Search

Your search keyword '"Audo I"' showing total 320 results
Start Over Author "Audo I"
320 results on '"Audo I"'

2. NMNAT1 mutations cause Leber congenital amaurosis.

Author

Moore, Anthony, Falk, MJ, Zhang, Q, Nakamaru-Ogiso, E, Kannabiran, C, Fonseca-Kelly, Z, Chakarova, C, Audo, I, Mackay, DS, Zeitz, C, and Borman, AD

Abstract

Leber congenital amaurosis (LCA) is an infantile-onset form of inherited retinal degeneration characterized by severe vision loss(1,2). Two-thirds of LCA cases are caused by mutations in 17 known disease-associated genes(3) (Retinal Information Network (Re

Published
2012

4. Tissue‐specific genotype–phenotype correlations among USH2A‐related disorders in the RUSH2A study

Author

Hufnagel, R.B., Liang, W., Duncan, J.L., Brewer, C.C., Audo, I., Ayala, A.R., Branham, K., Cheetham, J.K., Daiger, S.P., Durham, T.A., Guan, B., Heon, E, Hoyng, C.B., Iannaccone, A., Kay, C.N., Michaelides, M., Pennesi, M.E., Singh, M.S., and Ullah, E.

Subjects
Extracellular Matrix Proteins, genetic structures, Mutation, otorhinolaryngologic diseases, Genetics, Humans, Usher Syndromes, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], eye diseases, Genetic Association Studies, Retinitis Pigmentosa, Article, Genetics (clinical)
Abstract

Contains fulltext : 251572.pdf (Publisher’s version ) (Closed access) We assessed genotype-phenotype correlations among the visual, auditory, and olfactory phenotypes of 127 participants with Usher syndrome (USH2) (n =80) or nonsyndromic autosomal recessive retinitis pigmentosa (ARRP) (n = 47) due to USH2A variants, using clinical data and molecular diagnostics from the Rate of Progression in USH2A Related Retinal Degeneration (RUSH2A) study. USH2A truncating alleles were associated with USH2 and had a dose-dependent effect on hearing loss severity with no effect on visual loss severity within the USH2 subgroup. A group of missense alleles in an interfibronectin domain appeared to be hypomorphic in ARRP. These alleles were associated with later age of onset, larger visual field area, better sensitivity thresholds, and better electroretinographic responses. No effect of genotype on the severity of olfactory deficits was observed. This study unveils a unique, tissue-specific USH2A allelic hierarchy with important prognostic implications for patient counseling and treatment trial endpoints. These findings may inform clinical care or research approaches in others with allelic disorders or pleiotropic phenotypes.

Published
2022

7. Artificial intelligence extension of the OSCAR-IB criteria

Author

Petzold, A., Albrecht, P., Balcer, L., Bekkers, E., Brandt, A. U., Calabresi, P. A., Deborah, O. G., Graves, J. S., Green, A., Keane, P. A., Nij Bijvank, J. A., Sander, J. W., Paul, F., Saidha, S., Villoslada, P., Wagner, S. K., Yeh, E. A., Aktas, O., Antel, J., Asgari, N., Audo, I., Avasarala, J., Avril, D., Bagnato, F. R., Banwell, B., Bar-Or, A., Behbehani, R., Manterola, A. B., Bennett, J., Benson, L., Bernard, J., Bremond-Gignac, D., Britze, J., Burton, J., Calkwood, J., Carroll, W., Chandratheva, A., Cohen, J., Comi, G., Cordano, C., Costa, S., Costello, F., Courtney, A., Cruz-Herranz, A., Cutter, G., Crabb, D., Delott, L., De Seze, J., Diem, R., Dollfuss, H., El Ayoubi, N. K., Fasser, C., Finke, C., Fischer, D., Fitzgerald, K., Fonseca, P., Frederiksen, J. L., Frohman, E., Frohman, T., Fujihara, K., Cuellar, I. G., Galetta, S., Garcia-Martin, E., Giovannoni, G., Glebauskiene, B., Suarez, I. G., Jensen, G. P., Hamann, S., Hartung, H. -P., Havla, J., Hemmer, B., Huang, S. -C., Imitola, J., Jasinskas, V., Jiang, H., Kafieh, R., Kappos, L., Kardon, R., Keegan, D., Kildebeck, E., Kim, U. S., Klistorner, S., Knier, B., Kolbe, S., Korn, T., Krupp, L., Lagreze, W., Leocani, L., Levin, N., Liskova, P., Preiningerova, J. L., Lorenz, B., May, E., Miller, D., Mikolajczak, J., Said, S. M., Montalban, X., Morrow, M., Mowry, E., Murta, J., Navas, C., Nolan, R., Nowomiejska, K., Oertel, F. C., Oh, J., Oreja-Guevara, C., Orssaud, C., Osborne, B., Outteryck, O., Paiva, C., Palace, J., Papadopoulou, A., Patsopoulos, N., Pontikos, N., Preising, M., Prince, J., Reich, D., Rejdak, R., Ringelstein, M., Rodriguez de Antonio, L., Sahel, J. -A., Sanchez-Dalmau, B., Sastre-Garriga, J., Schippling, S., Schuman, J., Shindler, K., Shin, R., Shuey, N., Soelberg, K., Specovius, S., Suppiej, A., Thompson, A., Toosy, A., Torres, R., Touitou, V., Trauzettel-Klosinski, S., van der Walt, A., Vermersch, P., Vidal-Jordana, A., Waldman, A. T., Waters, C., Wheeler, R., White, O., Wilhelm, H., Winges, K. M., Wiegerinck, N., Wiehe, L., Wisnewski, T., Wong, S., Wurfel, J., Yaghi, S., You, Y., Yu, Z., Yu-Wai-Man, P., Zemaitien≐, R., Zimmermann, H., Albrecht P., Petzold A., Balcer, L., Bekkers, E., Brandt, A. U., Calabresi, P. A., Deborah, O. G., Graves, J. S., Green, A., Keane, P. A., Nij Bijvank, J. A., Sander, J. W., Paul, F., Saidha, S., Villoslada, P., Wagner, S. K., Yeh, E. A., Aktas, O., Antel, J., Asgari, N., Audo, I., Avasarala, J., Avril, D., Bagnato, F. R., Banwell, B., Bar-Or, A., Behbehani, R., Manterola, A. B., Bennett, J., Benson, L., Bernard, J., Bremond-Gignac, D., Britze, J., Burton, J., Calkwood, J., Carroll, W., Chandratheva, A., Cohen, J., Comi, G., Cordano, C., Costa, S., Costello, F., Courtney, A., Cruz-Herranz, A., Cutter, G., Crabb, D., Delott, L., De Seze, J., Diem, R., Dollfuss, H., El Ayoubi, N. K., Fasser, C., Finke, C., Fischer, D., Fitzgerald, K., Fonseca, P., Frederiksen, J. L., Frohman, E., Frohman, T., Fujihara, K., Cuellar, I. G., Galetta, S., Garcia-Martin, E., Giovannoni, G., Glebauskiene, B., Suarez, I. G., P. , Jensen, G., Hamann, S., Hartung, H. -P., Havla, J., Hemmer, B., Huang, S. -C., Imitola, J., Jasinskas, V., Jiang, H., Kafieh, R., Kappos, L., Kardon, R., Keegan, D., Kildebeck, E., Kim, U. S., Klistorner, S., Knier, B., Kolbe, S., Korn, T., Krupp, L., Lagreze, W., Leocani, L., Levin, N., Liskova, P., Preiningerova, J. L., Lorenz, B., May, E., Miller, D., Mikolajczak, J., Said, S. M., Montalban, X., Morrow, M., Mowry, E., Murta, J., Navas, C., Nolan, R., Nowomiejska, K., Oertel, F. C., Oh, J., Oreja-Guevara, C., Orssaud, C., Osborne, B., Outteryck, O., Paiva, C., Palace, J., Papadopoulou, A., Patsopoulos, N., Pontikos, N., Preising, M., Prince, J., Reich, D., Rejdak, R., Ringelstein, M., Rodriguez de Antonio, L., Sahel, J. -A., Sanchez-Dalmau, B., Sastre-Garriga, J., Schippling, S., Schuman, J., Shindler, K., Shin, R., Shuey, N., Soelberg, K., Specovius, S., Suppiej, A., Thompson, A., Toosy, A., Torres, R., Touitou, V., Trauzettel-Klosinski, S., van der Walt, A., Vermersch, P., Vidal-Jordana, A., Waldman, A. T., Waters, C., Wheeler, R., White, O., Wilhelm, H., Winges, K. M., Wiegerinck, N., Wiehe, L., Wisnewski, T., Wong, S., Wurfel, J., Yaghi, S., You, Y., Yu, Z., Yu-Wai-Man, P., Zemaitien≐, R., and Zimmermann, H.

