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Green DJ, Michaud V, Lasseaux E, Plaisant C, Fitzgerald T, Birney E, Black GC, Arveiler B, Sergouniotis PI. The co-occurrence of genetic variants in the TYR and OCA2 genes confers susceptibility to albinism. Nat Commun 2024; 15:8436. [PMID: 39349469 PMCID: PMC11443028 DOI: 10.1038/s41467-024-52763-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
Although rare genetic conditions are mostly caused by DNA sequence alterations that functionally disrupt individual genes, large-scale studies using genome sequencing have started to unmask additional complexity. Understanding how combinations of variants in different genes shape human phenotypes is expected to provide important insights into the clinical and genetic heterogeneity of rare disorders. Here, we use albinism, an archetypal rare condition associated with hypopigmentation, as an exemplar for the study of genetic interactions. We analyse data from the Genomics England 100,000 Genomes Project alongside a cohort of 1120 individuals with albinism, and investigate the effect of dual heterozygosity for the combination of two established albinism-related variants: TYR:c.1205 G > A (p.Arg402Gln) [rs1126809] and OCA2:c.1327 G > A (p.Val443Ile) [rs74653330]. As each of these changes alone is insufficient to cause disease when present in the heterozygous state, we sought evidence of synergistic effects. We show that, when both variants are present, the probability of receiving a diagnosis of albinism is significantly increased (odds ratio 12.8; 95% confidence interval 6.0 - 24.7; p-value 2.1 ×10-8). Further analyses in an independent cohort, the UK Biobank, support this finding and highlight that heterozygosity for the TYR:c.1205 G > A and OCA2:c.1327 G > A variant combination is associated with statistically significant alterations in visual acuity and central retinal thickness (traits that are considered albinism endophenotypes). The approach discussed in this report opens up new avenues for the investigation of oligogenic patterns in apparently Mendelian disorders.
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Affiliation(s)
- David J Green
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Vincent Michaud
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Claudio Plaisant
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Benoît Arveiler
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK.
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
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Chen C, Li J, Wang B, Wang Y, Yu X. TYR mutation in a Chinese population with oculocutaneous albinism: Molecular characteristics and ophthalmic manifestations. Exp Eye Res 2024; 239:109761. [PMID: 38145795 DOI: 10.1016/j.exer.2023.109761] [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: 08/22/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
Oculocutaneous albinism (OCA) is a rare inherited disorder characterized by a partial or complete reduction of melanin biosynthesis that leads to hypopigmentation in the skin, hair and eyes. The OCA1 subtype is caused by mutations in TYR. The purpose of this study was to investigate the genetic and clinical ophthalmic characteristics of TYR mutations in patients with OCA. Herein, 51 probands with a clinical diagnosis of OCA were enrolled. Whole-exome sequencing and comprehensive ophthalmic examinations were performed. Overall, TYR mutations were detected in 37.3% (19/51) in the patients with OCA. Fifteen patients had compound heterozygous variants, and four cases had homozygous variants. Eleven different pathogenic variants in TYR were detected in these 19 patients, with missense, insertion, delins and nonsense in 71.1% (27/38), 15.8% (6/38), 2.6% (1/38), and 10.5% (4/38), respectively. Clinical examinations revealed that 84.2% (16/19) of patients were OCA1A, and 15.8% (3/19) were OCA1B. Most TYR probands (52.6%, 10/19) had moderate vision impairment, 15.8% (3/19) had severe visual impairment, 10.5% (2/19) exhibited blindness, only 5.3% (1/19) had mild visual impairment and 15.8% (3/19) were not available. Photophobia and nystagmus were found in 100% (19/19) of the patients. In addition, grade 4 foveal hypoplasia was detected in 100% (12/12) of the patients. In conclusion: The TYR patients exhibited severe ocular phenotypes: the majority (93.8%, 15/16) of them had a moderate vision impairment or worse, and 100% (12/12) had severe grade 4 foveal hypoplasia. These novel findings could provide insight into the understanding of OCA.
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Affiliation(s)
- Chonglin Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Jun Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Bingqi Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yinghuan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xinping Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
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Kuht HJ, McLean RJ, Aamir A, Maconachie GDE, Gottlob I, Thomas MG. Albinism Associated With Torsional Nystagmus Masquerading as Spasmus Nutans. J Neuroophthalmol 2023; 43:e313-e315. [PMID: 34924531 DOI: 10.1097/wno.0000000000001417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Helen J Kuht
- The University of Leicester Ulverscroft Eye Unit (HJK, RJM, AA, GDEM, IG, MGT), Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, Leicester, United Kingdom; and Health Sciences School (GDEM), Division of Ophthalmology & Orthoptics, University of Sheffield, United Kingdom
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Kuht HJ, Thomas MG, McLean RJ, Sheth V, Proudlock FA, Gottlob I. Abnormal foveal morphology in carriers of oculocutaneous albinism. Br J Ophthalmol 2023; 107:1202-1208. [PMID: 35379600 PMCID: PMC10359511 DOI: 10.1136/bjophthalmol-2020-318192] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/18/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND/AIMS To investigate the foveal morphology in carriers of oculocutaneous albinism (OCA) using spectral domain optical coherence tomography (SD-OCT). A cross-sectional, observational study. METHODS Handheld SD-OCT (Envisu C2300) was used to acquire horizontal scans through the centre of the fovea in biological parents of patients with OCA (n=28; mean age±SD=40.43±8.07 years) and age-matched and ethnicity-matched controls (n=28; mean age±SD=38.04±10.27 years). Sequence analysis was performed for variants in known genes associated with OCA. Best-corrected visual acuity (BCVA), presence of foveal hypoplasia and grade, foveal, parafoveal and perifoveal thickness measurements of total retinal layers (TRL), inner retinal layers (IRL) and outer retinal layers (ORL) thickness were measured. RESULTS Foveal hypoplasia was identified in 32.14% of OCA carriers; grade 1 in all cases. OCA carriers demonstrated significant thicker TRL thickness (median difference: 13.46 µm, p=0.009) and IRL thickness (mean difference: 8.98 µm, p<0.001) at the central fovea compared with controls. BCVA of carriers was between -0.16 and 0.18 logMAR (mean: 0.0 logMAR). No significant differences in BCVA was noted between OCA carriers or controls (p=0.83). In the OCA carriers, we identified previously reported pathogenic variants in TYR, OCA2 and SLC45A2, novel OCA2 variants (n=3) and heterozygosity of the pathogenic TYR haplotype. CONCLUSION We have, for the first time, identified foveal abnormalities in OCA carriers. This provides clinical value, particularly in cases where limited phenotype data are available. Our findings raise the possibility that previously reported mild cases of foveal hypoplasia or isolated foveal hypoplasia could correspond to OCA carrier status.
