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Khan J, Asif S, Ghani S, Khan H, Arshad MW, Khan SA, Lin S, Baple EL, Salter C, Crosby AH, Rawlins L, Shabbir MI. Mutational spectrum associated with oculocutaneous albinism and Hermansky-Pudlak syndrome in nine Pakistani families. BMC Ophthalmol 2024; 24:345. [PMID: 39143519 PMCID: PMC11325792 DOI: 10.1186/s12886-024-03611-6] [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: 06/29/2023] [Accepted: 11/20/2023] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Oculocutaneous albinism (OCA) is a genetically heterogeneous condition that is associated with reduced or absent melanin pigment in the skin, hair, and eyes, resulting in reduced vision, high sensitivity to light, and rapid and uncontrolled eye movements. To date, seventeen genes have been associated with OCA including syndromic and non-syndromic forms of the condition. METHODS Whole exome sequencing (WES) was performed to identify pathogenic variants in nine Pakistani families with OCA, with validation and segregation of candidate variants performed using Sanger sequencing. Furthermore, the pathogenicity of the identified variants was assessed using various in-silico tools and 3D protein structural analysis software. RESULTS WES identified biallelic variants in three genes explaining the OCA in these families, including four variants in TYR, three in OCA2, and two in HPS1, including two novel variants c.667C > T: p.(Gln223*) in TYR, and c.2009 T > C: p.(Leu670Pro) in HPS1. CONCLUSIONS Overall, this study adds further knowledge of the genetic basis of OCA in Pakistani communities and facilitates improved management and counselling services for families suffering from severe genetic diseases in Pakistan.
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Affiliation(s)
- Jahangir Khan
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan
- Faculty of Basic and Applied Sciences, SA-Centre for Interdisciplinary Research in Basic Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan
| | - Saaim Asif
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, 45550, Pakistan
| | - Shamsul Ghani
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan
| | - Hamid Khan
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan
| | - Muhammad Waqar Arshad
- Department of Psychiatry, Yale University School of Medicine, VA CT Healthcare Center S116A2, West Haven, 06516, USA
| | - Shujaat Ali Khan
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan
| | - Siying Lin
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Emma L Baple
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Claire Salter
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Lettie Rawlins
- College of Medicine and Health, RILD Wellcome Wolfson Centre, University of Exeter, Royal Devon and Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, H-10, Islamabad, 44000, Pakistan.
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Shakil M, Akbar A, Aisha NM, Hussain I, Ullah MI, Atif M, Kaul H, Amar A, Latif MZ, Qureshi MA, Mahmood S. Delineating Novel and Known Pathogenic Variants in TYR, OCA2 and HPS-1 Genes in Eight Oculocutaneous Albinism (OCA) Pakistani Families. Genes (Basel) 2022; 13:genes13030503. [PMID: 35328057 PMCID: PMC8950407 DOI: 10.3390/genes13030503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 12/10/2022] Open
Abstract
Oculocutaneous albinism (OCA) is associated with a wide range of clinical presentations and has been categorized with syndromic and non-syndromic features. The most common causative genes in non-syndromic OCA are TYR and OCA2 and HSP1 is in the syndromic albinism. The objective of this study was to identify pathogenic variants in congenital OCA families from Pakistan. Eight consanguineous families were recruited, and clinical and ophthalmological examination was carried out to diagnose the disease. Whole blood was collected from the participating individuals, and genomic DNA was extracted for sequencing analysis. TruSight one-panel sequencing was carried out on one affected individual of each family, and termination Sanger sequencing was carried out to establish the co-segregation of the causative gene or genes. In silico analysis was conducted to predict the causative pathogenic variants. Two families were found to have novel genetic pathogenic variants, and six families harbored previously reported variants. One novel compound heterozygous pathogenic variant in the TYR gene, c.1002delA; p.Ala335LeufsTer20, a novel frameshift deletion pathogenic variant and c.832C>T; and p.Arg278Ter (a known pathogenic variant) were found in one family, whereas HPS1; c.437G>A; and p.Trp146Ter were detected in another family. The identification of new and previous pathogenic variants in TYR, OCA2, and HPS1 genes are causative of congenital OCA, and these findings are expanding the heterogeneity of OCA.