Subjects
0301 basic medicine, Big Data, medicine.medical_specialty, Neurology, media_common.quotation_subject, Big data, MEDLINE, Reviews, Socio-culturale, Neurosciences. Biological psychiatry. Neuropsychiatry, Review, Public domain, Retina, Cohort Studies, 03 medical and health sciences, Annotation, 0302 clinical medicine, Artificial Intelligence, medicine, Humans, Quality (business), RC346-429, Tomography, media_common, Image pattern recognition, business.industry, General Neuroscience, Nervous System Diseases, Tomography, Optical Coherence, Algorithms, 030104 developmental biology, Optical Coherence, Imaging technology, RC0321, Neurology. Diseases of the nervous system, Neurology (clinical), Artificial intelligence, sense organs, business, 030217 neurology & neurosurgery, RC321-571
Abstract

Artificial intelligence (AI)‐based diagnostic algorithms have achieved ambitious aims through automated image pattern recognition. For neurological disorders, this includes neurodegeneration and inflammation. Scalable imaging technology for big data in neurology is optical coherence tomography (OCT). We highlight that OCT changes observed in the retina, as a window to the brain, are small, requiring rigorous quality control pipelines. There are existing tools for this purpose. Firstly, there are human‐led validated consensus quality control criteria (OSCAR‐IB) for OCT. Secondly, these criteria are embedded into OCT reporting guidelines (APOSTEL). The use of the described annotation of failed OCT scans advances machine learning. This is illustrated through the present review of the advantages and disadvantages of AI‐based applications to OCT data. The neurological conditions reviewed here for the use of big data include Alzheimer disease, stroke, multiple sclerosis (MS), Parkinson disease, and epilepsy. It is noted that while big data is relevant for AI, ownership is complex. For this reason, we also reached out to involve representatives from patient organizations and the public domain in addition to clinical and research centers. The evidence reviewed can be grouped in a five‐point expansion of the OSCAR‐IB criteria to embrace AI (OSCAR‐AI). The review concludes by specific recommendations on how this can be achieved practically and in compliance with existing guidelines.

Published
2021

8. The landscape of submicroscopic structural variants at the OPN1LW/OPN1MW gene cluster on Xq28 underlying blue cone monochromacy

Author

Wissinger B, Baumann B, Buena-Atienza E, Ravesh Z, Cideciyan AV, Stingl K, Audo I, Meunier I, Bocquet B, Traboulsi EI, Hardcastle AJ, Gardner JC, Michaelides M, Branham KE, Rosenberg T, Andreasson S, Dollfus H, Birch D, Vincent AL, Martorell-Sampol L, Catala J, Kellner U, Rüther K, Lorenz B, Preising MN, Manfredini E, Zarate YA, Vijzelaar R, Zrenner E, Jacobson SG, and Kohl S

Subjects
gene conversion, BCM, human visual pigment genes, opsin gene deletion, locus control region
Abstract

Blue cone monochromacy (BCM) is an X-linked retinal disorder characterized by low vision, photoaversion, and poor color discrimination. BCM is due to the lack of long-wavelength-sensitive and middle-wavelength-sensitive cone photoreceptor function and caused by mutations in the OPN1LW/OPN1MW gene cluster on Xq28. Here, we investigated the prevalence and the landscape of submicroscopic structural variants (SVs) at single-base resolution in BCM patients. We found that about one-third (n = 73) of the 213 molecularly confirmed BCM families carry an SV, most commonly deletions restricted to the OPN1LW/OPN1MW gene cluster. The structure and precise breakpoints of the SVs were resolved in all but one of the 73 families. Twenty-two families-all from the United States-showed the same SV, and we confirmed a common ancestry of this mutation. In total, 42 distinct SVs were identified, including 40 previously unreported SVs, thereby quadrupling the number of precisely mapped SVs underlying BCM. Notably, there was no "region of overlap" among these SVs. However, 90% of SVs encompass the upstream locus control region, an essential enhancer element. Its minimal functional extent based on deletion mapping in patients was refined to 358 bp. Breakpoint analyses suggest diverse mechanisms underlying SV formation as well as in one case the gene conversion-based exchange of a 142-bp deletion between opsin genes. Using parsimonious assumptions, we reconstructed the composition and copy number of the OPN1LW/OPN1MW gene cluster prior to the mutation event and found evidence that large gene arrays may be predisposed to the occurrence of SVs at this locus.