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Affiliation(s)
- Helen J Kuht
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Mervyn G Thomas
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Rebecca J McLean
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Viral Sheth
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Frank A Proudlock
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Irene Gottlob
- Ulverscroft Eye Unit, Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- Cooper Medical School of Rowan University, Cooper Neurological Institute, Camden, New Jersey, USA
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Loftus SK, Gillis MF, Lundh L, Baxter LL, Wedel JC, Watkins-Chow DE, Donovan FX, Sergeev YV, Oetting WS, Pavan WJ, Adams DR. Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B. Am J Hum Genet 2023; 110:1123-1137. [PMID: 37327787 PMCID: PMC10357474 DOI: 10.1016/j.ajhg.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023] Open
Abstract
Oculocutaneous albinism (OCA) is a rare disorder of pigment production. Affected individuals have variably decreased global pigmentation and visual-developmental changes that lead to low vision. OCA is notable for significant missing heritability, particularly among individuals with residual pigmentation. Tyrosinase (TYR) is the rate-limiting enzyme in melanin pigment biosynthesis and mutations that decrease enzyme function are one of the most common causes of OCA. We present the analysis of high-depth short-read TYR sequencing data for a cohort of 352 OCA probands, ∼50% of whom were previously sequenced without yielding a definitive diagnostic result. Our analysis identified 66 TYR single-nucleotide variants (SNVs) and small insertion/deletions (indels), 3 structural variants, and a rare haplotype comprised of two common frequency variants (p.Ser192Tyr and p.Arg402Gln) in cis-orientation, present in 149/352 OCA probands. We further describe a detailed analysis of the disease-causing haplotype, p.[Ser192Tyr; Arg402Gln] ("cis-YQ"). Haplotype analysis suggests that the cis-YQ allele arose by recombination and that multiple cis-YQ haplotypes are segregating in OCA-affected individuals and control populations. The cis-YQ allele is the most common disease-causing allele in our cohort, representing 19.1% (57/298) of TYR pathogenic alleles in individuals with type 1 (TYR-associated) OCA. Finally, among the 66 TYR variants, we found several additional alleles defined by a cis-oriented combination of minor, potentially hypomorph-producing alleles at common variant sites plus a second, rare pathogenic variant. Together, these results suggest that identification of phased variants for the full TYR locus are required for an exhaustive assessment for potentially disease-causing alleles.
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Affiliation(s)
- Stacie K Loftus
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Meredith F Gillis
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank X Donovan
- Cancer Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Association of TYR SNP rs1042602 with Melanoma Risk and Prognosis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122004. [PMID: 36556369 PMCID: PMC9785037 DOI: 10.3390/life12122004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Cutaneous melanoma is the most aggressive of skin tumors. In order to discover new biomarkers that could help us improve prognostic prediction in melanoma patients, we have searched for germline DNA variants associated with melanoma progression. Thus, after exome sequencing of a set of melanoma patients and healthy control individuals, we identified rs1042602, an SNP within TYR, as a good candidate. After genotyping rs1042602 in 1025 patients and 773 healthy donors, we found that the rs1042602-A allele was significantly associated with susceptibility to melanoma (CATT test: p = 0.0035). Interestingly, we also observed significant differences between patients with good and bad prognosis (5 years of follow-up) (n = 664) (CATT test for all samples p = 0.0384 and for men alone p = 0.0054). Disease-free-survival (DFS) analyses also showed that patients with the A allele had shorter DFS periods. In men, the association remained significant even in a multivariate Cox Proportional-hazards model, which was adjusted for age at diagnosis, Breslow thickness, ulceration and melanoma subtype (HR 0.4; 95% confidence interval (CI) 0.20-0.83; p = 0.0139). Based on our results, we propose that rs1042602-A is a risk allele for melanoma, which also seems to be responsible for a poorer prognosis of the disease, particularly in men.
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The retinal pigmentation pathway in human albinism: Not so black and white. Prog Retin Eye Res 2022; 91:101091. [PMID: 35729001 DOI: 10.1016/j.preteyeres.2022.101091] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022]
Abstract
Albinism is a pigment disorder affecting eye, skin and/or hair. Patients usually have decreased melanin in affected tissues and suffer from severe visual abnormalities, including foveal hypoplasia and chiasmal misrouting. Combining our data with those of the literature, we propose a single functional genetic retinal signalling pathway that includes all 22 currently known human albinism disease genes. We hypothesise that defects affecting the genesis or function of different intra-cellular organelles, including melanosomes, cause syndromic forms of albinism (Hermansky-Pudlak (HPS) and Chediak-Higashi syndrome (CHS)). We put forward that specific melanosome impairments cause different forms of oculocutaneous albinism (OCA1-8). Further, we incorporate GPR143 that has been implicated in ocular albinism (OA1), characterised by a phenotype limited to the eye. Finally, we include the SLC38A8-associated disorder FHONDA that causes an even more restricted "albinism-related" ocular phenotype with foveal hypoplasia and chiasmal misrouting but without pigmentation defects. We propose the following retinal pigmentation pathway, with increasingly specific genetic and cellular defects causing an increasingly specific ocular phenotype: (HPS1-11/CHS: syndromic forms of albinism)-(OCA1-8: OCA)-(GPR143: OA1)-(SLC38A8: FHONDA). Beyond disease genes involvement, we also evaluate a range of (candidate) regulatory and signalling mechanisms affecting the activity of the pathway in retinal development, retinal pigmentation and albinism. We further suggest that the proposed pigmentation pathway is also involved in other retinal disorders, such as age-related macular degeneration. The hypotheses put forward in this report provide a framework for further systematic studies in albinism and melanin pigmentation disorders.
