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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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Sun G, Huang W, Wang L, Wu J, Zhao G, Ren H, Liu L, Kong X. Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment. Clin Chim Acta 2024; 561:119774. [PMID: 38852791 DOI: 10.1016/j.cca.2024.119774] [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: 03/31/2024] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Whole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory. MATERIALS AND METHODS We retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs). RESULTS Among the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults. CONCLUSIONS The proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.
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Affiliation(s)
- Gege Sun
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlin Wu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanan Ren
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Jiang B, Zhang H, Kan Y, Gao X, Du Z, Liu Q. Novel compound heterozygous mutations in OCA2 gene were identified in a Chinese family with oculocutaneous albinism. Mol Genet Genomic Med 2024; 12:e2297. [PMID: 37882226 PMCID: PMC10767448 DOI: 10.1002/mgg3.2297] [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: 05/09/2023] [Revised: 08/18/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Oculocutaneous albinism (OCA) is a group of rare autosomal recessive disorders characterized by clinical genetic heterogeneity. OCA type II (OMIM: 203200) is the most common subtype among African and African Americans, primarily caused by pathogenic variants in the OCA2 (HGNC ID: 8101) gene. In this study, we presented a Chinese family with OCA and reported two novel variants in the OCA2 gene. METHODS Whole-exome sequencing (WES) was performed to identify pathogenic variants in the proband. The candidate variants were subsequently validated using Sanger sequencing and QPCR assay. Additionally, bioinformatics analyses were employed to predict the deleteriousness and conservation of the identified mutations. RESULTS In the 16-year-old male proband, two novel compound heterozygous OCA2 variants, NM_000275.3: c.1640T>G (NP_000266.2: p.L547R) and an exons 10-19 deletion variant, were identified. Meanwhile, a reported heterozygous variant c.1441G>A/p.A481T (NM_000275.3, NP_000266.2) in the OCA2 gene was also found in the proband. Sanger sequencing confirmed that the two variants c.1441G>A/p.A481T and c.1640T>G/p.L547R were inherited from his father. Moreover, qPCR assay revealed that the exons 10-19 deletion was inherited from the mother, his sister also carried this variant. Fortunately, the variant was not detected in the amniotic fluid of the proband's sister. Multiple online bioinformatics tools predicted the variant c.1640T>G to be damaging, leading to the replacement of a highly conserved leucine with an arginine. The gross exon 10-19 deletion in the OCA2 gene resulted in a truncated, non-functional protein losing the 3-9 transmembrane α-helices domains. According to the American College of Medical Genetics and Genomics classification, these three variants in the OCA2 gene were evaluated as likely pathogenic. CONCLUSION This study has identified two novel compound variants in the OCA2 gene and a previously reported variant in a Chinese family with OCA. By expanding the mutation spectrum of the OCA2 gene, our findings contribute to a better understanding of the genetic basis of OCA.
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Affiliation(s)
- Beilei Jiang
- Prenatal Diagnosis CenterBinhu District of Hefei First People's HospitalHefeiAnhuiChina
| | - Hua Zhang
- Prenatal Diagnosis CenterBinhu District of Hefei First People's HospitalHefeiAnhuiChina
| | - Yuling Kan
- Central LaboratoryBinzhou People's HospitalBinzhouShandongChina
| | - Xueping Gao
- Yinfeng Gene Technology Co, LtdJinanShandongChina
| | - Zhaoli Du
- Yinfeng Gene Technology Co, LtdJinanShandongChina
| | - Quan Liu
- Prenatal Diagnosis CenterBinhu District of Hefei First People's HospitalHefeiAnhuiChina
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AlAbdi L, Alshammari M, Helaby R, Khan AO, Alkuraya FS. PMEL is mutated in oculocutaneous albinism. Hum Genet 2023; 142:139-144. [PMID: 36166100 DOI: 10.1007/s00439-022-02489-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/17/2022] [Indexed: 01/18/2023]
