct sequence analysis of KLF1, HBA1, HBA2 and HBB genes from 212 healthy Saudis (88 subjects: HbA2 < 3; 72 subjects: HbA2 = 3.1 to 3.9; 52 subjects HbA2 > 4.3). RESULTS The presence of the borderline HbA2 level is not specific to any type of β-thalassemia variation or β+-thalassemia variations in Saudis. Two exonic (c.304T>C and c.544T>C) and two 3' untranslated region (3'UTR) (c.*296G>A and c.*277C>G) variations have been identified in the KLF1 gene for the first time from an Arab population. None of these four variations in KLF1 genes are significantly associated with the Saudis with borderline HbA2. α Globin genotype, -α23.7/α1α2, is found to be the most frequent (55.55%) among healthy Saudis with borderline HbA2 compared with the other groups (HbA2 < 3 = 20.45%; HbA2 > 4.3 = 13.51%). CONCLUSIONS Further studies are necessary to determine the influence of other factors on the presence of borderline HbA2 in 41.67% of Saudis.
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Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), University of Dammam, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), University of Dammam, Dammam, Saudi Arabia
| | - Ahmed M. Al-Muslami
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), University of Dammam, Dammam, Saudi Arabia
| | | | | | - Ahmed M. Al-Suliman
- Al-Omran Scientific Chair for Hematological Diseases Prevalent in the Al-Ahssa Area, King Faisal University, Al-Ahssa, Saudi Arabia
| | - Mohammed S. Al-Madan
- Department of Pediatrics, King Fahd Hospital of the University, Al-Khobar, Saudi Arabia
| | - Amein K. Al-Ali
- Department of Biochemistry, University of Dammam, Dammam, Saudi Arabia
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12
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Borgio JF, Abdulazeez S, Almandil NB, Naserullah ZA, Al-Jarrash S, Al-Suliman AM, Elfakharay HI, Qaw FS, Alabdrabalnabi FI, Alkhalifah MA, Shakil Akhtar M, Qutub H, Al-Ali AK. The ‑α3.7 deletion in α‑globin genes increases the concentration of fetal hemoglobin and hemoglobin A2 in a Saudi Arabian population. Mol Med Rep 2017; 17:1879-1884. [PMID: 29138844 DOI: 10.3892/mmr.2017.8033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/29/2017] [Indexed: 11/06/2022] Open
Abstract
The regions of Al‑Qatif and Al‑Ahssa in the Eastern Province of Saudi Arabia are known for their high prevalence of hemoglobinopathies, including β‑thalassemia and sickle cell anemia. Previously, the α‑gene deletion has been demonstrated as highly prevalent among populations residing in these two regions. The present study was conducted in order to investigate the implications of the α‑globin gene deletion on fetal hemoglobin (HbF) and hemoglobin α2 (HbA2) concentrations in patients with transfusion‑dependent β‑thalassemia. A total of 166 Saudi patients with transfusion‑dependent β‑thalassemia and 337 healthy Saudi patients were included in the study. The ‑α3.7, ‑α4.2, -‑FIL, -‑SEA, -‑MED and -‑(20.5) gene deletions were identified using multiplex α‑globin deletion polymerase chain reaction. The present study revealed that the ‑α3.7 gene deletion is the most prevalent (43.5%) in the Saudi populations that were analyzed and is characterized by the deletion of 3,804 base pairs. Numerous genotypes, namely ‑3.7α2/α1α2, ‑3.7α2/α1α12, ‑3.7α2/‑3.7α2, ‑3.7α2HphI/α1α2HphI, ‑3.7α2/α1‑4.2, ‑3.7α2/α1polyA‑1α2, ‑3.7α12/α1α12, ‑‑FIL/‑3.7α2 and ‑3.7α2/‑3.7α2Hb Villiers le Bel were also identified in the investigated population. Furthermore, a gradual increase in the concentration of HbF and HbA2 in patients with β‑thalassemia and the number of α‑gene deletions was demonstrated; whereas in healthy patients the level of HbA2 was demonstrated to decrease as the number of α‑gene deletions increased. Therefore, it can be concluded that the high HbF concentration in the present study is predominantly associated with other mutations associated with β‑thalassemia rather than α‑globin deletions. Furthermore, the results of the present study also revealed novel α‑gene deletion genotypes prevalent in the population studied, namely α1α2/α1α2HphI, α1α2HphI/α1α2HphI, α1α2/α1α2Hb Handsworth, ‑3.7α2HphI/α1α2HphI, ‑3.7α2/‑3.7α2Hb Villiers le Bel and ‑-MED/α1α2HphI.