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Expanding the Spectrum of Oculocutaneous Albinism: Does Isolated Foveal Hypoplasia Really Exist? Int J Mol Sci 2022; 23:ijms23147825. [PMID: 35887175 PMCID: PMC9317384 DOI: 10.3390/ijms23147825] [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: 05/14/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/05/2023] Open
Abstract
Oculocutaneous albinism is an autosomal recessive disorder characterized by the presence of typical ocular features, such as foveal hypoplasia, iris translucency, hypopigmented fundus oculi and reduced pigmentation of skin and hair. Albino patients can show significant clinical variability; some individuals can present with only mild depigmentation and subtle ocular changes. Here, we provide a retrospective review of the standardized clinical charts of patients firstly addressed for evaluation of foveal hypoplasia and slightly subnormal visual acuity, whose diagnosis of albinism was achieved only after extensive phenotypic and genotypic characterization. Our report corroborates the pathogenicity of the two common TYR polymorphisms p.(Arg402Gln) and p.(Ser192Tyr) when both are located in trans with a pathogenic TYR variant and aims to expand the phenotypic spectrum of albinism in order to increase the detection rate of the albino phenotype. Our data also suggest that isolated foveal hypoplasia should be considered a clinical sign instead of a definitive diagnosis of an isolated clinical entity, and we recommend deep phenotypic and molecular characterization in such patients to achieve a proper diagnosis.
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Michaud V, Lasseaux E, Green DJ, Gerrard DT, Plaisant C, Fitzgerald T, Birney E, Arveiler B, Black GC, Sergouniotis PI. The contribution of common regulatory and protein-coding TYR variants to the genetic architecture of albinism. Nat Commun 2022; 13:3939. [PMID: 35803923 PMCID: PMC9270319 DOI: 10.1038/s41467-022-31392-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Genetic diseases have been historically segregated into rare Mendelian disorders and common complex conditions. Large-scale studies using genome sequencing are eroding this distinction and are gradually unmasking the underlying complexity of human traits. Here, we analysed data from the Genomics England 100,000 Genomes Project and from a cohort of 1313 individuals with albinism aiming to gain insights into the genetic architecture of this archetypal rare disorder. We investigated the contribution of protein-coding and regulatory variants both rare and common. We focused on TYR, the gene encoding tyrosinase, and found that a high-frequency promoter variant, TYR c.-301C>T [rs4547091], modulates the penetrance of a prevalent, albinism-associated missense change, TYR c.1205G>A (p.Arg402Gln) [rs1126809]. We also found that homozygosity for a haplotype formed by three common, functionally-relevant variants, TYR c.[-301C;575C>A;1205G>A], is associated with a high probability of receiving an albinism diagnosis (OR>82). This genotype is also associated with reduced visual acuity and with increased central retinal thickness in UK Biobank participants. Finally, we report how the combined analysis of rare and common variants can increase diagnostic yield and can help inform genetic counselling in families with albinism.
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Affiliation(s)
- Vincent Michaud
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - David J Green
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Dave T Gerrard
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Claudio Plaisant
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK
| | - Benoît Arveiler
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France.
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France.
| | - Graeme C Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
| | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Cambridge, UK.
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
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Kuht HJ, Maconachie GDE, Han J, Kessel L, van Genderen MM, McLean RJ, Hisaund M, Tu Z, Hertle RW, Gronskov K, Bai D, Wei A, Li W, Jiao Y, Smirnov V, Choi JH, Tobin MD, Sheth V, Purohit R, Dawar B, Girach A, Strul S, May L, Chen FK, Heath Jeffery RC, Aamir A, Sano R, Jin J, Brooks BP, Kohl S, Arveiler B, Montoliu L, Engle EC, Proudlock FA, Nishad G, Pani P, Varma G, Gottlob I, Thomas MG. Genotypic and Phenotypic Spectrum of Foveal Hypoplasia: A Multicenter Study. Ophthalmology 2022; 129:708-718. [PMID: 35157951 PMCID: PMC9341240 DOI: 10.1016/j.ophtha.2022.02.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 01/01/2023] Open
Abstract
PURPOSE To characterize the genotypic and phenotypic spectrum of foveal hypoplasia (FH). DESIGN Multicenter, observational study. PARTICIPANTS A total of 907 patients with a confirmed molecular diagnosis of albinism, PAX6, SLC38A8, FRMD7, AHR, or achromatopsia from 12 centers in 9 countries (n = 523) or extracted from publicly available datasets from previously reported literature (n = 384). METHODS Individuals with a confirmed molecular diagnosis and availability of foveal OCT scans were identified from 12 centers or from the literature between January 2011 and March 2021. A genetic diagnosis was confirmed by sequence analysis. Grading of FH was derived from OCT scans. MAIN OUTCOME MEASURES Grade of FH, presence or absence of photoreceptor specialization (PRS+ vs. PRS-), molecular diagnosis, and visual acuity (VA). RESULTS The most common genetic etiology for typical FH in our cohort was albinism (67.5%), followed by PAX6 (21.8%), SLC38A8 (6.8%), and FRMD7 (3.5%) variants. AHR variants were rare (0.4%). Atypical FH was seen in 67.4% of achromatopsia cases. Atypical FH in achromatopsia had significantly worse VA than typical FH (P < 0.0001). There was a significant difference in the spectrum of FH grades based on the molecular diagnosis (chi-square = 60.4, P < 0.0001). All SLC38A8 cases were PRS- (P = 0.003), whereas all FRMD7 cases were PRS+ (P < 0.0001). Analysis of albinism subtypes revealed a significant difference in the grade of FH (chi-square = 31.4, P < 0.0001) and VA (P = 0.0003) between oculocutaneous albinism (OCA) compared with ocular albinism (OA) and Hermansky-Pudlak syndrome (HPS). Ocular albinism and HPS demonstrated higher grades of FH and worse VA than OCA. There was a significant difference (P < 0.0001) in VA between FRMD7 variants compared with other diagnoses associated with FH. CONCLUSIONS We characterized the phenotypic and genotypic spectrum of FH. Atypical FH is associated with a worse prognosis than all other forms of FH. In typical FH, our data suggest that arrested retinal development occurs earlier in SLC38A8, OA, HPS, and AHR variants and later in FRMD7 variants. The defined time period of foveal developmental arrest for OCA and PAX6 variants seems to demonstrate more variability. Our findings provide mechanistic insight into disorders associated with FH and have significant prognostic and diagnostic value.