Abstract
Oculocutaneous albinism (OCA) is a group of Mendelian disorders characterized by hypopigmentation of skin, hair and pigmented ocular structures. While much of the genetic heterogeneity of OCA has been resolved, many patients still lack a molecular diagnosis following exome sequencing. Here, we report a consanguineous family in which the index patient presented with OCA and Hirschsprung disease but tested negative for known genetic causes of OCA. Instead, he was found to have a homozygous presumptive loss of function variant in PMEL. PMEL encodes a scaffolding protein that is essential for the normal maturation of melanosomes and normal deposition of the melanin pigment therein. Numerous PMEL vertebrate ortholog mutants have been reported and all were characterized by conspicuous pigmentary abnormalities. We suggest that the patient we report is the first human equivalent of PMEL loss of function.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muneera Alshammari
- Pediatric Department, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Oculo-Cutaneous Albinism Type 4 (OCA4): Phenotype-Genotype Correlation. Genes (Basel) 2022; 13:genes13122198. [PMID: 36553465 PMCID: PMC9777904 DOI: 10.3390/genes13122198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/04/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Albinism is a genetic disorder, present worldwide, caused by mutations in genes affecting melanin production or transport in the skin, hair and eyes. To date, mutations in at least 20 different genes have been identified. Oculo-cutaneous Albinism type IV (OCA4) is the most frequent form in Asia but has been reported in all populations, including Europeans. Little is known about the genotype-phenotype correlation. We identified two main phenotypes via the analysis of 30 OCA4 patients with a molecularly proven diagnosis. The first, found in 20 patients, is clinically indistinguishable from the classical OCA1 phenotype. The genotype-to-phenotype correlation suggests that this phenotype is associated with homozygous or compound heterozygous nonsense or deletion variants with frameshift leading to translation interruption in the SLC45A2 gene. The second phenotype, found in 10 patients, is characterized by very mild hypopigmentation of the hair (light brown or even dark hair) and skin that is similar to the general population. In this group, visual acuity is variable, but it can be subnormal, foveal hypoplasia can be low grade or even normal, and nystagmus may be lacking. These mild to moderate phenotypes are associated with at least one missense mutation in SLC45A2.
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Ullah MI. Clinical and Mutation Spectrum of Autosomal Recessive Non-Syndromic Oculocutaneous Albinism (nsOCA) in Pakistan: A Review. Genes (Basel) 2022; 13:genes13061072. [PMID: 35741834 PMCID: PMC9222488 DOI: 10.3390/genes13061072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
Oculocutaneous albinism (OCA) is an autosomal recessive syndromic and non-syndromic defect with deficient or a complete lack of the melanin pigment. The characteristics of OCA appears in skin, hair, and eyes with variable degree of pigmentation. Clinical manifestations of OCA include nystagmus, photophobia, reduced visual acuity, hypo-plastic macula, and iris trans-illumination. There are eight OCA types (OCA1–8) documented with non-syndromic characteristics. Molecular studies identified seven genes linked to the OCA phenotype (TYR, OCA2, TYRP1, SLC45A2, SLC24A5, C10orf11, and DCT) and one locus (OCA5) in consanguineous and sporadic albinism. The complications of OCA result in skin cancer and variable syndromes such as Hermansky–Pudlak syndrome (HPS) Chediak–Higashi syndrome (CHS). In the Pakistani population, autosomal recessive non-syndromic OCA is common and is associated with a large number of consanguineous families, and mutations in genes of non-syndromic types are reported. This review highlights the updates on the genetic mutation of OCA genes reported from Pakistani families. Several studies reported the genetic mutations in OCA1, OCA2, OCA3, OCA4, and OCA6 albinism in Pakistani families. A locus, OCA5, was also reported from the Pakistani population, but the gene has not been identified. A new type of OCA8 was identified due to the DCT gene mutation, and it is also reviewed here.