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Affiliation(s)
- J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Sayed Abdulazeez
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Sana Al-Jarrash
- Dammam Maternity and Child Hospital, Dammam 32253, Saudi Arabia
| | - Ahmed M Al-Suliman
- Al‑Omran Scientific Chair for Hematological Diseases Prevalent in The Al‑Ahssa Area, King Faisal University, Al‑Ahssa 31982, Saudi Arabia
| | | | - Fuad S Qaw
- Department of Biochemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | | | - Mohammed Shakil Akhtar
- Department of Biochemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Hatem Qutub
- King Fahd Hospital of The University, Al‑Khobar 34445, Saudi Arabia
| | - Amein K Al-Ali
- Al‑Omran Scientific Chair for Hematological Diseases Prevalent in The Al‑Ahssa Area, King Faisal University, Al‑Ahssa 31982, Saudi Arabia
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13
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Impact of annotation error in α-globin genes on molecular diagnosis. PLoS One 2017; 12:e0185270. [PMID: 29049312 PMCID: PMC5648127 DOI: 10.1371/journal.pone.0185270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/08/2017] [Indexed: 11/21/2022] Open
Abstract
Background Recent studies on the variants in duplicated human alpha globin genes (HBA2 and HBA1) actively target the α-globin gene as molecular modulators for the treatment of β-thalassemia major. Identification of the exact position of variant in HBA1, HBA2 or its patchworks is mandatory to support the therapeutic aims in β-thalassemia major, by identifying specific modulators for the reactivation of fetal hemoglobin production. Hence, accurate identification of the variants in α-globin genes is crucial for the proper diagnosis, treatment and genetic counseling. Method The objective was to reveal the annotation errors produced in α-globin gene sequence analysis while using different analytic tools. An HBA2 gene sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert have been taken as examples to prove annotation error in α-globin gene from different analytic tools. Results and discussion Although various bioinformatics tools used to predict variants are usually of high reliability, the current study using the an alpha globin 2 sequence with the HBA2:c.95+2_95+6delTGAGG variant and a recently reported HBA12 gene convert, has showcased ambiguous outputs among the three bioinformatics tools used and against the manual analytical method adopted. Conclusions This report emphasizes the necessity for caution in the usage of DNA sequence analysis tools during molecular diagnosis and the importance of the selection of more appropriate tools for analysis. Furthermore, ethnic specific sequences should be considered as reference sequence for the analysis to bypass sequence dissimilarities among diverse populations.
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Pécriaux A, Paillard C, Galoisy A, Riou J, Le metayer N, Wajcman H, Pissard S. Evidence for a gene conversion in a Hb Arya Carrier [α codon 47 Asp>Asn, Hb A1(or Hb A2):c.142 G>A]. Int J Lab Hematol 2017; 39:e55-e59. [DOI: 10.1111/ijlh.12609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Pécriaux
- Department of genetics; APHP, GHU Henri Mondor; Creteil France
| | - C. Paillard
- Service d'hématologie oncologie pédiatrique; CHU Hautepierre and Laboratoire d'Immuno Rhumatologie Moléculaire; INSERM UMR_S1109; Faculté de Médecine; Fédération Hospitalo-Universitaire OMICARE; Fédération de Médecine Translationnelle de Strasbourg (FMTS); Université de Strasbourg; Strasbourg France
| | - A. Galoisy
- Laboratoire d'hématologie UF6344; CHU de Hautepierre; Strasbourg France
| | - J. Riou
- Department of genetics; APHP, GHU Henri Mondor; Creteil France
| | - N. Le metayer
- Department of genetics; APHP, GHU Henri Mondor; Creteil France
| | - H. Wajcman
- IMRB Inserm U 955eq2, and GReX; GHU Henri Mondor; Creteil France
| | - S. Pissard
- Department of genetics; APHP, GHU Henri Mondor; Creteil France
- IMRB Inserm U 955eq2, and GReX; GHU Henri Mondor; Creteil France
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Existence of HbF Enhancer Haplotypes at HBS1L-MYB Intergenic Region in Transfusion-Dependent Saudi β-Thalassemia Patients. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1972429. [PMID: 28280727 PMCID: PMC5322420 DOI: 10.1155/2017/1972429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/14/2016] [Accepted: 01/16/2017] [Indexed: 12/21/2022]
Abstract