Published
2022

9. The need for widely available genomic testing in rare eye diseases: an ERN-EYE position statement

Author

Black G. C., Sergouniotis P., Sodi A., Leroy B. P., Van Cauwenbergh C., Liskova P., Gronskov K., Klett A., Kohl S., Taurina G., Sukys M., Haer-Wigman L., Nowomiejska K., Marques J. P., Leroux D., Cremers F. P. M., De Baere E., Dollfus H., Ashworth J., Audo I., Bacci G., Balciuniene V. J., Bargiacchi S., Bertelsen M., Black G., Boon C., Bremond-Gignac D., Buzzonetti L., Calvas P., Thomsen A. C., Chirita-Emandi A., Chokoshvili D., Cremers F., Daly A., Downes S., Fasolo A., Fasser C., Fischer D., Fortunato P., Gelzinis A., Hall G., Hamann S., Heon E., Iarossi G., Iberg C., Jouanjan G., Kaariainen H., Kahn K., Keegan D., Laengsfeld M., Leon A., Leroux B., Lorenz B., Maggi R., Mauring L., Melico P., Meunier I., Mohand-Said S., Monterosso C., Morandi P., Parmeggiani F., Passerini I., Pelletier V., Peluso F., Perdomo Y., Rapizzi E., Roos L., Roosing S., Rozet J. -M., Simonelli F., Sowden J., Stingl K., Suppiej A., Testa F., Tracewska A., Traficante G., Valeina S., Wheeler-Schilling T., Yu-Wai-Man P., Zeitz C., Zemaitiene R., Leroux, Dorothée [0000-0002-1412-6611], Apollo - University of Cambridge Repository, Ophthalmology, ANS - Complex Trait Genetics, Black, G. C., Sergouniotis, P., Sodi, A., Leroy, B. P., Van Cauwenbergh, C., Liskova, P., Gronskov, K., Klett, A., Kohl, S., Taurina, G., Sukys, M., Haer-Wigman, L., Nowomiejska, K., Marques, J. P., Leroux, D., Cremers, F. P. M., De Baere, E., Dollfus, H., Ashworth, J., Audo, I., Bacci, G., Balciuniene, V. J., Bargiacchi, S., Bertelsen, M., Black, G., Boon, C., Bremond-Gignac, D., Buzzonetti, L., Calvas, P., Thomsen, A. C., Chirita-Emandi, A., Chokoshvili, D., Cremers, F., Daly, A., Downes, S., Fasolo, A., Fasser, C., Fischer, D., Fortunato, P., Gelzinis, A., Hall, G., Hamann, S., Heon, E., Iarossi, G., Iberg, C., Jouanjan, G., Kaariainen, H., Kahn, K., Keegan, D., Laengsfeld, M., Leon, A., Leroux, B., Lorenz, B., Maggi, R., Mauring, L., Melico, P., Meunier, I., Mohand-Said, S., Monterosso, C., Morandi, P., Parmeggiani, F., Passerini, I., Pelletier, V., Peluso, F., Perdomo, Y., Rapizzi, E., Roos, L., Roosing, S., Rozet, J. -M., Simonelli, F., Sowden, J., Stingl, K., Suppiej, A., Testa, F., Tracewska, A., Traficante, G., Valeina, S., Wheeler-Schilling, T., Yu-Wai-Man, P., Zeitz, C., and Zemaitiene, R.

Subjects
0301 basic medicine, Eye Diseases, lcsh:Medicine, CHILDREN, Position statement, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], MOLECULAR-GENETICS, 0302 clinical medicine, HISTORY, Health care, Medicine and Health Sciences, Genetics(clinical), Pharmacology (medical), Child, Genetics (clinical), medicine.diagnostic_test, General Medicine, Genomics, Europe, TRIALS, ERN-EYE, Rare eye diseases, medicine.symptom, Genetic and genomic testing, Human, medicine.medical_specialty, Visual impairment, LEBER CONGENITAL AMAUROSIS, Socio-culturale, DIAGNOSIS, 03 medical and health sciences, Rare Diseases, medicine, Humans, Genetic Testing, Intensive care medicine, Genetic testing, business.industry, CLINICAL-FEATURES, lcsh:R, Rare eye disease, Eye Disease, Human genetics, Clinical trial, 030104 developmental biology, Genomic, 030221 ophthalmology & optometry, Personalized medicine, business, Rare disease
Abstract

Background Rare Eye Diseases (RED) are the leading cause of visual impairment and blindness for children and young adults in Europe. This heterogeneous group of conditions includes over 900 disorders ranging from relatively prevalent disorders such as retinitis pigmentosa to very rare entities such as developmental eye anomalies. A significant number of patients with RED have an underlying genetic etiology. One of the aims of the European Reference Network for Rare Eye Diseases (ERN–EYE) is to facilitate improvement in diagnosis of RED in European member states. Main body Technological advances have allowed genetic and genomic testing for RED. The outcome of genetic testing allows better understanding of the condition and allows reproductive and therapeutic options. The increase of the number of clinical trials for RED has provided urgency for genetic testing in RED. A survey of countries participating in ERN-EYE demonstrated that the majority are able to access some forms of genomic testing. However, there is significant variability, particularly regarding testing as part of clinical service. Some countries have a well-delineated rare disease pathway and have a national plan for rare diseases combined or not with a national plan for genomics in medicine. In other countries, there is a well-established organization of genetic centres that offer reimbursed genomic testing of RED and other rare diseases. Clinicians often rely upon research-funded laboratories or private companies. Notably, some member states rely on cross-border testing by way of an academic research project. Consequently, many clinicians are either unable to access testing or are confronted with long turnaround times. Overall, while the cost of sequencing has dropped, the cumulative cost of a genomic testing service for populations remains considerable. Importantly, the majority of countries reported healthcare budgets that limit testing. Short conclusion Despite technological advances, critical gaps in genomic testing remain in Europe, especially in smaller countries where no formal genomic testing pathways exist. Even within larger countries, the existing arrangements are insufficient to meet the demand and to ensure access. ERN-EYE promotes access to genetic testing in RED and emphasizes the clinical need and relevance of genetic testing in RED.

Published
2021

13. Deep-intronic variants in CNGB3 cause achromatopsia by pseudoexon activation

Author

Weisschuh, N. Sturm, M. Baumann, B. Audo, I. Ayuso, C. Bocquet, B. Branham, K. Brooks, B.P. Catalá-Mora, J. Giorda, R. Heckenlively, J.R. Hufnagel, R.B. Jacobson, S.G. Kellner, U. Kitsiou-Tzeli, S. Matet, A. Martorell Sampol, L. Meunier, I. Rudolph, G. Sharon, D. Stingl, K. Streubel, B. Varsányi, B. Wissinger, B. Kohl, S.

Abstract

Our comprehensive cohort of 1100 unrelated achromatopsia (ACHM) patients comprises a considerable number of cases (~5%) harboring only a single pathogenic variant in the major ACHM gene CNGB3. We sequenced the entire CNGB3 locus in 33 of these patients to find a second variant which eventually explained the patients’ phenotype. Forty-seven intronic CNGB3 variants were identified in 28 subjects after a filtering step based on frequency and the exclusion of variants found in cis with pathogenic alleles. In a second step, in silico prediction tools were used to filter out those variants with little odds of being deleterious. This left three variants that were analyzed using heterologous splicing assays. Variant c.1663–1205G>A, found in 14 subjects, and variant c.1663-2137C>T, found in two subjects, were indeed shown to exert a splicing defect by causing pseudoexon insertion into the transcript. Subsequent screening of further unsolved CNGB3 subjects identified four additional cases harboring the c.1663–1205G>A variant which makes it the eighth most frequent CNGB3 variant in our cohort. Compound heterozygosity could be validated in ten cases. Our study demonstrates that whole gene sequencing can be a powerful approach to identify the second pathogenic allele in patients apparently harboring only one disease-causing variant. © 2019 Wiley Periodicals, Inc.