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Affiliation(s)
- Helen J Kuht
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Foveal Development Investigators Group
| | - Gail D E Maconachie
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Academic Unit of Ophthalmology and Orthoptics, University of Sheffield, Sheffield, United Kingdom; Foveal Development Investigators Group
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea; Foveal Development Investigators Group
| | - Line Kessel
- Department of Ophthalmology, Rigshospitalet, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Foveal Development Investigators Group
| | - Maria M van Genderen
- Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, The Netherlands; Bartiméus Diagnostic Centre for Complex Visual Disorders, Zeist, The Netherlands; Foveal Development Investigators Group
| | - Rebecca J McLean
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Michael Hisaund
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Zhanhan Tu
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Foveal Development Investigators Group
| | - Richard W Hertle
- Department of Ophthalmology, The Rebecca D. Considine Research Institute and The Children's Vision Center, Akron Children's Hospital, Akron, Ohio; Department of Surgery, The Northeastern Ohio Medical University, Rootstown, Ohio; Foveal Development Investigators Group
| | - Karen Gronskov
- Department of Clinical Genetics, Rigshospitalet-Kennedy Center, Glostrup, Denmark; Foveal Development Investigators Group
| | - Dayong Bai
- Department of Ophthalmology, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China; Foveal Development Investigators Group
| | - Aihua Wei
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Foveal Development Investigators Group
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; Rare Disease Center, National Center for Children's Health; MOE Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, Capital Medical University, Beijing, China; Foveal Development Investigators Group
| | - Yonghong Jiao
- Beijing Tongren Eye Centre, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China; Foveal Development Investigators Group
| | - Vasily Smirnov
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, Paris, France; Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France; Foveal Development Investigators Group
| | - Jae-Hwan Choi
- Department of Neurology, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea; Foveal Development Investigators Group
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom; Foveal Development Investigators Group
| | - Viral Sheth
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Academic Unit of Ophthalmology and Orthoptics, University of Sheffield, Sheffield, United Kingdom
| | - Ravi Purohit
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Basu Dawar
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Ayesha Girach
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Sasha Strul
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota; Foveal Development Investigators Group
| | - Laura May
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota; Foveal Development Investigators Group
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Crawley, Australia; Foveal Development Investigators Group
| | - Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Crawley, Australia; Foveal Development Investigators Group
| | - Abdullah Aamir
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Ronaldo Sano
- Retina and Vitreous Sector of Santa Casa de Misericórdia de São Paulo, São Paulo, Brazil; Foveal Development Investigators Group
| | - Jing Jin
- Sidney Kimmel Medical College of Thomas Jefferson University, Nemours Children's Health, Philadelphia, Pennsylvania; Nemours Children's Health, Wilmington, Delaware
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland; Foveal Development Investigators Group
| | - Susanne Kohl
- Centre for Ophthalmology, Institute for Ophthalmic Research, University Tübingen, Tübingen, Germany; Foveal Development Investigators Group
| | - Benoit Arveiler
- Rare Diseases, Genetics and Metabolism, INSERM U1211, University of Bordeaux, Bordeaux, France; Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, France; Foveal Development Investigators Group
| | - Lluis Montoliu
- National Centre for Biotechnology (CNB-CSIC) and CIBERER-ISCIII, Madrid, Spain; Foveal Development Investigators Group
| | - Elizabeth C Engle
- Departments of Neurology and Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts; Howard Hughes Medical Institute, Chevy Chase, Maryland; Foveal Development Investigators Group
| | - Frank A Proudlock
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Garima Nishad
- International Institute of Information Technology, Hyderabad, India
| | - Prateek Pani
- International Institute of Information Technology, Hyderabad, India
| | - Girish Varma
- International Institute of Information Technology, Hyderabad, India; Foveal Development Investigators Group
| | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Foveal Development Investigators Group; Cooper Neurological Institute, Cooper Medical School of Rowan University, Camden, New Jersey
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom; Foveal Development Investigators Group.
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11
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Lin S, Sanchez-Bretaño A, Leslie JS, Williams KB, Lee H, Thomas NS, Callaway J, Deline J, Ratnayaka JA, Baralle D, Schmitt MA, Norman CS, Hammond S, Harlalka GV, Ennis S, Cross HE, Wenger O, Crosby AH, Baple EL, Self JE. Evidence that the Ser192Tyr/Arg402Gln in cis Tyrosinase gene haplotype is a disease-causing allele in oculocutaneous albinism type 1B (OCA1B). NPJ Genom Med 2022; 7:2. [PMID: 35027574 PMCID: PMC8758782 DOI: 10.1038/s41525-021-00275-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/19/2021] [Indexed: 01/09/2023] Open
Abstract
Oculocutaneous albinism type 1 (OCA1) is caused by pathogenic variants in the TYR (tyrosinase) gene which encodes the critical and rate-limiting enzyme in melanin synthesis. It is the most common OCA subtype found in Caucasians, accounting for ~50% of cases worldwide. The apparent 'missing heritability' in OCA is well described, with ~25-30% of clinically diagnosed individuals lacking two clearly pathogenic variants. Here we undertook empowered genetic studies in an extensive multigenerational Amish family, alongside a review of previously published literature, a retrospective analysis of in-house datasets, and tyrosinase activity studies. Together this provides irrefutable evidence of the pathogenicity of two common TYR variants, p.(Ser192Tyr) and p.(Arg402Gln) when inherited in cis alongside a pathogenic TYR variant in trans. We also show that homozygosity for the p.(Ser192Tyr)/p.(Arg402Gln) TYR haplotype results in a very mild, but fully penetrant, albinism phenotype. Together these data underscore the importance of including the TYR p.(Ser192Tyr)/p.(Arg402Gln) in cis haplotype as a pathogenic allele causative of OCA, which would likely increase molecular diagnoses in this missing heritability albinism cohort by 25-50%.
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Affiliation(s)
- Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Aida Sanchez-Bretaño
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
| | - Katie B Williams
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - Helena Lee
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Southampton Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - N Simon Thomas
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Jonathan Callaway
- Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - James Deline
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - J Arjuna Ratnayaka
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Melanie A Schmitt
- University of Wisconsin School of Medicine and Public Health, Department of Ophthalmology & Visual Sciences, Madison, WI, USA
| | - Chelsea S Norman
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The Rosalind Franklin Institute, Rutherford Appleton Laboratories, Harwell Science and Innovation Campus, Didcot, UK
| | - Sheri Hammond
- Center for Special Children, Vernon Memorial Healthcare, La Farge, WI, USA
| | - Gaurav V Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK
- Rajarshi Shahu College of Pharmacy, Malvihir, Buldana, India
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Harold E Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Olivia Wenger
- New Leaf Clinic, PO Box 336, 16014 East Chestnut Street, Mount Eaton, OH, 44691, USA
- Department of Pediatrics, Akron Children's Hospital, 214 West Bowery Street, Akron, OH, 44308, USA
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK.