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Affiliation(s)
- Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 75471, Aljouf, Saudi Arabia
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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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Dhangar S, Panchal P, Ghatanatti J, Suralkar J, Shah A, Vundinti BR. Novel deletion of exon 3 in TYR gene causing Oculocutaneous albinism 1B in an Indian family along with intellectual disability associated with chromosomal copy number variations. BMC Med Genomics 2022; 15:2. [PMID: 34980106 PMCID: PMC8722050 DOI: 10.1186/s12920-021-01152-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Oculocutaneous albinism (OCA) is an autosomal recessive disorder characterized by hypo-pigmentation of skin, hair, and eyes. The OCA clinical presentation is due to a deficiency of melanin biosynthesis. Intellectual disability (ID) in OCA cases is a rare clinical presentation and appropriate diagnosis of ID is challenging through clinical examination. We report an Indian family with a rare co-inheritance of OCA1B and ID due to a novel TYR gene variant and chromosomal copy number variations. Methods We have done a study on three siblings (2 males and 1 female) of a family where all of them presented with hypopigmented skin, hair and eyes. The male children and their father was affected with ID. Targeted exome sequencing and multiplex ligation-dependent probe amplification analysis were carried out to identify the OCA1B and ID associated genomic changes. Further Array-CGH was performed using SurePrint G3 Human CGH + SNP, 8*60 K array. Results A rare homozygous deletion of exon 3 in TYR gene causing OCA1B was identified in all three children. The parents were found to be heterozygous carriers. The Array-CGH analysis revealed paternally inherited heterozygous deletion (1.9 MB) of 15q11.1-> 15q11.2 region in all three children. Additionally, paternally inherited heterozygous deletion (2.6 MB) of 10q23.2-> 10q23.31 region was identified in the first male child; this may be associated with ID as the father and the child both presented with ID. While the 2nd male child had a denovo duplication of 13q31.1-> 13q31.3 chromosomal region. Conclusion A rare homozygous TYR gene exon 3 deletion in the present study is the cause of OCA1B in all three children, and the additional copy number variations are associated with the ID. The study highlights the importance of combinational genetic approaches for diagnosing two different co-inherited disorders (OCA and ID). Hence, OCA cases with additional clinical presentation need to be studied in-depth for the appropriate management of the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01152-1.
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Affiliation(s)
- Somprakash Dhangar
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India
| | - Purvi Panchal
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India
| | - Jagdeeshwar Ghatanatti
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India
| | - Jitendra Suralkar
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India
| | - Anjali Shah
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India
| | - Babu Rao Vundinti
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th floor, new multistoried building, K.E.M Hospital campus, Parel, Mumbai, 400012, India.
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9
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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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Jiang Y, Li S, Xiao X, Sun W, Zhang Q. Genotype-Phenotype of Isolated Foveal Hypoplasia in a Large Cohort: Minor Iris Changes as an Indicator of PAX6 Involvement. Invest Ophthalmol Vis Sci 2021; 62:23. [PMID: 34415986 PMCID: PMC8383911 DOI: 10.1167/iovs.62.10.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Foveal hypoplasia (FVH) is defined as the lack of fovea with a relatively preserved neuroretina, occurring either as an isolated FVH (IFVH) condition or associated with other diseases. This study aimed to systemically molecularly characterize IFVH. Methods Genetic defects in 33 families with IFVH were analyzed by exome sequencing. Variants in three genes (PAX6, SLC38A8, and AHR) were selected and evaluated with multistep bioinformatic tools. Results Mutations in the three genes were identified in 69.7% (23/33) of families with IFVH and infantile nystagmus, including 18 families with PAX6 mutations, 5 with SLC38A8 mutations, but none with AHR mutations. Clinical data from 32 patients in the 23 families showed FVH, infantile nystagmus, and full iris. Careful follow-up visits revealed subtle changes in iris in 9 of 14 patients with PAX6 variants. The PAX6 variants of the 18 families (15 missense and one stop-loss) were mostly located in the C-terminal region of the paired box domain. Variants in AHR, SLC38A8, and PAX6 contributed to IFVH in one (2%), 25 (45%), and 30 (53%) families with identified genetic defects (23 families in this study and 33 reported previously), respectively. Conclusions PAX6 and SLC38A8 mutations are the main cause of IFVH based on our data and a systematic review. IFVH-associated PAX6 variants are mostly missense with a specific location, indicating a specific correlation of these variants with IFVH but not with typical aniridia. Full iris with subtle structural abnormalities is more common in patients with PAX6-associated IFVH, suggesting a potential diagnostic indicator.
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Affiliation(s)
- Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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11
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Loftus SK, Lundh L, Watkins-Chow DE, Baxter LL, Pairo-Castineira E, Nisc Comparative Sequencing Program, Jackson IJ, Oetting WS, Pavan WJ, Adams DR. A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus. Hum Mutat 2021; 42:1239-1253. [PMID: 34246199 DOI: 10.1002/humu.24257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022]
Abstract
Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.