Background and Objectives. β-Thalassemia and sickle cell disease are genetic disorders characterized by reduced and abnormal β-globin chain production, respectively. The elevation of fetal hemoglobin (HbF) can ameliorate the severity of these disorders. In sickle cell disease patients, the HbF level elevation is associated with three quantitative trait loci (QTLs), BCL11A, HBG2 promoter, and HBS1L-MYB intergenic region. This study elucidates the existence of the variants in these three QTLs to determine their association with HbF levels of transfusion-dependent Saudi β-thalassemia patients. Materials and Methods. A total of 174 transfusion-dependent β-thalassemia patients and 164 healthy controls from Eastern Province of Saudi Arabia were genotyped for fourteen single nucleotide polymorphisms (SNPs) from the three QTL regions using TaqMan assay on real-time PCR. Results. Genotype analysis revealed that six alleles of HBS1L-MYB QTL (rs9376090C p = 0.0009, rs9399137C p = 0.008, rs4895441G p = 0.004, rs9389269C p = 0.008, rs9402686A p = 0.008, and rs9494142C p = 0.002) were predominantly associated with β-thalassemia. In addition, haplotype analysis revealed that haplotypes of HBS1L-MYB (GCCGCAC p = 0.022) and HBG2 (GTT p = 0.009) were also predominantly associated with β-thalassemia. Furthermore, the HBS1L-MYB region also exhibited association with the high HbF cohort. Conclusion. The stimulation of HbF gene expression may provide alternative therapies for the amelioration of the disease severity of β-thalassemia.
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16
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Alyousef YM, Borgio JF, AbdulAzeez S, Al-Masoud N, Al-Ali AA, Al-Shwaimi E, Al-Ali AK. Association of MBL2 Gene Polymorphism with Dental Caries in Saudi Children. Caries Res 2016; 51:12-16. [PMID: 27894112 DOI: 10.1159/000450963] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/20/2016] [Indexed: 11/19/2022] Open
Abstract
The high prevalence of dental caries in children worldwide is a major oral health problem which requires early intervention. Dental caries is mainly caused by the action of acids produced by bacteria in addition to many other factors. Recent genetic studies have reported that a number of genes are associated with the susceptibility to dental caries. The majority of these genes are associated with inflammation, increased susceptibility to infection, and dentine matrix formation. Using the TaqMan assay and direct DNA sequencing, the prevalence of 6 single-nucleotide polymorphisms (SNPs) in MMP9, MBL2, MMP2, and TIMP2 genes was determined in 102 children with caries and in 100 age-matched caries-free controls. Out of the 6 SNPs tested in the 4 selected genes, only rs11003125 in the MBL2 gene was shown to be associated with a high prevalence of caries in our cohort. In addition, haplotype analysis of the 6 SNPs tested revealed that certain haplotypes, namely GT of rs11003125G and rs7501477T and GT of rs7096206G and rs7501477T, were found to be associated with a high prevalence of dental caries in our cohort, while haplotype AG of rs17576A and rs7501477G was found to have a protective effect against dental caries. In conclusion, the data indicate that rs11003125 in the MBL2 gene was shown to be associated with a high prevalence of caries in our cohort, and 2 haplotypes are also involved in the increased susceptibility to dental caries.
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Affiliation(s)
- Yousef M Alyousef
- College of Dentistry, Institute for Research and Medical Consultation (IRMC), University of Dammam, Dammam, Saudi Arabia
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Abstract
Alpha-thalassemia (α-thal) is a disorder caused by the deletion of single or double α-globin genes, and/or point mutations in the α-globin genes. There are 2 common types of α-globin genes; HBA2 and HBA1. Recently, it has been discovered that the HBA2 gene is replaced by a unique HBA12 gene convert in 5.7% of the Saudi population. The α-globin genes have been emerging as a molecular target for the treatment of β-thalassemia (β-thal). Hence, it is essential to understand the molecular nature of α-globin genes to treat the most prevalent hemoglobin disorders, such as sickle cell disease, α-thal, and β-thal prevalent in the Kingdom of Saudi Arabia. Thirty-two different α-globin genotypes have been observed in the Saudi population. This review outlines the classification of the α-globin genes on the basis of their molecular nature and complex combinations of α-globin genes, and their variants predominant in Saudis.