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, UK.
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Gladstone Road, Exeter, UK.
| | - Jay E Self
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
- Southampton Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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12
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Ayala GD, Linderman RE, Valenzuela RK, Woertz EN, Brilliant M, Tarima S, Carroll J. Assessing Foveal Structure in Individuals with TYR R402Q and S192Y Hypomorphic Alleles. OPHTHALMOLOGY SCIENCE 2021; 1:100077. [PMID: 36246950 PMCID: PMC9560529 DOI: 10.1016/j.xops.2021.100077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 10/31/2022]
Abstract
Purpose Design Participants Methods Main Outcome Measures Results Conclusions
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13
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Aamir A, Kuht HJ, Grønskov K, Brooks BP, Thomas MG. Clinical utility gene card for oculocutaneous (OCA) and ocular albinism (OA)-an update. Eur J Hum Genet 2021; 29:1577-1583. [PMID: 33504991 PMCID: PMC8484472 DOI: 10.1038/s41431-021-00809-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/12/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Affiliation(s)
- Abdullah Aamir
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester, LE2 7LX, UK
| | - Helen J Kuht
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester, LE2 7LX, UK
| | - Karen Grønskov
- Rigshospitalet, Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Bethesda, MD, USA
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester, LE2 7LX, UK.
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14
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Koirala M, Shashikala HBM, Jeffries J, Wu B, Loftus SK, Zippin JH, Alexov E. Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. Int J Mol Sci 2021; 22:ijms22158273. [PMID: 34361043 PMCID: PMC8347052 DOI: 10.3390/ijms22158273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.
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Affiliation(s)
- Mahesh Koirala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - H. B. Mihiri Shashikala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Jacob Jeffries
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Bohua Wu
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Branch, National Institutes of Health, Bethesda, MD 22066, USA;
| | - Jonathan H. Zippin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
- Correspondence:
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15
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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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16
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Duwell EJ, Woertz EN, Mathis J, Carroll J, DeYoe EA. Aberrant visual population receptive fields in human albinism. J Vis 2021; 21:19. [PMID: 34007988 PMCID: PMC8142699 DOI: 10.1167/jov.21.5.19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Retinotopic organization is a fundamental feature of visual cortex thought to play a vital role in encoding spatial information. One important aspect of normal retinotopy is the representation of the right and left hemifields in contralateral visual cortex. However, in human albinism, many temporal retinal afferents decussate aberrantly at the optic chiasm resulting in partially superimposed representations of opposite hemifields in each hemisphere of visual cortex. Previous functional magnetic resonance imaging (fMRI) studies in human albinism suggest that the right and left hemifield representations are superimposed in a mirror-symmetric manner. This should produce imaging voxels which respond to two separate locations mirrored across the vertical meridian. However, it is not yet clear how retino-cortical miswiring in albinism manifests at the level of single voxel population receptive fields (pRFs). Here, we used pRF modeling to fit both single and dual pRF models to the visual responses of voxels in visual areas V1 to V3 of five subjects with albinism. We found that subjects with albinism (but not controls) have sizable clusters of voxels with unequivocal dual pRFs consistently corresponding to, but not fully coextensive with, regions of hemifield overlap. These dual pRFs were typically positioned at locations roughly mirrored across the vertical meridian and were uniquely clustered within a portion of the visual field for each subject.
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Affiliation(s)
- Ethan J Duwell
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA.,
| | - Erica N Woertz
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.,
| | - Jedidiah Mathis
- Department of Neurology, Medical College of Wisconsin, USA.,
| | - Joseph Carroll
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, USA.,
| | - Edgar A DeYoe
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, USA.,
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17
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Chan HW, Schiff ER, Tailor VK, Malka S, Neveu MM, Theodorou M, Moosajee M. Prospective Study of the Phenotypic and Mutational Spectrum of Ocular Albinism and Oculocutaneous Albinism. Genes (Basel) 2021; 12:508. [PMID: 33808351 PMCID: PMC8065601 DOI: 10.3390/genes12040508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/15/2021] [Accepted: 03/26/2021] [Indexed: 02/07/2023] Open
Abstract
Albinism encompasses a group of hereditary disorders characterized by reduced or absent ocular pigment and variable skin and/or hair involvement, with syndromic forms such as Hermansky-Pudlak syndrome and Chédiak-Higashi syndrome. Autosomal recessive oculocutaneous albinism (OCA) is phenotypically and genetically heterogenous (associated with seven genes). X-linked ocular albinism (OA) is associated with only one gene, GPR143. We report the clinical and genetic outcomes of 44 patients, from 40 unrelated families of diverse ethnicities, with query albinism presenting to the ocular genetics service at Moorfields Eye Hospital NHS Foundation Trust between November 2017 and October 2019. Thirty-six were children (≤ 16 years) with a median age of 31 months (range 2-186), and eight adults with a median age of 33 years (range 17-39); 52.3% (n = 23) were male. Genetic testing using whole genome sequencing (WGS, n = 9) or a targeted gene panel (n = 31) gave an overall diagnostic rate of 42.5% (44.4% (4/9) with WGS and 41.9% (13/31) with panel testing). Seventeen families had confirmed mutations in TYR (n = 9), OCA2, (n = 4), HPS1 (n = 1), HPS3 (n = 1), HPS6 (n = 1), and GPR143 (n = 1). Molecular diagnosis of albinism remains challenging due to factors such as missing heritability. Differential diagnoses must include SLC38A8-associated foveal hypoplasia and syndromic forms of albinism.
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Affiliation(s)
- Hwei Wuen Chan
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
- Department of Ophthalmology, National University Singapore, Singapore S118177, Singapore
| | - Elena R. Schiff
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Vijay K. Tailor
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
- Experimental Psychology, University College London, London WC1H 0AP, UK
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
| | - Magella M. Neveu
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Maria Theodorou
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
| | - Mariya Moosajee
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK; (H.W.C.); (E.R.S.); (V.K.T.); (S.M.); (M.M.N.); (M.T.)