Published
2020

15. Deciphering the natural history of SCA7 in children

Author

Bah, M. G., primary, Rodriguez, D., additional, Cazeneuve, C., additional, Mochel, F., additional, Devos, D., additional, Suppiej, A., additional, Roubertie, A., additional, Meunier, I., additional, Gitiaux, C., additional, Curie, A., additional, Klapczynski, F., additional, Allani‐Essid, N., additional, Carneiro, M., additional, Van Minkelen, R., additional, Kievit, A., additional, Fluss, J., additional, Leheup, B., additional, Ratbi, L., additional, Héron, D., additional, Gras, D., additional, Do Cao, J., additional, Pichard, S., additional, Strubi‐Villaume, I., additional, Audo, I., additional, Lesca, G., additional, Charles, P., additional, Dubois, F., additional, Comet‐Didierjean, P., additional, Capri, Y., additional, Barondiot, C., additional, Barathon, M., additional, Ewenczyk, C., additional, Durr, A., additional, and Mignot, C., additional

Published
2020
Full Text
View/download PDF

17. An ontological foundation for ocular phenotypes and rare eye diseases

Author

Sergouniotis, Panagiotis I., Maxime, Emmanuel, Leroux, Dorothée, Olry, Annie, Thompson, Rachel, Rath, Ana, Robinson, Peter N., Dollfus, Hélèneashworth, Jl, Audo, I, Balciuniene, Vj, Banin, E, Black, Gc, Böhringer, D, Boon, Cjf, Bremond-Gignac, D, Calvas, P, Castela, G, Dagnelie, G, Dollfus, H, Downes, Sm, Fasolo, A, Fasser, C, Gelzinis, A, Goetz, K, Hamann, S, Héon, E, Iarossi, G, Kawasaki, A, Keegan, D, Kessel, L, Khan, K, Klett, A, Köhler, S, Leroux, D, Leroy, Bp, Lisch, W, Liskova, P, Lorenz, B, Maggi, R, Maxime, E, Meunier, I, Mohand-Said, S, Nowomiejska, K, Perdomo, Y, Petzold, A, Preising, M, Robinson, Pn, Scholl, Hpn, Sergouniotis, Pi, Sodi, A, Stingl, K, Studer, F, Suppiej, A, Thompson, R, Touitou, V, Traboulsi, E, Trumpaitis, J, Tuft, Sj, Vaclavik, V, Valeina, S, Van Cauwenbergh, C, Verloes, A, Vighetto, A, Wheeler, R, Wheeler-Schilling, T, Yu-Wai-Man, P, Zobor, D, Zrenner, E., Sergouniotis, Panagiotis I [0000-0003-0986-4123], Apollo - University of Cambridge Repository, University of Manchester [Manchester], Plateforme d'information et de services pour les maladies rares et les médicaments orphelins (Orphanet), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Broussais-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO) et Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Newcastle University [Newcastle], The Jackson Laboratory for Genomic Medicine, Laboratoire de Génétique Médicale (LGM), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), and European Project: 0305444(2003)

Subjects
0301 basic medicine, Eye Diseases, Computer science, Evidence-based precision medicine, Rare eye disease, Human phenotype ontology, Orphanet rare disease ontology, lcsh:Medicine, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 030105 genetics & heredity, Ontology (information science), Terminology, NO, Open Biomedical Ontologies, MESH: Eye Diseases / classificationHumans Precision Medicine / methods* Rare Diseases / classification, 03 medical and health sciences, 0302 clinical medicine, Rare Diseases, Human Phenotype Ontology, Eye Diseases/classification, Humans, Pharmacology (medical), Precision Medicine, Letter to the Editor, MESH: Humans Precision Medicine / methods, Genetics (clinical), Information exchange, Evidence-Based Medicine, Orphanet rare disease ontology, Rare Diseases/classification, MESH: Computational Biology / methods, lcsh:R, Computational Biology, Human phenotype ontology, Biological Ontologies, Precision Medicine/methods, General Medicine, Evidence-based medicine, Rare eye disease, Computational Biology/methods, Data science, MESH: Rare Diseases / classification, 3. Good health, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Evidence-based precision medicine, Eye disorder, MESH: Biological Ontologies, MESH: Evidence-Based Medicine, 030217 neurology & neurosurgery
Abstract

Background The optical accessibility of the eye and technological advances in ophthalmic diagnostics have put ophthalmology at the forefront of data-driven medicine. The focus of this study is rare eye disorders, a group of conditions whose clinical heterogeneity and geographic dispersion make data-driven, evidence-based practice particularly challenging. Inter-institutional collaboration and information sharing is crucial but the lack of standardised terminology poses an important barrier. Ontologies are computational tools that include sets of vocabulary terms arranged in hierarchical structures. They can be used to provide robust terminology standards and to enhance data interoperability. Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings) and the Orphanet Rare Disease Ontology (ORDO; includes rare disease nomenclature/nosology). Methods A variety of approaches were used including automated matching to existing resources and extensive manual curation. To achieve the latter, a study group including clinicians, patient representatives and ontology developers from 17 countries was formed. A broad range of terms was discussed and validated during a dedicated workshop attended by 60 members of the group. Results A comprehensive, structured and well-defined set of terms has been agreed on including 1106 terms relating to ocular phenotypes (HPO) and 1202 terms relating to rare eye disease nomenclature (ORDO). These terms and their relevant annotations can be accessed in http://www.human-phenotype-ontology.org/ and http://www.orpha.net/; comments, corrections, suggestions and requests for new terms can be made through these websites. This is an ongoing, community-driven endeavour and both HPO and ORDO are regularly updated. Conclusions To our knowledge, this is the first effort of such scale to provide terminology standards for the rare eye disease community. We hope that this work will not only improve coding and standardise information exchange in clinical care and research, but also it will catalyse the transition to an evidence-based precision ophthalmology paradigm. Electronic supplementary material The online version of this article (10.1186/s13023-018-0980-6) contains supplementary material, which is available to authorized users.