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Affiliation(s)
- J Francis Borgio
- Center for Research and Medical Consultation, University of Dammam, Dammam, Kingdom of Saudi Arabia. E-mail.
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Intronic Polymorphisms in the CDKN2B-AS1 Gene Are Strongly Associated with the Risk of Myocardial Infarction and Coronary Artery Disease in the Saudi Population. Int J Mol Sci 2016; 17:395. [PMID: 26999117 PMCID: PMC4813250 DOI: 10.3390/ijms17030395] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 01/01/2023] Open
Abstract
Recent genome-wide association studies identified single nucleotide polymorphisms (SNPs) on the chromosome 9p21.3 conferring the risk for CAD (coronary artery disease) in individuals of Caucasian ancestry. We performed a genetic association study to investigate the effect of 12 candidate SNPs within 9p21.3 locus on the risk of CAD in the Saudi population of the Eastern Province of Saudi Arabia. A total of 250 Saudi CAD patients who had experienced an myocardial infarction (MI) and 252 Saudi age-matched healthy controls were genotyped using TaqMan assay. Controls with evidenced lack of CAD provided 90% of statistical power at the type I error rate of 0.05. Five percent of the results were rechecked for quality control using Sanger sequencing, the results of which concurred with the TaqMan genotyping results. Association analysis of 12 SNPs indicated a significant difference in the genotype distribution for four SNPs between cases and controls (rs564398 p = 0.0315, χ2 = 4.6, odds ratio (OD) = 1.5; rs4977574 p = 0.0336, χ2 = 4.5, OD = 1.4; rs2891168 p = 1.85 × 10 − 10, χ2 = 40.6, OD = 2.1 and rs1333042 p = 5.14 × 10 − 9, χ2 = 34.1, OD = 2.2). The study identified three protective haplotypes (TAAG p = 1.00 × 10 − 4; AGTA p = 0.022 and GGGCC p = 0.0175) and a risk haplotype (TGGA p = 2.86 × 10 − 10) for the development of CAD. This study is in line with others that indicated that the SNPs located in the intronic region of the CDKN2B-AS1 gene are associated with CAD.
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In-Silico Computing of the Most Deleterious nsSNPs in HBA1 Gene. PLoS One 2016; 11:e0147702. [PMID: 26824843 PMCID: PMC4733110 DOI: 10.1371/journal.pone.0147702] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/07/2016] [Indexed: 01/30/2023] Open
Abstract
Background α-Thalassemia (α-thal) is a genetic disorder caused by the substitution of single amino acid or large deletions in the HBA1 and/or HBA2 genes. Method Using modern bioinformatics tools as a systematic in-silico approach to predict the deleterious SNPs in the HBA1 gene and its significant pathogenic impact on the functions and structure of HBA1 protein was predicted. Results and Discussion A total of 389 SNPs in HBA1 were retrieved from dbSNP database, which includes: 201 non-coding synonymous (nsSNPs), 43 human active SNPs, 16 intronic SNPs, 11 mRNA 3′ UTR SNPs, 9 coding synonymous SNPs, 9 5′ UTR SNPs and other types. Structural homology-based method (PolyPhen) and sequence homology-based tool (SIFT), SNPs&Go, PROVEAN and PANTHER revealed that 2.4% of the nsSNPs are pathogenic. Conclusions A total of 5 nsSNPs (G60V, K17M, K17T, L92F and W15R) were predicted to be responsible for the structural and functional modifications of HBA1 protein. It is evident from the deep comprehensive in-silico analysis that, two nsSNPs such as G60Vand W15R in HBA1 are highly deleterious. These “2 pathogenic nsSNPs” can be considered for wet-lab confirmatory analysis.