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Affiliation(s)
- Muhammad Shakil
- Department of Biochemistry, University of Health Sciences (UHS), Lahore 54600, Pakistan;
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Abida Akbar
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Nazish Mahmood Aisha
- Department of Biochemistry, Services Institute of Medical Sciences, Lahore 54600, Pakistan;
| | - Intzar Hussain
- Department of Ophthalmology Services, Institute of Medical Sciences, Lahore 54600, Pakistan;
| | - Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 75471, Saudi Arabia; (M.I.U.); (M.A.)
| | - Muhammad Atif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 75471, Saudi Arabia; (M.I.U.); (M.A.)
| | - Haiba Kaul
- Genetics Discipline, Department of Animal Breeding and Genetics, Faculty of Animal Production and Technology, Ravi Campus, University of Veterinary and Animal Sciences, Pattoki 55300, Pakistan;
| | - Ali Amar
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
| | - Muhammad Zahid Latif
- Department of Community Medicine and Medical Education, Azra Naheed Medical College, The Superior University, Lahore 54600, Pakistan; (M.Z.L.); (M.A.Q.)
| | - Muhammad Atif Qureshi
- Department of Community Medicine and Medical Education, Azra Naheed Medical College, The Superior University, Lahore 54600, Pakistan; (M.Z.L.); (M.A.Q.)
| | - Saqib Mahmood
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
- Institute of Biomedical & Allied Health Sciences, University of Health Sciences Lahore, Lahore 54600, Pakistan
- Correspondence:
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Ma L, Zhu J, Wang J, Huang Y, Zhang J, Wang C, Zhou Y, Peng D. Genetic Analysis of 28 Chinese Families With Tyrosinase-Positive Oculocutaneous Albinism. Front Genet 2021; 12:715437. [PMID: 34707637 PMCID: PMC8544823 DOI: 10.3389/fgene.2021.715437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/30/2021] [Indexed: 11/28/2022] Open
Abstract
Background Tyrosinase-positive oculocutaneous albinism (OCA, type II, OCA2) is an autosomal recessive genetic disease in which the biosynthesis of melanin decreases in the skin, hair, and eyes. OCA2 disease is caused by mutations in OCA2 gene. The gene product plays a role in regulating the pH of melanosomes. Up to now, hundreds of OCA2 mutations have been reported and novel variants are still being discovered. Methods In this study, we reviewed the records of OCA2 patients who had conducted albinism genetic testing, and then analyzed the clinical and genetic information of 28 OCA2 patients who had been genetically diagnosed by using Sanger sequencing and next-generation sequencing. Results In this study, we reported 31 variants screened from 28 Chinese OCA2 families, and characterized the detailed molecular and clinical presentations. There were 12 novel variants among all detected variants, including 3 missense variants (p.G393V, p.T482A, and p.R720P), 4 frameshift variants (p.R53Gfs∗49, p.N279Kfs∗17, p.I469Lfs∗4, p.I655Nfs∗12), 2 splicing variants (c.1637-2A > G, c.1951 + 1G > C), 2 stopgain variants (p.L278X, p.W652X) and 1 insertion variants (p.P315LinsT). One potential cluster of missense variants was implicated indicating the important roles of the underlying domains in OCA2 pathogenesis. Conclusion Our results were beneficial for diagnosis and precision clinical management for OCA2-related disorder, and this study expanded the mutation spectrum of oculocutaneous albinism.