Published
2019

19. Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration

Author

Waksmunski, AR, Grunin, M, Kinzy, TG, Igo, RP, Haines, JL, Bailey, JNC, Fritsche, LG, Igl, W, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, M, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Ouyang, H, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Stark, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-A, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, S, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, A, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Iyengar, SK, Weber, BHF, Abecasis, GR, Heid, IM, Waksmunski, AR, Grunin, M, Kinzy, TG, Igo, RP, Haines, JL, Bailey, JNC, Fritsche, LG, Igl, W, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, M, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Ouyang, H, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Stark, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-A, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, S, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, A, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Iyengar, SK, Weber, BHF, Abecasis, GR, and Heid, IM

Abstract

PURPOSE: Age-related macular degeneration (AMD) is the worldwide leading cause of blindness among the elderly. Although genome-wide association studies (GWAS) have identified AMD risk variants, their roles in disease etiology are not well-characterized, and they only explain a portion of AMD heritability. METHODS: We performed pathway analyses using summary statistics from the International AMD Genomics Consortium's 2016 GWAS and multiple pathway databases to identify biological pathways wherein genetic association signals for AMD may be aggregating. We determined which genes contributed most to significant pathway signals across the databases. We characterized these genes by constructing protein-protein interaction networks and performing motif analysis. RESULTS: We determined that eight genes (C2, C3, LIPC, MICA, NOTCH4, PLCG2, PPARA, and RAD51B) "drive" the statistical signals observed across pathways curated in the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and Gene Ontology (GO) databases. We further refined our definition of statistical driver gene to identify PLCG2 as a candidate gene for AMD due to its significant gene-level signals (P < 0.0001) across KEGG, Reactome, GO, and NetPath pathways. CONCLUSIONS: We performed pathway analyses on the largest available collection of advanced AMD cases and controls in the world. Eight genes strongly contributed to significant pathways from the three larger databases, and one gene (PLCG2) was central to significant pathways from all four databases. This is, to our knowledge, the first study to identify PLCG2 as a candidate gene for AMD based solely on genetic burden. Our findings reinforce the utility of integrating in silico genetic and biological pathway data to investigate the genetic architecture of AMD.

Published
2019

25. ARL2BP mutations account for 0.1% of autosomal recessive rod-cone dystrophies with the report of a novel splice variant

Author

Audo, I., primary, El Shamieh, S., additional, Méjécase, C., additional, Michiels, C., additional, Demontant, V., additional, Antonio, A., additional, Condroyer, C., additional, Boyard, F., additional, Letexier, M., additional, Saraiva, J.-P., additional, Blanchard, S., additional, Mohand-Saïd, S., additional, Sahel, J.-A., additional, and Zeitz, C., additional

Published
2017
Full Text
View/download PDF

26. Variabilité du phénotype dans la dystrophie maculaire de Best

Author

Zerbib, J., Giuseppe Querques, Massamba, N., Santacrose, R., Maraglione, M., Delphin, N., Audo, I., Rozet, Jm, Kaplan, J., Souied, E., Zerbib, J, Querques, Giuseppe, Massamba, N, Santacrose, R, Maraglione, M, Delphin, N, Audo, I, Rozet, Jm, Kaplan, J, and Souied, E.

Published
2012

27. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, L.G., Igl, W., Bailey, J.N., Grassmann, F., Sengupta, S, Bragg-Gresham, J.L., Burdon, K.P., Hebbring, S.J., Wen, C., Gorski, M., Kim, I.K., Cho, D., Zack, D., Souied, E., Scholl, H.P., Bala, E., Lee, K.E., Hunter, D.J., Sardell, R.J., Mitchell, P., Merriam, J.E., Cipriani, V., Hoffman, J.D., Schick, T., Lechanteur, Y.T., Guymer, R.H., Johnson, M.P., Jiang, Y., Stanton, C.M., Buitendijk, G.H., Zhan, X., Kwong, A.M., Boleda, A., Brooks, M., Gieser, L., Ratnapriya, R., Branham, K.E., Foerster, J.R., Heckenlively, J.R., Othman, M.I., Vote, B.J., Liang, H.H., Souzeau, E., McAllister, I.L., Isaacs, T., Hall, J., Lake, S., Mackey, D.A., Constable, I.J., Craig, J.E., Kitchner, T.E., Yang, Z, Su, Z., Luo, H., Chen, D., Ouyang, H., Flagg, K., Lin, D., Mao, G., Ferreyra, H., Stark, K., Strachwitz, C.N. von, Wolf, A., Brandl, C., Rudolph, G., Olden, M., Morrison, M.A., Morgan, D.J., Schu, M., Ahn, J., Silvestri, G., Tsironi, E.E., Park, K.H., Farrer, L.A., Orlin, A., Brucker, A., Li, M., Curcio, C.A., Mohand-Said, S., Sahel, J.A., Audo, I., Benchaboune, M., Cree, A.J., Rennie, C.A., Goverdhan, S.V., Grunin, M., Hagbi-Levi, S., Campochiaro, P., Katsanis, N., Holz, F.G., Blond, F., Blanche, H., Deleuze, J.F., Igo, R.P., Jr., Truitt, B., Peachey, N.S., Meuer, S.M., Myers, C.E., Moore, E.L., Klein, R., Hollander, A.I. den, Saksens, N.T.M., Hoyng, C.B., Jong, E.K. de, et al., Fritsche, L.G., Igl, W., Bailey, J.N., Grassmann, F., Sengupta, S, Bragg-Gresham, J.L., Burdon, K.P., Hebbring, S.J., Wen, C., Gorski, M., Kim, I.K., Cho, D., Zack, D., Souied, E., Scholl, H.P., Bala, E., Lee, K.E., Hunter, D.J., Sardell, R.J., Mitchell, P., Merriam, J.E., Cipriani, V., Hoffman, J.D., Schick, T., Lechanteur, Y.T., Guymer, R.H., Johnson, M.P., Jiang, Y., Stanton, C.M., Buitendijk, G.H., Zhan, X., Kwong, A.M., Boleda, A., Brooks, M., Gieser, L., Ratnapriya, R., Branham, K.E., Foerster, J.R., Heckenlively, J.R., Othman, M.I., Vote, B.J., Liang, H.H., Souzeau, E., McAllister, I.L., Isaacs, T., Hall, J., Lake, S., Mackey, D.A., Constable, I.J., Craig, J.E., Kitchner, T.E., Yang, Z, Su, Z., Luo, H., Chen, D., Ouyang, H., Flagg, K., Lin, D., Mao, G., Ferreyra, H., Stark, K., Strachwitz, C.N. von, Wolf, A., Brandl, C., Rudolph, G., Olden, M., Morrison, M.A., Morgan, D.J., Schu, M., Ahn, J., Silvestri, G., Tsironi, E.E., Park, K.H., Farrer, L.A., Orlin, A., Brucker, A., Li, M., Curcio, C.A., Mohand-Said, S., Sahel, J.A., Audo, I., Benchaboune, M., Cree, A.J., Rennie, C.A., Goverdhan, S.V., Grunin, M., Hagbi-Levi, S., Campochiaro, P., Katsanis, N., Holz, F.G., Blond, F., Blanche, H., Deleuze, J.F., Igo, R.P., Jr., Truitt, B., Peachey, N.S., Meuer, S.M., Myers, C.E., Moore, E.L., Klein, R., Hollander, A.I. den, Saksens, N.T.M., Hoyng, C.B., Jong, E.K. de, and et al.