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- The Francis Crick Institute, London NW1 1AT, UK
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18
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de Bruijn SE, Fadaie Z, Cremers FPM, Kremer H, Roosing S. The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. Int J Mol Sci 2021; 22:2943. [PMID: 33799353 PMCID: PMC7998853 DOI: 10.3390/ijms22062943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
The identification of pathogenic variants in monogenic diseases has been of interest to researchers and clinicians for several decades. However, for inherited diseases with extremely high genetic heterogeneity, such as hearing loss and retinal dystrophies, establishing a molecular diagnosis requires an enormous effort. In this review, we use these two genetic conditions as examples to describe the initial molecular genetic identification approaches, as performed since the early 90s, and subsequent improvements and refinements introduced over the years. Next, the history of DNA sequencing from conventional Sanger sequencing to high-throughput massive parallel sequencing, a.k.a. next-generation sequencing, is outlined, including their advantages and limitations and their impact on identifying the remaining genetic defects. Moreover, the development of recent technologies, also coined "third-generation" sequencing, is reviewed, which holds the promise to overcome these limitations. Furthermore, we outline the importance and complexity of variant interpretation in clinical diagnostic settings concerning the massive number of different variants identified by these methods. Finally, we briefly mention the development of novel approaches such as optical mapping and multiomics, which can help to further identify genetic defects in the near future.
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Affiliation(s)
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Hannie Kremer
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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19
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Kessel L, Kjer B, Lei U, Duno M, Grønskov K. Genotype-phenotype associations in Danish patients with ocular and oculocutaneous albinism. Ophthalmic Genet 2021; 42:230-238. [PMID: 33612058 DOI: 10.1080/13816810.2021.1881979] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND The study aimed to describe genotype-phenotype associations in patients with oculocutaneous and ocular-only albinism and to evaluate a set of diagnostic criteria proposed recently by Kruijt et al. MATERIALS AND METHODS Genotype-phenotype associations in patients with a clinical diagnosis of albinism were studied based on imaging of hair and ocular features (nystagmus, iris color and translucency, fundus pigmentation and foveal development) and self-evaluated skin type. Patients were sub-grouped based on genetic findings. RESULTS Patients with biallelic variants in TYR (n = 29), OCA2 (n = 22), other albinism genes (n = 13) or monoallelic variants in GPR143 (n = 13) were included as were 15 patients with a pure clinical diagnosis but no genetic findings. In descending order the most common findings were: foveal hypoplasia (any hypoplasia 95.2%, severe 88.0%), nystagmus (93.5%), iris translucency (any translucency 80.2%, moderate to severe 31.5%), misrouting on VEP (80.0%): fundus hypopigmentation (any hypopigmentation: 75.8%, severe 30.1%), fair skin type (73.8%), blue irides (62.0%), blonde hair (57.5%), and unpigmented eye lashes (39.1%). There were no phenotypic differences between the different genetic subgroups of albinism but patients with a pathogenic haplotype in TYR in combination with a classic variant had less iris translucency than patients with two classic variants in TYR. CONCLUSIONS Ocular developmental features were the most common findings whereas phenotypic features related to pigmentation were less common findings but there were no genotype-phenotype correlations. All patients with a genetically confirmed diagnosis of albinism fulfilled the diagnostic criteria by Kruijt irrespective of genetic subtype.
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Affiliation(s)
- Line Kessel
- Department of Ophthalmology, Rigshospitalet-Kennedy Center, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen Denmark
| | - Birgit Kjer
- Department of Ophthalmology, Rigshospitalet-Kennedy Center, Denmark
| | - Ulrikke Lei
- Department of Clinical Medicine, University of Copenhagen, Copenhagen Denmark.,Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Denmark
| | - Morten Duno
- Department of Clinical Genetics, Rigshospitalet-Kennedy Center, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet-Kennedy Center, Denmark
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20
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Discordant phenotypes in twins with infantile nystagmus. Sci Rep 2021; 11:2826. [PMID: 33531592 PMCID: PMC7854608 DOI: 10.1038/s41598-021-82368-0] [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] [Received: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 11/08/2022] Open
Abstract
Infantile nystagmus (IN) may result from aetiologies including albinism and FRMD7 mutations. IN has low prevalence, and twins with IN are rare. Whilst discordant presentation has been previously reported for IN, we present for the first time the comprehensive assessment of diagnostically discordant monozygotic twins. From a cohort of over 2000 patients, we identified twins and triplets discordant for nystagmus. Using next-generation sequencing, high-resolution infra-red pupil tracking and optical coherence tomography, we characterised differences in genotype and phenotype. Monozygotic twins (n = 1), dizygotic twins (n = 3) and triplets (n = 1) were included. The monozygotic twins had concordant TYR variants. No causative variants were identified in the triplets. Dizygotic twins had discordant variants in TYR, OCA2 and FRMD7. One unaffected co-twin demonstrated sub-clinical nystagmus. Foveal hypoplasia (FH) was noted in four of five probands. Both co-twins of the monozygotic pair and triplets displayed FH. In three families, at least one parent had FH without nystagmus. FH alone may be insufficient to develop nystagmus. Whilst arrested optokinetic reflex pathway development is implicated in IN, discordant twins raise questions regarding where differences in development have arisen. In unaffected monozygotes therefore, genetic variants may predispose to oculomotor instability, with variable expressivity possibly responsible for the discordance observed.
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21
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Mock JR, Dial CF, Tune MK, Gilmore RC, O'Neal WK, Dang H, Doerschuk CM. Impact of Regulatory T Cells on Type 2 Alveolar Epithelial Cell Transcriptomes during Resolution of Acute Lung Injury and Contributions of IFN-γ. Am J Respir Cell Mol Biol 2020; 63:464-477. [PMID: 32543909 DOI: 10.1165/rcmb.2019-0399oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
By enhancing tissue repair and modulating immune responses, Foxp3+ regulatory T cells (Tregs) play essential roles in resolution from lung injury. The current study investigated the effects that Tregs exert directly or indirectly on the transcriptional profiles of type 2 alveolar epithelial (AT2) cells during resolution in an experimental model of acute lung injury. Purified AT2 cells were isolated from uninjured mice or mice recovering from LPS-induced lung injury, either in the presence of Tregs or in Treg-depleted mice, and transcriptome profiling identified differentially expressed genes. Depletion of Tregs resulted in altered expression of 49 genes within AT2 cells during resolution, suggesting that Tregs present in this microenvironment influence AT2-cell function. Biological processes from Gene Ontology enriched in the absence of Tregs included those describing responses to IFN. Neutralizing IFN-γ in Treg-depleted mice reversed the effect of Treg depletion on inflammatory macrophages and B cells by preventing the increase in inflammatory macrophages and the decrease in B cells. Our results provide insight into the effects of Tregs on AT2 cells. Tregs directly or indirectly impact many AT2-cell functions, including IFN type I and II-mediated signaling pathways. Inhibition of IFN-γ expression and/or function may be one mechanism through which Tregs accelerate resolution after acute lung injury.