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Affiliation(s)
- Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | | | - Ian J Jackson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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12
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Genetic Causes of Oculocutaneous Albinism in Pakistani Population. Genes (Basel) 2021; 12:genes12040492. [PMID: 33800529 PMCID: PMC8066997 DOI: 10.3390/genes12040492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/30/2022] Open
Abstract
Melanin pigment helps protect our body from broad wavelength solar radiation and skin cancer. Among other pigmentation disorders in humans, albinism is reported to manifest in both syndromic and nonsyndromic forms as well as with varying inheritance patterns. Oculocutaneous albinism (OCA), an autosomal recessive nonsyndromic form of albinism, presents as partial to complete loss of melanin in the skin, hair, and iris. OCA has been known to be caused by pathogenic variants in seven different genes, so far, according to all the currently published population studies. However, the detection rate of alleles causing OCA varies from 50% to 90%. One of the significant challenges of uncovering the pathological variant underlying disease etiology is inter- and intra-familial locus heterogeneity. This problem is especially pertinent in highly inbred populations. As examples of such familial locus heterogeneity, we present nine consanguineous Pakistani families with segregating OCA due to variants in one or two different known albinism-associated genes. All of the identified variants are predicted to be pathogenic, which was corroborated by several in silico algorithms and association with diverse clinical phenotypes. We report an individual affected with OCA carries heterozygous, likely pathogenic variants in TYR and OCA2, raising the question of a possible digenic inheritance. Altogether, our study highlights the significance of exome sequencing for the complete genetic diagnosis of inbred families and provides the ramifications of potential genetic interaction and digenic inheritance of variants in the TYR and OCA2 genes.
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13
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Pennamen P, Tingaud-Sequeira A, Gazova I, Keighren M, McKie L, Marlin S, Gherbi Halem S, Kaplan J, Delevoye C, Lacombe D, Plaisant C, Michaud V, Lasseaux E, Javerzat S, Jackson I, Arveiler B. Dopachrome tautomerase variants in patients with oculocutaneous albinism. Genet Med 2021; 23:479-487. [PMID: 33100333 DOI: 10.1038/s41436-020-00997-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Albinism is a clinically and genetically heterogeneous condition. Despite analysis of the 20 known genes, ~30% patients remain unsolved. We aimed to identify new genes involved in albinism. METHODS We sequenced a panel of genes with known or predicted involvement in melanogenesis in 230 unsolved albinism patients. RESULTS We identified variants in the Dopachrome tautomerase (DCT) gene in two patients. One was compound heterozygous for a 14-bp deletion in exon 9 and c.118T>A p.(Cys40Ser). The second was homozygous for c.183C>G p.(Cys61Trp). Both patients had mild hair and skin hypopigmentation, and classical ocular features. CRISPR-Cas9 was used in C57BL/6J mice to create mutations identical to the missense variants carried by the patients, along with one loss-of-function indel. When bred to homozygosity the three mutations revealed hypopigmentation of the coat, milder for Cys40Ser compared with Cys61Trp or the frameshift mutation. Histological analysis identified significant hypopigmentation of the retinal pigmented epithelium (RPE) indicating that defective RPE melanogenesis could be associated with eye and vision defects. DCT loss of function in zebrafish embryos elicited hypopigmentation both in melanophores and RPE cells. CONCLUSION DCT is the gene for a new type of oculocutaneous albinism that we propose to name OCA8.
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Affiliation(s)
- Perrine Pennamen
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France
| | - Angèle Tingaud-Sequeira
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Iveta Gazova
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | | | - Lisa McKie
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Sandrine Marlin
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, Paris Descartes, Sorbonne Paris Cité University, Paris, France
| | - Souad Gherbi Halem
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, Paris Descartes, Sorbonne Paris Cité University, Paris, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, Imagine Institute, Paris Descartes, Sorbonne Paris Cité University, Paris, France
| | - Cédric Delevoye
- Institut Curie, PSL Research University, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Didier Lacombe
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Claudio Plaisant
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France
| | - Vincent Michaud
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France
| | - Eulalie Lasseaux
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France
| | - Sophie Javerzat
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France
| | - Ian Jackson
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Benoit Arveiler
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France.
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France.