Abstract

Item does not contain fulltext, Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 x 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 x 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016

28. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, L.G. (Lars), Igl, W. (Wilmar), Cooke Bailey, J.N. (Jessica N.), Grassmann, F. (Felix), Sengupta, S. (Sebanti), Bragg-Gresham, J.L. (Jennifer L.), Burdon, K.P. (Kathryn P.), Hebbring, S.J. (Scott J.), Wen, C. (Cindy), Gorski, M. (Mathias), Kim, I.K. (Ivana), Cho, D. (David), Zack, D. (Donald), Souied, E.H. (Eric), Scholl, H.P.N. (Hendrik), Bala, E. (Elisa), ELee, K. (Kristine), Hunter, D. (David), Sardell, R.J. (Rebecca J.), Mitchell, P. (Paul), Merriam, J.E. (Joanna), Cipriani, F. (Francesco), Hoffman, J.D. (Joshua D.), Schick, T. (Tina), Lechanteur, Y.T.E. (Yara T. E.), Guymer, R.H. (Robyn), Johnson, M.P. (Matthew), Jiang, Y., Stanton, C.M. (Chloe), Buitendijk, G.H.S. (Gabrielle), Zhan, X. (Xiaowei), Kwong, A.M. (Alan M.), Boleda, A. (Alexis), Brooks, M. (Matthew), Gieser, L. (Linn), Ratna Priya, R. (Rinki), Branham, K.E. (Kari), Foerster, J.R. (Johanna R.), Heckenlively, J.R. (John), Othman, M.I. (Mohammad), Vote, B.J. (Brendan J.), Liang, H.H. (Helena Hai), Souzeau, E. (Emmanuelle), McAllister, I.L. (Ian L.), Isaacs, T. (Timothy), Hall, J. (Janette), Lake, S. (Stewart), Mackey, D.A. (David), Constable, I.J. (Ian J.), Craig, J.E. (Jamie E.), Kitchner, T.E. (Terrie E.), Yang, Z. (Zhenglin), Su, Z. (Zhiguang), Luo, H. (Hongrong), Chen, D. (Daniel), Ouyang, H. (Hong), Flagg, K. (Ken), Lin, D. (Danni), Mao, G. (Guanping), Ferreyra, H.A. (Henry), Stark, K. (Klaus), Strachwitz, C. (Claudia) von, Wolf, A. (Armin), Brandl, C. (Caroline), Rudolph, G. (Guenther), Olden, M. (Matthias), Morrison, M.A. (Margaux), Morgan, D.J. (Denise), Schu, M. (Matthew), Ahn, J. (Jeeyun), Silvestri, G. (Giuliana), Tsironi, E.E. (Evangelia), Park, K.H. (Kyu Hyung), Farrer, L.A. (Lindsay), Orlin, A. (Anton), Brucker, A. (Alexander), Curcio, C.A. (Christine A.), Mohand-Sa'd, S. (Saddek), Sahel, J.-A. (José-Alain), Audo, I. (Isabelle), Benchaboune, M. (Mustapha), Cree, A.J. (Angela), Rennie, C.A. (Christina A.), Goverdhan, S.V. (Srinivas V.), Grunin, M. (Michelle), Hagbi-Levi, S. (Shira), Campochiaro, B. (Betsy), Katsanis, N. (Nicholas), Holz, F.G. (Frank), Blond, F. (Frédéric), Blanché, H. (Hél'ne), Deleuze, J.-F. (Jean-Fran'ois), Igo Jr., R.P. (Robert), Truitt, B.J. (Barbara), Peachey, N.S. (Neal ), Meuer, S.M. (Stacy), Myers, C.E. (Chelsea), Moore, E.L. (Emily L.), Klein, R. (Ronald), Hauser, M.A. (Michael), Postel, E.A. (Eric), Courtenay, M.D. (Monique D.), Schwartz, S.M. (Stephen), Kovach, J.L. (Jaclyn), Scott, W.K. (William), Liew, G. (Gerald), Tan, A.G. (Ava G.), Gopinath, B. (Bamini), Smith, T. (Tim), Khan, J.C. (Jane), Shahid, M. (Mohammad), Moore, A.T. (Anthony), McGrath, J.A. (J Allie), Laux, R. (Reneé), Brantley, M.A. (Milam), Agarwal, A. (Anita), Ersoy, L. (Lebriz), Caramoy, A. (Albert), Langmann, T. (Thomas), Saksens, N.T.M. (Nicole T.), Jong, E.K. (Eiko Kde), Hoyng, C.B. (Carel), Cain, M.S. (Melinda), Richardson, A.J. (Andrea), Martin, T.M. (Tammy M.), Blangero, J. (John), Weeks, D.E. (Daniel), Dhillon, B. (Bal), Duijn, C.M. (Cornelia) van, Doheny, K.F. (Kimberly), Romm, J. (Jane), Klaver, C.C.W. (Caroline), Hayward, C. (Caroline), Gorin, M.B. (Michael B.), Klein, M.L. (Michael), Baird, P.N. (Paul), Hollander, A.I. (Anneke), Fauser, S. (Sascha), WYates, J.R. (John R.), Allikmets, R. (Rando), Wang, J.J. (Jie Jin), Schaumberg, D.A. (Debra), Klein, B.E.K. (Barbara), Hagstrom, S.A. (Stephanie), Chowers, Y. (Yehuda), Lotery, A.J. (Andrew), Léveillard, T. (Thierry), Zhang, K. (Kang), Brilliant, M.H. (Murray H.), Hewit, A.W. (Alex), Swaroop, A. (Anand), Chew, E.Y. (Emily Y.), Pericak-Vance, M.A. (Margaret), DeAngelis, M.M. (Margaret), Stambolian, D. (Dwight), Haines, J.L. (Jonathan), Iyengar, S.K. (Sudha), Weber, B.H.F. (Bernhard), Abecasis, G.R. (Gonçalo), Heid, I.M. (Iris), Li, M. (Mingyao), Fritsche, L.G. (Lars), Igl, W. (Wilmar), Cooke Bailey, J.N. (Jessica N.), Grassmann, F. (Felix), Sengupta, S. (Sebanti), Bragg-Gresham, J.L. (Jennifer L.), Burdon, K.P. (Kathryn P.), Hebbring, S.J. (Scott J.), Wen, C. (Cindy), Gorski, M. (Mathias), Kim, I.K. (Ivana), Cho, D. (David), Zack, D. (Donald), Souied, E.H. (Eric), Scholl, H.P.N. (Hendrik), Bala, E. (Elisa), ELee, K. (Kristine), Hunter, D. (David), Sardell, R.J. (Rebecca J.), Mitchell, P. (Paul), Merriam, J.E. (Joanna), Cipriani, F. (Francesco), Hoffman, J.D. (Joshua D.), Schick, T. (Tina), Lechanteur, Y.T.E. (Yara T. E.), Guymer, R.H. (Robyn), Johnson, M.P. (Matthew), Jiang, Y., Stanton, C.M. (Chloe), Buitendijk, G.H.S. (Gabrielle), Zhan, X. (Xiaowei), Kwong, A.M. (Alan M.), Boleda, A. (Alexis), Brooks, M. (Matthew), Gieser, L. (Linn), Ratna Priya, R. (Rinki), Branham, K.E. (Kari), Foerster, J.R. (Johanna R.), Heckenlively, J.R. (John), Othman, M.I. (Mohammad), Vote, B.J. (Brendan J.), Liang, H.H. (Helena Hai), Souzeau, E. (Emmanuelle), McAllister, I.L. (Ian L.), Isaacs, T. (Timothy), Hall, J. (Janette), Lake, S. (Stewart), Mackey, D.A. (David), Constable, I.J. (Ian J.), Craig, J.E. (Jamie E.), Kitchner, T.E. (Terrie E.), Yang, Z. (Zhenglin), Su, Z. (Zhiguang), Luo, H. (Hongrong), Chen, D. (Daniel), Ouyang, H. (Hong), Flagg, K. (Ken), Lin, D. (Danni), Mao, G. (Guanping), Ferreyra, H.A. (Henry), Stark, K. (Klaus), Strachwitz, C. (Claudia) von, Wolf, A. (Armin), Brandl, C. (Caroline), Rudolph, G. (Guenther), Olden, M. (Matthias), Morrison, M.A. (Margaux), Morgan, D.J. (Denise), Schu, M. (Matthew), Ahn, J. (Jeeyun), Silvestri, G. (Giuliana), Tsironi, E.E. (Evangelia), Park, K.H. (Kyu Hyung), Farrer, L.A. (Lindsay), Orlin, A. (Anton), Brucker, A. (Alexander), Curcio, C.A. (Christine A.), Mohand-Sa'd, S. (Saddek), Sahel, J.-A. (José-Alain), Audo, I. (Isabelle), Benchaboune, M. (Mustapha), Cree, A.J. (Angela), Rennie, C.A. (Christina A.), Goverdhan, S.V. (Srinivas V.), Grunin, M. (Michelle), Hagbi-Levi, S. (Shira), Campochiaro, B. (Betsy), Katsanis, N. (Nicholas), Holz, F.G. (Frank), Blond, F. (Frédéric), Blanché, H. (Hél'ne), Deleuze, J.-F. (Jean-Fran'ois), Igo Jr., R.P. (Robert), Truitt, B.J. (Barbara), Peachey, N.S. (Neal ), Meuer, S.M. (Stacy), Myers, C.E. (Chelsea), Moore, E.L. (Emily L.), Klein, R. (Ronald), Hauser, M.A. (Michael), Postel, E.A. (Eric), Courtenay, M.D. (Monique D.), Schwartz, S.M. (Stephen), Kovach, J.L. (Jaclyn), Scott, W.K. (William), Liew, G. (Gerald), Tan, A.G. (Ava G.), Gopinath, B. (Bamini), Smith, T. (Tim), Khan, J.C. (Jane), Shahid, M. (Mohammad), Moore, A.T. (Anthony), McGrath, J.A. (J Allie), Laux, R. (Reneé), Brantley, M.A. (Milam), Agarwal, A. (Anita), Ersoy, L. (Lebriz), Caramoy, A. (Albert), Langmann, T. (Thomas), Saksens, N.T.M. (Nicole T.), Jong, E.K. (Eiko Kde), Hoyng, C.B. (Carel), Cain, M.S. (Melinda), Richardson, A.J. (Andrea), Martin, T.M. (Tammy M.), Blangero, J. (John), Weeks, D.E. (Daniel), Dhillon, B. (Bal), Duijn, C.M. (Cornelia) van, Doheny, K.F. (Kimberly), Romm, J. (Jane), Klaver, C.C.W. (Caroline), Hayward, C. (Caroline), Gorin, M.B. (Michael B.), Klein, M.L. (Michael), Baird, P.N. (Paul), Hollander, A.I. (Anneke), Fauser, S. (Sascha), WYates, J.R. (John R.), Allikmets, R. (Rando), Wang, J.J. (Jie Jin), Schaumberg, D.A. (Debra), Klein, B.E.K. (Barbara), Hagstrom, S.A. (Stephanie), Chowers, Y. (Yehuda), Lotery, A.J. (Andrew), Léveillard, T. (Thierry), Zhang, K. (Kang), Brilliant, M.H. (Murray H.), Hewit, A.W. (Alex), Swaroop, A. (Anand), Chew, E.Y. (Emily Y.), Pericak-Vance, M.A. (Margaret), DeAngelis, M.M. (Margaret), Stambolian, D. (Dwight), Haines, J.L. (Jonathan), Iyengar, S.K. (Sudha), Weber, B.H.F. (Bernhard), Abecasis, G.R. (Gonçalo), Heid, I.M. (Iris), and Li, M. (Mingyao)