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Affiliation(s)
- Linya Ma
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Jianjian Zhu
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Jing Wang
- Changsha Kingmed Center for Clinical Laboratory, Changsha, China
| | - Yazhou Huang
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Jibo Zhang
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Chao Wang
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Yuan Zhou
- Department of Medical Genetics, Changde First People's Hospital, Changde, China
| | - Dan Peng
- Department of Medical Genetics, Changde First People's Hospital, Changde, China.,Affiliated Hospital of Changde City, University of South China, Hengyang, China
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Wang X, Liu A, Lu Y, Hu Q. Novel compound heterozygous mutations in the SPTA1 gene, causing hereditary spherocytosis in a neonate with Coombs‑negative hemolytic jaundice. Mol Med Rep 2019; 19:2801-2807. [PMID: 30816434 PMCID: PMC6423610 DOI: 10.3892/mmr.2019.9947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022] Open
Abstract
Hereditary spherocytosis (HS) is a common heterogeneous type of inherited hemolytic anemia characterized by jaundice and splenomegaly. Diagnosis of HS in neonates is considered unreliable, and is generally based on positive family history, spherocytes in peripheral smears, increased osmotic fragility, and jaundice. In the present study, routine laboratory tests, next‑generation sequencing, and Sanger sequencing were applied to diagnose a neonatal patient with Coombs‑negative hemolytic jaundice. The neonate had no family history of HS; however, spherocytes were observed in peripheral smears, and the patient exhibited Coombs‑negative and severe hemolytic jaundice, normal mean corpuscular hemoglobin concentration (MCHC) and mean corpuscular volume (MCV), normal glucose‑6‑phosphate dehydrogenase activity, negative thalassemia genetic mutation screening results, and negative autoimmune antibody tests. Novel compound heterozygous mutations in the spectrin‑α, erythrocytic 1 (SPTA1) gene (c.3897‑1G>C and c.5029G>A) were identified. The SPTA1 c.3897‑1G>C mutation in intron 27‑1, which disrupted the consensus splice site, was inherited from his asymptomatic mother, and the SPTA1 c.5029G>A (p.Gly1677Arg) mutation in trans with the SPTA1 c.3897‑1G>C mutation was inherited from his asymptomatic father. Sanger sequencing of mRNA reverse transcribed into cDNA identified a deletion of the first 10 nucleotides of exon 28, confirming the splicing mutation. In conclusion, the present study reports a rare case of autosomal‑recessive HS with a severe clinical phenotype, but normal MCHC and MCV.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Aiguo Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Qun Hu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Wang Y, Zhou YF, Shen N, Zhu YW, Tan K, Wang X. Identification of a Homozygous Missense Mutation in the TYR Gene in a Chinese Family with OCA1. Curr Med Sci 2018; 38:932-936. [PMID: 30341532 DOI: 10.1007/s11596-018-1965-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/20/2018] [Indexed: 12/28/2022]
Abstract
Oculocutaneous albinism (OCA) is an autosomal recessive pigmentation abnormality, characterized by variable hair, skin, and ocular hypopigmentation. OCA1 is the most frequent subtype of OCA, caused by mutations in the tyrosinase gene (TYR). In this study, we investigated the genetic mutation of a Chinese family with a female OCA patient who came for genetic counseling before pregnancy. Complete physical examination was performed, and DNA from blood samples was collected from the family members. Mutations of TYR, OCA2, and SLC45A2 genes were examined in the proband, and verified in her parents by Sanger sequencing. Large deletion or duplication of TYR and OCA2 genes was detected by multiplex ligation-dependent probe amplification (MLPA). A homozygous TYR c.307T>C (p.Cys103Arg) missense mutation was identified in the proband, and both parents were heterozygous carriers. No large deletion or duplication was found in the proband. This mutation was absent in 1000G, ExAC, or HGMD database, and multiple lines of in silico tools supported a deleterious effect. These results suggest that TYR c.307T>C mutation might be responsible for OCA1, and our study further expands the mutation spectrum of OCA1 in the Chinese population.