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14
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Self JE, Lee H. Novel therapeutics in nystagmus: what has the genetics taught us so far? THERAPEUTIC ADVANCES IN RARE DISEASE 2021; 2:2633004021998714. [PMID: 37181109 PMCID: PMC10032456 DOI: 10.1177/2633004021998714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 05/16/2023]
Abstract
Nystagmus is a disorder characterised by uncontrolled, repetitive, to-and-fro movement of the eyes. It can occur as a seemingly isolated disorder but is most commonly the first, or most obvious, feature in a host of ophthalmic and systemic disorders. The number of underlying causes is vast, and recent improvements in the provision of genetic testing have shown that many conditions can include nystagmus as a feature, but that phenotypes overlap significantly. Therefore, an increase in the understanding of the genetic causes of nystagmus has shown that successful novel therapeutics for 'nystagmus' can target either specific underlying disorders and mechanisms (aiming to treat the underlying condition as a whole), or a final common pathway (aiming to treat the nystagmus directly). Plain language summary Novel treatments for a disorder of eye movement (nystagmus): what has the genetics taught us so far? Nystagmus is a disorder of eye movement characterised by uncontrolled, to-and-fro movements. It can occur as an isolated disorder, in conditions affecting other parts of the eye, in conditions affecting multiple other parts of the body or secondary to neurological diseases (brain diseases). In recent years, advances in genetic testing methods and increase in genetic testing in healthcare systems have provided a greater understanding of the underlying causes of nystagmus. They have highlighted the bewildering number of genetic causes that can result in what looks like a very similar eye movement disorder.In recent years, new classes of drugs have been developed for some of the causes of nystagmus, and some new drugs have been developed for other conditions which have the potential to work in certain types of nystagmus. For these reasons, genetics has taught us that identifying new possible treatments for nystagmus can either be dependent on identifying the underlying genetic cause and aiming to treat that, or aiming to treat the nystagmus per se by targeting a final common pathway. A toolkit based on specific treatments for specific conditions is more to have meaningful impact on 'nystagmus' than pursuing a panacea based on a 'one size fits all' approach.
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Affiliation(s)
- Jay E Self
- Clinical and Experimental Sciences, Faculty of
Medicine, University of Southampton, Tremona Road, Southampton SO16 6YD,
UK
- University Hospital Southampton, Southampton,
UK
| | - Helena Lee
- Clinical and Experimental Sciences, Faculty of
Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton, Southampton,
UK
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15
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Bibi N, Ullah A, Darwesh L, Khan W, Khan T, Ullah K, Khan B, Ahmad W. Identification and Computational Analysis of Novel TYR and SLC45A2 Gene Mutations in Pakistani Families With Identical Non-syndromic Oculocutaneous Albinism. Front Genet 2020; 11:749. [PMID: 32849781 PMCID: PMC7385404 DOI: 10.3389/fgene.2020.00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/23/2020] [Indexed: 12/19/2022] Open
Abstract
Non-syndromic oculocutaneous albinism (nsOCA) is an inherited disorder of melanin biosynthesis with autosomal recessive mode of inheritance, presenting either hypopigmented or depigmented skin, hair, and eyes. It is genetically heterogeneous with seven loci (OCA1–OCA7) reported to date. In the present study, we have reported three consanguineous families (A, B, C) presenting identical nsOCA phenotypes. Sanger sequencing revealed a novel [NM_000372.5: c.826 T > C, p.(Cys276Arg)] and a recurrent variant [NM_000372.5: c.832C > T, p.(Arg278∗)] in tyrosinase (TYR) in families A and B, respectively. Microsatellite marker-based homozygosity mapping linked family C to OCA4. Sequence analysis identified a novel insertion variant (NM_016180.5: c.1331_1332insA) in the SLC45A2. Further, in silico mutagenesis and dynamic simulation approaches revealed that a novel Cys276Arg variant abolished the cysteine bridge and might contribute toward decreased stability of the TYR protein. Our study expands the mutation spectrum of the TYR and SLC45A2 genes and emphasizes that molecular investigations are essential for accurate disease diagnosis.