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10 -8) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10 -10). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016
Full Text
View/download PDF

29. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Author

Fritsche, LG, Igl, W, Bailey, JNC, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, MI, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Hong, O, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Starke, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-M, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, SV, Grunin, M, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Igo, RP, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, AI, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Haines, JL, Iyengar, SK, Weber, BHF, Abecasis, GR, Heid, IM, Fritsche, LG, Igl, W, Bailey, JNC, Grassmann, F, Sengupta, S, Bragg-Gresham, JL, Burdon, KP, Hebbring, SJ, Wen, C, Gorski, M, Kim, IK, Cho, D, Zack, D, Souied, E, Scholl, HPN, Bala, E, Lee, KE, Hunter, DJ, Sardell, RJ, Mitchell, P, Merriam, JE, Cipriani, V, Hoffman, JD, Schick, T, Lechanteur, YTE, Guymer, RH, Johnson, MP, Jiang, Y, Stanton, CM, Buitendijk, GHS, Zhan, X, Kwong, AM, Boleda, A, Brooks, M, Gieser, L, Ratnapriya, R, Branham, KE, Foerster, JR, Heckenlively, JR, Othman, MI, Vote, BJ, Liang, HH, Souzeau, E, McAllister, IL, Isaacs, T, Hall, J, Lake, S, Mackey, DA, Constable, IJ, Craig, JE, Kitchner, TE, Yang, Z, Su, Z, Luo, H, Chen, D, Hong, O, Flagg, K, Lin, D, Mao, G, Ferreyra, H, Starke, K, von Strachwitz, CN, Wolf, A, Brandl, C, Rudolph, G, Olden, M, Morrison, MA, Morgan, DJ, Schu, M, Ahn, J, Silvestri, G, Tsironi, EE, Park, KH, Farrer, LA, Orlin, A, Brucker, A, Li, M, Curcio, CA, Mohand-Said, S, Sahel, J-M, Audo, I, Benchaboune, M, Cree, AJ, Rennie, CA, Goverdhan, SV, Grunin, M, Hagbi-Levi, S, Campochiaro, P, Katsanis, N, Holz, FG, Blond, F, Blanche, H, Deleuze, J-F, Igo, RP, Truitt, B, Peachey, NS, Meuer, SM, Myers, CE, Moore, EL, Klein, R, Hauser, MA, Postel, EA, Courtenay, MD, Schwartz, SG, Kovach, JL, Scott, WK, Liew, G, Tan, AG, Gopinath, B, Merriam, JC, Smith, RT, Khan, JC, Shahid, H, Moore, AT, McGrath, JA, Laux, R, Brantley, MA, Agarwal, A, Ersoy, L, Caramoy, A, Langmann, T, Saksens, NTM, de Jong, EK, Hoyng, CB, Cain, MS, Richardson, AJ, Martin, TM, Blangero, J, Weeks, DE, Dhillon, B, van Duijn, CM, Doheny, KF, Romm, J, Klaver, CCW, Hayward, C, Gorin, MB, Klein, ML, Baird, PN, den Hollander, AI, Fauser, S, Yates, JRW, Allikmets, R, Wang, JJ, Schaumberg, DA, Klein, BEK, Hagstrom, SA, Chowers, I, Lotery, AJ, Leveillard, T, Zhang, K, Brilliant, MH, Hewitt, AW, Swaroop, A, Chew, EY, Pericak-Vance, MA, DeAngelis, M, Stambolian, D, Haines, JL, Iyengar, SK, Weber, BHF, Abecasis, GR, and Heid, IM