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Affiliation(s)
- Jason R Mock
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine.,Marsico Lung Institute, and
| | - Catherine F Dial
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine.,Marsico Lung Institute, and
| | - Miriya K Tune
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine.,Marsico Lung Institute, and
| | | | - Wanda K O'Neal
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine.,Marsico Lung Institute, and
| | | | - Claire M Doerschuk
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine.,Marsico Lung Institute, and.,Center for Airways Disease, University of North Carolina, Chapel Hill, North Carolina
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22
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Current and emerging treatments for albinism. Surv Ophthalmol 2020; 66:362-377. [PMID: 33129801 DOI: 10.1016/j.survophthal.2020.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/07/2020] [Accepted: 10/21/2020] [Indexed: 12/24/2022]
Abstract
Albinism is a group of rare inherited disorders arising from impairment of melanin biosynthesis. The reduction of melanin synthesis leads to hypopigmentation of the skin and eyes. A wide range of ophthalmic manifestations arise from albinism, including reduction of visual acuity, nystagmus, strabismus, iris translucency, foveal hypoplasia, fundus hypopigmentation, and abnormal decussation of retinal ganglion cell axons at the optic chiasm. Currently, albinism is incurable, and treatment aims either surgically or pharmacologically to optimize vision and protect the skin; however, novel therapies that aim to directly address the molecular errors of albinism, such as l-dihydroxyphenylalanine and nitisinone, are being developed and have entered human trials though with limited success. Experimental gene-based strategies for editing the genetic errors in albinism have also met early success in animal models. The emergence of these new therapeutic modalities represents a new era in the management of albinism. We focus on the known genetic subtypes, clinical assessment, and existing and emerging therapeutic options for the nonsyndromic forms of albinism.
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23
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Rayner JE, Duffy DL, Smit DJ, Jagirdar K, Lee KJ, De’Ambrosis B, Smithers BM, McMeniman EK, McInerney-Leo AM, Schaider H, Stark MS, Soyer HP, Sturm RA. Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants. PLoS One 2020; 15:e0238529. [PMID: 32966289 PMCID: PMC7510969 DOI: 10.1371/journal.pone.0238529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
Amelanotic/hypomelanotic melanoma is a clinicopathologic subtype with absent or minimal melanin. This study assessed previously reported coding variants in albinism genes (TYR, OCA2, TYRP1, SLC45A2, SLC24A5, LRMDA) and common intronic, regulatory variants of OCA2 in individuals with amelanotic/hypomelanotic melanoma, pigmented melanoma cases and controls. Exome sequencing was available for 28 individuals with amelanotic/hypomelanotic melanoma and 303 individuals with pigmented melanoma, which were compared to whole exome data from 1144 Australian controls. Microarray genotyping was available for a further 17 amelanotic/hypomelanotic melanoma, 86 pigmented melanoma, 147 melanoma cases (pigmentation unknown) and 652 unaffected controls. Rare deleterious variants in TYR/OCA1 were more common in amelanotic/hypomelanotic melanoma cases than pigmented melanoma cases (set mixed model association tests P = 0.0088). The OCA2 hypomorphic allele p.V443I was more common in melanoma cases (1.8%) than controls (1.0%, X2 P = 0.02), and more so in amelanotic/hypomelanotic melanoma (4.4%, X2 P = 0.007). No amelanotic/hypomelanotic melanoma cases carried an eye and skin darkening haplotype of OCA2 (including rs7174027), present in 7.1% of pigmented melanoma cases (P = 0.0005) and 9.4% controls. Variants in TYR and OCA2 may play a role in amelanotic/hypomelanotic melanoma susceptibility. We suggest that somatic loss of function at these loci could contribute to the loss of tumor pigmentation, consistent with this we found a higher rate of somatic mutation in TYR/OCA2 in amelanotic/hypomelanotic melanoma vs pigmented melanoma samples (28.6% vs 3.0%; P = 0.021) from The Cancer Genome Atlas Skin Cutaneous Melanoma collection.
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Affiliation(s)
- Jenna E. Rayner
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - David L. Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - Darren J. Smit
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Katie J. Lee
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Brian De’Ambrosis
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
- South East Dermatology, Annerley, Brisbane, Qld, Australia
| | - B. Mark Smithers
- Queensland Melanoma Project, School of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Erin K. McMeniman
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Helmut Schaider
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Mitchell S. Stark
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - H. Peter Soyer
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- * E-mail:
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24
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Hvid K, Nissen KR, Bayat A, Roos L, Grønskov K, Kessel L. Prevalence and causes of infantile nystagmus in a large population-based Danish cohort. Acta Ophthalmol 2020; 98:506-513. [PMID: 32067411 DOI: 10.1111/aos.14354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/31/2019] [Indexed: 01/14/2023]
Abstract
PURPOSE The aim of this study was to provide a population-based estimate on the prevalence of infantile nystagmus and to describe the causes in the Capital Region of Denmark. METHODS Review of medical records of children with infantile nystagmus born in the period 1 January 2010 through 31 December 2017 and living in the Capital Region of Denmark. We used birth registry data from Statistics Denmark and the National Danish Birth Registry to calculate the prevalence of nystagmus in children born at term and prematurely. RESULTS A total of 103 patients (52 males/51 females) with infantile nystagmus were included. The overall prevalence of infantile nystagmus was 6.1 per 10 000 live births. It was higher in premature children (28.4/10 000 live births) than children born at term (4.4/10 000), p < 0.0001, and highest in children born extremely preterm, (97.3/10 000). The most common cause of infantile nystagmus was ocular disease (44%) followed by idiopathic nystagmus (32%), neurological disorders and genetic syndromes (20%) and prematurity without retinopathy of prematurity as the only cause (4%). CONCLUSIONS In this study, we provide the prevalence of infantile nystagmus based on national medical records in which all residents are accounted for. Our findings show a prevalence of 6.1 per 10 000 live births but six times higher among children born preterm than born at term. Ocular disease was the leading cause of infantile nystagmus with albinism and ocular malformations as the most frequent. In 1/3 of patients, no cause could be identified.