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Affiliation(s)
- Nousheen Bibi
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Asmat Ullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Lubna Darwesh
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Waqas Khan
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Tanzeela Khan
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Kalim Ullah
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Bushra Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
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16
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Chuan Z, Yan Y, Hao S, Zhang Q, Zhou B, Feng X, Wang X, Liu F, Zheng L, Cao Z, Ma X. Mutation Analysis of 63 Northwest Chinese Probands with Oculocutaneous Albinism. Curr Eye Res 2020; 46:140-143. [PMID: 32552135 DOI: 10.1080/02713683.2020.1781192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
PURPOSE To identify the mutational spectrum of 63 northwest Chinese probands with Oculocutaneous albinism (OCA), and identify correlations between phenotype and genotype. METHODS We recruited 63 clinically diagnosed with OCA patients in Gansu Provincial Maternal and Child Health Care Hospital. Mutation screening analysis was performed by direct sequencing and NGS-target sequencing to screen the variants on genes related to OCA. PolyPhen2 and PROVEN tools were used to predict the possible functional role of the novel variants. We assessed the pathogenicity of the novel mutations according to the clinical interpretation of genetic variants by ACMG/AMP 2015 guideline. RESULTS By molecular testing, 56 of the OCA probands were diagnosed as OCA 1, three were OCA 2 and one was OCA 4. The most common variants of TYR were c.929insC(33.7%), c.896 G > A(12.5%), c.832 C > T(9.6%).We found five novel variants of TYR that have not previously been reported. CONCLUSIONS We make an accurate diagnosis and classification for the OCA probands. Our result enlarged the mutational spectrum of TYR and SLC45A2. These findings could be useful for genetic counseling and gene diagnosis of OCA in Northwest of China.
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Affiliation(s)
- Zhang Chuan
- Graduate School of Peking Union Medical College , Beijing, China.,National Research Institute for Family Planning , Beijing, China.,Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Yousheng Yan
- National Research Institute for Family Planning , Beijing, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Qinghua Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Bingbo Zhou
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Xuan Feng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Xing Wang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Furong Liu
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital , Lanzhou, China
| | - Zongfu Cao
- Graduate School of Peking Union Medical College , Beijing, China.,National Research Institute for Family Planning , Beijing, China.,National Human Genetic Resources Center , Beijing, China
| | - Xu Ma
- Graduate School of Peking Union Medical College , Beijing, China.,National Research Institute for Family Planning , Beijing, China.,National Human Genetic Resources Center , Beijing, China
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17
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Schidlowski L, Liebert F, Iankilevich PG, Rebellato PRO, Rocha RA, Almeida NAP, Jain A, Wu Y, Itan Y, Rosati R, Prando C. Non-syndromic Oculocutaneous Albinism: Novel Genetic Variants and Clinical Follow Up of a Brazilian Pediatric Cohort. Front Genet 2020; 11:397. [PMID: 32411182 PMCID: PMC7198815 DOI: 10.3389/fgene.2020.00397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Oculocutaneous albinism (OCA) is a genetic disorder characterized by skin, hair, and eye hypopigmentation due to a reduction or absence of melanin. Clinical manifestations include vision problems and a high susceptibility to skin cancer. In its non-syndromic form, OCA is associated with six genes and one chromosomal region. Because OCA subtypes are not always clinically distinguishable, molecular analysis has become an important tool for classifying types of OCA, which facilitates genetic counseling and can guide the development of new therapies. We studied eight Brazilian individuals aged 1.5–18 years old with clinical diagnosis of OCA. Assessment of ophthalmologic characteristics showed results consistent with albinism, including reduced visual acuity, nystagmus, and loss of stereoscopic vision. We also observed the appearance of the strabismus and changes in static refraction over a 2-year period. Dermatologic evaluation showed that no participants had preneoplastic skin lesions, despite half of the participants reporting insufficient knowledge about skin care in albinism. Whole-exome and Sanger sequencing revealed eight different mutations: six in the TYR gene and two in the SLC45A2 gene, of which one was novel and two were described in a population study but were not previously associated with the OCA phenotype. We performed two ophthalmological evaluations, 2 years apart; and one dermatological evaluation. To the best of our knowledge, this is the first study to perform clinical follow-up and genetic analysis of a Brazilian cohort with albinism. Here, we report three new OCA causing mutations.