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Affiliation(s)
- Yan Wang
- Department of Neurosurgery, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi-Fan Zhou
- Reproductive Medicine Center, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Na Shen
- Department of Laboratory Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yao-Wu Zhu
- Department of Laboratory Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kun Tan
- Department of Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiong Wang
- Department of Laboratory Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Arshad MW, Harlalka GV, Lin S, D'Atri I, Mehmood S, Shakil M, Hassan MJ, Chioza BA, Self JE, Ennis S, O'Gorman L, Norman C, Aman T, Ali SS, Kaul H, Baple EL, Crosby AH, Ullah MI, Shabbir MI. Mutations in TYR and OCA2 associated with oculocutaneous albinism in Pakistani families. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Mutational analysis of a Chinese family with oculocutaneous albinism type 2. Oncotarget 2017; 8:70345-70355. [PMID: 29050284 PMCID: PMC5642559 DOI: 10.18632/oncotarget.19697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/01/2017] [Indexed: 11/25/2022] Open
Abstract
Oculocutaneous albinism (OCA) is an autosomal recessive disorder characterized by hypopigmentation of the skin, hair, and eyes accompanied with ophthalmologic abnormalities. Molecular genetic test can confirm the diagnosis of the four subtypes of OCA (OCA1-4). Herein, we report a Chinese family with two patients affected by OCA. Mutations of TYR, OCA2, TYRP1, and SLC45A2 were examined by using PCR-sequencing. Large deletions or duplications of TYR and OCA2 were examined by Multiplex Ligation-dependent Probe Amplification (MLPA) assay. Compound heterozygous mutations of OCA2, (c.808-3C>G and c.2080-2A>G), were identified in both patients characterized with yellow hair and milky skin, heterochromia iridis, and nystagmus. Several computer-assisted approaches predicted that c.808-3C>G and c.2080-2A>G in OCA2 might potentially be pathogenic splicing mutations. No exon rearrangement (deletion/duplication) of TYR and OCA2 was observed in the patients by MLPA analysis. This study suggests that compound heterozygous mutations, (c.808-3C>G and c.2080-2A>G), in OCA2 may be responsible for partial clinical manifestations of OCA.
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Wang X, Yi B, Mu K, Shen N, Zhu Y, Hu Q, Lu Y. Identification of a novel de novo ANK1 R1426* nonsense mutation in a Chinese family with hereditary spherocytosis by NGS. Oncotarget 2017; 8:96791-96797. [PMID: 29228571 PMCID: PMC5722523 DOI: 10.18632/oncotarget.18243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/15/2017] [Indexed: 12/22/2022] Open
Abstract
Hereditary spherocytosis (HS) is an inherited heterogeneous hemolytic anemia, characterized by the presence of spherical-shaped erythrocytes on the peripheral blood smear, and the clinical manifestation ranges from asymptomatic to severely anemic, and transfusion-dependent patients. Mutations in at least five genes (ANK1, EPB42, SLC4A1, SPTA1, and SPTB) have been identified so far, and mutations of ANK1 gene are responsible for the majority of all HS cases. In this study, targeted next generation sequencing (NGS) was applied to identify a novel de novo ANK1 c.4276C>T (p.R1426*) nonsense mutation in a Chinese family with a patient of HS who was diagnosed clinically with only 10% spherical-shaped erythrocytes in the peripheral blood and received splenectomy. Sanger sequencing further confirmed that only the patient carried heterozygous ANK1 c.4276C>T nonsense mutation, while none of his parents or his young brother carried this mutation. Moreover, consistent with the genetic findings, the anemia was ameliorated after splenectomy. RBCs increased from 2.74 × 1012/L pre-surgery to 4.76 × 1012/L one month post-surgery, and hemoglobin increased from 66g/L to 126g/L respectively. This is the first report of ANK1 c.4276C>T (p.R1426*) heterozygous nonsense mutation responsible for HS. Our results also demonstrate that targeted NGS may provide a powerful approach for rapid genetic test of HS.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bin Yi
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ketao Mu
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qun Hu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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