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Affiliation(s)
- Karen Hvid
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kamilla Rothe Nissen
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Allan Bayat
- Danish Epilepsy Centre, Dianalund, Denmark.,Department of Pediatrics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Laura Roos
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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25
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Ganguly K, Dutta T, Saha A, Sarkar D, Sil A, Ray K, Sengupta M. Mapping the TYR gene reveals novel and previously reported variants in Eastern Indian patients highlighting preponderance of the same changes in multiple unrelated ethnicities. Ann Hum Genet 2020; 84:303-312. [PMID: 32115698 DOI: 10.1111/ahg.12376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 11/30/2022]
Abstract
Oculocutaneous albinism (OCA) is a group of congenital autosomal recessive disorders with seven known subtypes (OCA1-OCA7) characterized by loss or absence of pigmentation in the skin, hair, and eyes. OCA1, caused by pathogenic variations in the tyrosinase (TYR) gene, has been documented to be the most prevalent subtype across the world including India. In the present study, we recruited 53 OCA-affected individuals from 45 unrelated families belonging to 20 different marriage groups/ethnicities of 15 different districts of West Bengal. We took a targeted sequencing-based approach to find the causal variations in the TYR gene. We report here identification of two novel potentially pathogenic variations [NM_000372.4:c.614C>T, NP_000363.1:p.(Pro205Leu), and NM_000372.4:c.1036+1=/G>T], one novel synonymous TYR variant [NM_000372.4:c.204=/A>G, NP_000363.1:p.(Gln68=)], two pathogenic variations documented for the first time in Indian OCA cases [NM_000372.4:c.1147G>A, NP_000363.1:p.(Asp383Asn), and NM_000372.4:c.585G>A, NP_000363.1:p.(Trp195*)], along with nine previously reported pathogenic variants in 36 out of 53 (∼68%) patients recruited. We report common haplotype backgrounds for the two most prevalent variations [NM_000372.4:c.124G>A, NM_000372.4:c.832C>T] in cases belonging to different marriage/ethnic groups, suggesting a possible founder effect. To our knowledge, this is the most comprehensive genetic study on OCA1 from India, firmly establishing OCA1 as the commonest form of albinism in this part of the world.
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Affiliation(s)
- Kausik Ganguly
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Tithi Dutta
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Arpan Saha
- Department of Genetics, University of Calcutta, Kolkata, India
| | - Devroop Sarkar
- Joypur Block Primary Health Centre, Howrah, West Bengal, India
| | - Asim Sil
- Vivekananda Mission Ashram Netra Niramay Niketan, Purba Medinipur, West Bengal, India
| | - Kunal Ray
- ATGC Diagnostics, Kolkata, West Bengal, India
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, Kolkata, India
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26
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Campbell P, Ellingford JM, Parry NRA, Fletcher T, Ramsden SC, Gale T, Hall G, Smith K, Kasperaviciute D, Thomas E, Lloyd IC, Douzgou S, Clayton-Smith J, Biswas S, Ashworth JL, Black GCM, Sergouniotis PI. Clinical and genetic variability in children with partial albinism. Sci Rep 2019; 9:16576. [PMID: 31719542 PMCID: PMC6851142 DOI: 10.1038/s41598-019-51768-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022] Open
Abstract
Individuals who have ocular features of albinism and skin pigmentation in keeping with their familial background present a considerable diagnostic challenge. Timely diagnosis through genomic testing can help avert diagnostic odysseys and facilitates accurate genetic counselling and tailored specialist management. Here, we report the clinical and gene panel testing findings in 12 children with presumed ocular albinism. A definitive molecular diagnosis was made in 8/12 probands (67%) and a possible molecular diagnosis was identified in a further 3/12 probands (25%). TYR was the most commonly mutated gene in this cohort (75% of patients, 9/12). A disease-causing TYR haplotype comprised of two common, functional polymorphisms, TYR c.[575 C > A;1205 G > A] p.[(Ser192Tyr);(Arg402Gln)], was found to be particularly prevalent. One participant had GPR143-associated X-linked ocular albinism and another proband had biallelic variants in SLC38A8, a glutamine transporter gene associated with foveal hypoplasia and optic nerve misrouting without pigmentation defects. Intriguingly, 2/12 individuals had a single, rare, likely pathogenic variant in each of TYR and OCA2 - a significant enrichment compared to a control cohort of 4046 individuals from the 100,000 genomes project pilot dataset. Overall, our findings highlight that panel-based genetic testing is a clinically useful test with a high diagnostic yield in children with partial/ocular albinism.
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Affiliation(s)
- Patrick Campbell
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Neil R A Parry
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Georgina Hall
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | | | | | - I Chris Lloyd
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Susmito Biswas
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jane L Ashworth
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C M Black
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Panagiotis I Sergouniotis
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Manchester Royal Eye Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
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27
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A small gene sequencing panel realises a high diagnostic rate in patients with congenital nystagmus following basic phenotyping. Sci Rep 2019; 9:13229. [PMID: 31519934 PMCID: PMC6744446 DOI: 10.1038/s41598-019-49368-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/26/2019] [Indexed: 11/08/2022] Open
Abstract
Nystagmus is a disorder of uncontrolled eye movement and can occur as an isolated trait (idiopathic INS, IINS) or as part of multisystem disorders such as albinism, significant visual disorders or neurological disease. Eighty-one unrelated patients with nystagmus underwent routine ocular phenotyping using commonly available phenotyping methods and were grouped into four sub-cohorts according to the level of phenotyping information gained and their findings. DNA was extracted and sequenced using a broad utility next generation sequencing (NGS) gene panel. A clinical subpanel of genes for nystagmus/albinism was utilised and likely causal variants were prioritised according to methods currently employed by clinical diagnostic laboratories. We determine the likely underlying genetic cause for 43.2% of participants with similar yields regardless of prior phenotyping. This study demonstrates that a diagnostic workflow combining basic ocular phenotyping and a clinically available targeted NGS panel, can provide a high diagnostic yield for patients with infantile nystagmus, enabling access to disease specific management at a young age and reducing the need for multiple costly, often invasive tests. By describing diagnostic yield for groups of patients with incomplete phenotyping data, it also permits the subsequent design of ‘real-world’ diagnostic workflows and illustrates the changing role of genetic testing in modern diagnostic workflows for heterogeneous ophthalmic disorders.
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