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Affiliation(s)
- Laire Schidlowski
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
| | - Fernando Liebert
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
| | | | | | | | | | - Aayushee Jain
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yuval Itan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Roberto Rosati
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
| | - Carolina Prando
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil.,Hospital Pequeno Príncipe, Curitiba, Brazil
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18
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Shakil M, Harlalka GV, Ali S, Lin S, D'Atri I, Hussain S, Nasir A, Shahzad MA, Ullah MI, Self JE, Baple EL, Crosby AH, Mahmood S. Tyrosinase (TYR) gene sequencing and literature review reveals recurrent mutations and multiple population founder gene mutations as causative of oculocutaneous albinism (OCA) in Pakistani families. Eye (Lond) 2019; 33:1339-1346. [PMID: 30996339 PMCID: PMC7005860 DOI: 10.1038/s41433-019-0436-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 01/21/2019] [Accepted: 03/25/2019] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To investigate eight previously unreported Pakistani families with genetically undefined OCA for mutations in TYR. METHODS Sanger sequencing of TYR has been performed in eight families with OCA phenotype. Mutation analysis was performed to establish the pathogenic role of novel mutation. Bioinformatics analysis was performed to predict the structural and functional impacts on protein due to the mutation. RESULTS In this study, we identified six likely pathogenic variants of TYR (c.272 G>A, c.308 G>A, c.346C>T, c.715 C>T, c.832 C>T and c.1255 G>A), including one novel variant (c.308 G>A; p.Cys103Tyr), segregating as appropriate in each family. Cys103 lies in the highly conserved region of the tyrosinase enzyme, and p.Cys103Tyr is predicted to disturb enzymatic function via alteration of the configurational orientation of TYR leading to a more rigid polypeptide structure. We have also reviewed the mutation spectrum of TYR in Pakistani ethnicity. Published data on OCA families proposed that ~40% have been associated with genetic variations in the TYR gene. The mutations reported in this study have now been described with varying frequencies in Pakistani families, including very rare/unique mutations. CONCLUSION A literature review of TYR gene mutations in Pakistani populations, combined with our genetic data, identified a number of gene mutations likely to represent regional ancestral founder mutations of relevance to Pakistani populations, in addition to sporadic and recurrent 'hotspot' mutations present repeatedly in other regions worldwide.
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Affiliation(s)
- Muhammad Shakil
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
- Department of Biochemistry, Services Institute of Medical Sciences, Services Hospital, Lahore, Pakistan
| | - Gaurav V Harlalka
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Shamshad Ali
- Department of Ophthalmology, Services Institute of Medical Sciences, Services Hospital, Lahore, Pakistan
| | - Siying Lin
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Ilaria D'Atri
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Shabbir Hussain
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Muhammad Aiman Shahzad
- Department of Human Genetics and Molecular Biology, University of Health Sciences (UHS), Lahore, Pakistan
| | - Muhammad Ikram Ullah
- Department of Biochemistry, University of Health Sciences (UHS), Lahore, Pakistan
- Department of Clinical Laboratory Sciences, Jouf University, Sakaka-2014, Saudi Arabia
| | - Jay E Self
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Emma L Baple
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Saqib Mahmood
- Department of Human Genetics and Molecular Biology, University of Health Sciences (UHS), Lahore, Pakistan.
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences (UHS), Lahore, Pakistan.
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19
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Wang H, Wan Y, Yang Y, Li H, Mao L, Gao S, Xu J, Wang J. Novel compound heterozygous mutations in OCA2 gene associated with non-syndromic oculocutaneous albinism in a Chinese Han patient: a case report. BMC MEDICAL GENETICS 2019; 20:130. [PMID: 31345173 PMCID: PMC6659248 DOI: 10.1186/s12881-019-0850-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/19/2019] [Indexed: 11/24/2022]
Abstract
Background Oculocutaneous albinism (OCA) is a group of rare genetically heterogeneous disorders. The present study aimed to identify the genetic cause of a Chinese Han family with non-syndromic oculocutaneous albinism (OCA). Case presentation Here, we report an 11-month-old male proband from a Chinese Han non-consanguineous family, who presented with milky skin, yellow white hair, nystagmus, astigmatism, and hypermetropia. We performed the targeted next-generation sequencing (NGS) on the proband and identified two novel compound heterozygous variants (c.1865 T > C (p.Leu622Pro) and exons 17–21 deletion) in OCA2 gene associated with OCA type 2 (OCA2, OMIM 203200). Meanwhile, a previously reported heterozygous mutation (c.4805G > A) in MYO7 gene related with Usher syndrome type 1B was found. The online tools SIFT, PolyPhen-2, and Mutation Taster predicted variant c.1865 T > C was probably damaging. The residue p.Leu622 was in a highly conserved region among species by CLUSTALW. Three-dimensional homology model with I-TASSER indicated that p.Leu622Pro variant disturbed the formation of the α-helix, resulting in a random coil structure. The gross deletion (exons 17–21) in OCA2 gene has was not been reported previously. These two novel variants in OCA2 gene were inherited from each parent respectively, after verification by Sanger sequencing and quantitative PCR (qPCR) in the family. Conclusions This study indicates the two novel compound heterozygous mutations in OCA2 gene may be responsible for clinical manifestations of OCA2. It expands the mutation spectrum of OCA2 gene and is helpful to screen for large deletions with targeted NGS protocol in monogenic disease. It also assists the genetic counselling, carrier screening and personalized healthcare of the disease. Electronic supplementary material The online version of this article (10.1186/s12881-019-0850-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hairong Wang
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China
| | - Yang Wan
- Department of Obstetrics and Gynecology, Fuyang People's Hospital, Fuyang, 236000, China
| | - Yun Yang
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hao Li
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China
| | - Liangwei Mao
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China.,College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shuyang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jingjing Xu
- Prenatal diagnosis center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230071, China
| | - Jing Wang
- Prenatal diagnosis center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230071, China.