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Borgio JF, AbdulAzeez S, Naserullah ZA, Al-Jarrash S, Al-Ali RA, Al-Madan MS, Al-Muhanna F, Al-Suliman AM, Al-Nafie A, Steinberg MH, Al-Ali AK. Mutations in the β-globin gene from a Saudi population: an update. Int J Lab Hematol 2016; 38:e38-40. [PMID: 26822801 DOI: 10.1111/ijlh.12463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- J F Borgio
- Institute for Research & Medical Consultation, University of Dammam, Dammam, Saudi Arabia. ,
| | - S AbdulAzeez
- Institute for Research & Medical Consultation, University of Dammam, Dammam, Saudi Arabia
| | - Z A Naserullah
- Dammam Maternity and Child Hospital, Dammam, Saudi Arabia
| | - S Al-Jarrash
- Dammam Maternity and Child Hospital, Dammam, Saudi Arabia
| | - R A Al-Ali
- King Fahd Hospital of the University, University of Dammam, Al-Khobar, Saudi Arabia
| | - M S Al-Madan
- King Fahd Hospital of the University, University of Dammam, Al-Khobar, Saudi Arabia
| | - F Al-Muhanna
- King Fahd Hospital of the University, University of Dammam, Al-Khobar, Saudi Arabia
| | - A M Al-Suliman
- King Fahd Hospital, King Faisal University, Al-Ahssa, Saudi Arabia
| | - A Al-Nafie
- King Fahd Hospital of the University, University of Dammam, Al-Khobar, Saudi Arabia
| | - M H Steinberg
- Centre of Excellence in Sickle Cell Disease, Boston University School of Medicine, Boston, MA, USA
| | - A K Al-Ali
- Institute for Research & Medical Consultation, University of Dammam, Dammam, Saudi Arabia.,King Fahd Hospital, King Faisal University, Al-Ahssa, Saudi Arabia
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Turner A, Sasse J, Varadi A. Development and validation of a high throughput, closed tube method for the determination of haemoglobin alpha gene (HBA1 and HBA2) numbers by gene ratio assay copy enumeration-PCR (GRACE-PCR). BMC MEDICAL GENETICS 2015; 16:115. [PMID: 26683685 PMCID: PMC4683937 DOI: 10.1186/s12881-015-0258-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 12/04/2015] [Indexed: 11/13/2022]
Abstract
BACKGROUND Deletions of the α-globin genes are the most common genetic abnormalities in the world. Currently multiplex Gap-PCRs are frequently used to identify specific sets of common deletions. However, these assays require significant post-amplification hands on time and cannot be used to identify novel or unexpected deletions. The aim of the current study was to develop a rapid screening test for the detection of all deletions of the α-globin genes that can be integrated into a high volume clinical laboratory workflow. METHODS A gene ratio assay copy enumeration (GRACE) PCR method was developed by simultaneous amplification of targets in the α-globin genes (HBA1 and HBA2) and the chloride channel voltage sensitive 7 (CLCN7) reference gene. A novel application of High Resolution Melting (HRM) analysis then allowed rapid determination of α-globin gene copy numbers. The assay was validated using 105 samples with previously determined and 62 samples with unknown α-globin genotypes. RESULTS The GRACE-PCR assay detected abnormal α-globin gene copy numbers in 108 of the 167 samples evaluated. The results were consistent with those from a commercial reverse hybridization assay and no allele drop out was observed. CONCLUSIONS We have successfully developed and validated a GRACE-PCR screening test for the detection of deletions and duplications of the α-globin genes. The assay is based on copy number determination and has the ability to detect both known and novel deletions of the α-globin genes. It is a closed tube technique; consequently the risk of amplicon contamination is negligible. Amplification, detection and analysis can be completed within one hour, making it faster, cheaper and simpler than other existing tests and thus well suited as a rapid first step in a clinical laboratory workflow.
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Affiliation(s)
- Andrew Turner
- Department of Pathology and Laboratory Medicine, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates.
| | - Jurgen Sasse
- Department of Pathology and Laboratory Medicine, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates.
| | - Aniko Varadi
- Department of Biological, Biomedical and Analytical Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK.
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Al-Nafie AN, Borgio JF, AbdulAzeez S, Al-Suliman AM, Qaw FS, Naserullah ZA, Al-Jarrash S, Al-Madan MS, Al-Ali RA, AlKhalifah MA, Al-Muhanna F, Steinberg MH, Al-Ali AK. Co-inheritance of novel ATRX gene mutation and globin (α & β) gene mutations in transfusion dependent beta-thalassemia patients. Blood Cells Mol Dis 2015; 55:27-9. [DOI: 10.1016/j.bcmd.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/28/2015] [Indexed: 12/22/2022]
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