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Gul H, Shah AH, Harripaul R, Mikhailov A, Prajapati K, Khan E, Ullah F, Zubair M, Ali MZ, Shah AH, Salman S, Khan S, Vincent JB, Khan MA. Genetic studies of multiple consanguineous Pakistani families segregating oculocutaneous albinism identified novel and reported mutations. Ann Hum Genet 2019; 83:278-284. [PMID: 30868578 DOI: 10.1111/ahg.12307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 02/05/2019] [Accepted: 02/18/2019] [Indexed: 11/28/2022]
Abstract
Oculocutaneous albinism (OCA) is an autosomal-recessive disorder of a defective melanin pathway. The condition is characterized by hypopigmentation of hair, dermis, and ocular tissue. Genetic studies have reported seven nonsyndromic OCA genes, among which Pakistani OCA families mostly segregate TYR and OCA2 gene mutations. Here in the present study, we investigate the genetic factors of eight consanguineous OCA families from Pakistan. Genetic analysis was performed through single-nucleotide polymorphism (SNP) genotyping (for homozygosity mapping), whole exome sequencing (for mutation identification), Sanger sequencing (for validation and segregation analysis), and quantitative PCR (qPCR) (for copy number variant [CNV] validation). Genetic mapping in one family identified a novel homozygous deletion mutation of the entire TYRP1 gene, and a novel deletion of exon 19 in the OCA2 gene in two apparently unrelated families. In three further families, we identified homozygous mutations in TYR (NM_000372.4:c.1424G > A; p.Trp475*), NM_000372.4:c.895C > T; p.Arg299Cys), and SLC45A2 (NM_016180:c.1532C > T; p.Ala511Val). For the remaining two families, G and H, compound heterozygous TYR variants NM_000372.4:c.1037-7T > A, NM_000372.4:c.1255G > A (p.Gly419Arg), and NM_000372.4:c.1255G > A (p.Gly419Arg) and novel variant NM_000372.4:c.248T > G; (p.Val83Gly), respectively, were found. Our study further extends the evidence of TYR and OCA2 as genetic mutation hot spots in Pakistani families. Genetic screening of additional OCA cases may also contribute toward the development of Pakistani specific molecular diagnostic tests, genetic counseling, and personalized healthcare.
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Affiliation(s)
- Hadia Gul
- Department of Biological Sciences, Faculty of Sciences, Gomal University, D.I. Khan, Pakistan
| | - Abdul Haleem Shah
- Department of Biological Sciences, Faculty of Sciences, Gomal University, D.I. Khan, Pakistan
| | - Ricardo Harripaul
- Molecular Neuro-Psychiatry and Development Lab (MiND), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Anna Mikhailov
- Molecular Neuro-Psychiatry and Development Lab (MiND), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Kamalben Prajapati
- Molecular Neuro-Psychiatry and Development Lab (MiND), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Ejazullah Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Pakistan
| | - Farman Ullah
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Pakistan
| | - Muhammad Zubair
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Pakistan.,Department of Cell and Developmental Biology, School of Life Sciences, University of Science and Technology, Hefei, China
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Pakistan
| | - Ayesha Haleem Shah
- Department of Biological Sciences, Faculty of Sciences, Gomal University, D.I. Khan, Pakistan
| | - Said Salman
- Department of Plant Breeding and Genetics, Ghazi University, D.G. Khan, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - John B Vincent
- Molecular Neuro-Psychiatry and Development Lab (MiND), Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Pakistan
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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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