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Published
2016

31. Next-generation sequencing confirms the implication ofSLC24A1in autosomal-recessive congenital stationary night blindness

Author

Neuillé, M., primary, Malaichamy, S., additional, Vadalà, M., additional, Michiels, C., additional, Condroyer, C., additional, Sachidanandam, R., additional, Srilekha, S., additional, Arokiasamy, T., additional, Letexier, M., additional, Démontant, V., additional, Sahel, J.-A., additional, Sen, P., additional, Audo, I., additional, Soumittra, N., additional, and Zeitz, C., additional

Published
2016
Full Text
View/download PDF

32. Adult-onset foveomacular vitelliform dystrophy: A fresh perspective

Author

Chowers, I., Tiosano, L., Audo, I., Grunin, M., Boon, C.J.F., Chowers, I., Tiosano, L., Audo, I., Grunin, M., and Boon, C.J.F.

Abstract

Item does not contain fulltext, Adult-onset foveomacular vitelliform dystrophy (AFVD) was first described by Gass four decades ago. AFVD is characterized by subretinal vitelliform macular lesions and is usually diagnosed after the age of 40. The lesions gradually increase and then decrease in size over the years, leaving an area of atrophic outer retina and retinal pigment epithelium. This process is accompanied by a loss of visual acuity. Vitelliform lesions are hyperautofluorescent and initially have a dome-shaped appearance on optical coherence tomography. The electro-oculogram and full-field electroretinogram are typically normal, indicating localized retinal pathology. Phenocopies are also associated with other ocular disorders, such as vitreomacular traction, age-related macular degeneration, pseudodrusen, and central serous chorioretinopathy. A minority of AFVD patients have a mutation in the PRPH2, BEST1, IMPG1, or IMPG2 genes. A single-nucleotide polymorphism in the HTRA1 gene has also been associated with this phenotype. Accordingly, the phenotype can arise from alterations in the photoreceptors, retinal pigment epithelium, and/or interphotoreceptor matrix depending on the underlying gene defect. Excess photoreceptor outer segment production and/or impaired outer segment uptake due to impaired phagocytosis are likely underlying mechanisms. At present, no cure is available for AFVD. Thus, the current challenges in the field include identifying the underlying cause in the majority of AFVD cases and the development of effective therapeutic approaches.

Published
2015

33. Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome

Author

Bujakowska, K.M., Zhang, Q, Siemiatkowska, A.M., Liu, Q., Place, E., Falk, M.J., Consugar, M., Lancelot, M.E., Antonio, A., Lonjou, C., Carpentier, W., Mohand-Said, S., Hollander, A.I. den, Cremers, F.P.M., Leroy, B.P., Gai, X., Sahel, J.A., Born, L.I. van den, Collin, R.W.J., Zeitz, C., Audo, I., Pierce, E.A., Bujakowska, K.M., Zhang, Q, Siemiatkowska, A.M., Liu, Q., Place, E., Falk, M.J., Consugar, M., Lancelot, M.E., Antonio, A., Lonjou, C., Carpentier, W., Mohand-Said, S., Hollander, A.I. den, Cremers, F.P.M., Leroy, B.P., Gai, X., Sahel, J.A., Born, L.I. van den, Collin, R.W.J., Zeitz, C., Audo, I., and Pierce, E.A.

Abstract

Item does not contain fulltext, Primary cilia are sensory organelles present on most mammalian cells. The assembly and maintenance of primary cilia are facilitated by intraflagellar transport (IFT), a bidirectional protein trafficking along the cilium. Mutations in genes coding for IFT components have been associated with a group of diseases called ciliopathies. These genetic disorders can affect a variety of organs including the retina. Using whole exome sequencing in three families, we identified mutations in Intraflagellar Transport 172 Homolog [IFT172 (Chlamydomonas)] that underlie an isolated retinal degeneration and Bardet-Biedl syndrome. Extensive functional analyses of the identified mutations in cell culture, rat retina and in zebrafish demonstrated their hypomorphic or null nature. It has recently been reported that mutations in IFT172 cause a severe ciliopathy syndrome involving skeletal, renal, hepatic and retinal abnormalities (Jeune and Mainzer-Saldino syndromes). Here, we report for the first time that mutations in this gene can also lead to an isolated form of retinal degeneration. The functional data for the mutations can partially explain milder phenotypes; however, the involvement of modifying alleles in the IFT172-associated phenotypes cannot be excluded. These findings expand the spectrum of disease associated with mutations in IFT172 and suggest that mutations in genes originally reported to be associated with syndromic ciliopathies should also be considered in subjects with non-syndromic retinal dystrophy.

Published
2015

34. Methods in Genetics in inherited retinal disorders and Gene therapy trials

Author

Zeitz, Christina, Shamieh, S. El, Audo, I., and Sahel, J.-A.

Subjects
ddc: 610, natural sciences, 610 Medical sciences, Medicine
Abstract

Inherited retinal disorders (IRD) are clinically and genetically heterogeneous with more than 150 gene defects accounting for the diversity of disease phenotypes. Over the past two decades, three main approaches including Sanger sequencing, arrayed primer extension (APEX) chip technology and homozygosity[for full text, please go to the a.m. URL], 26. Jahrestagung der Retinologischen Gesellschaft

Published
2013

35. A novel nonsense variant in <italic>REEP6</italic> is involved in a sporadic rod‐cone dystrophy case.

Author

Méjécase, C., Mohand‐saïd, S., El Shamieh, S., Antonio, A., Condroyer, C., Blanchard, S., Letexier, M., Saraiva, J.‐p., Sahel, J.‐a., Audo, I., and Zeitz, C.

Subjects
RETINITIS pigmentosa, NONSENSE mutation, EXOMES, NUCLEOTIDE sequencing, PATHOLOGICAL physiology
Abstract

Rod‐cone dystrophy (RCD), also called retinitis pigmentosa, is the most common form of progressive inherited retinal disorders secondary to photoreceptor degeneration. It is a genetically heterogeneous disease characterized by night blindness, followed by visual field constriction and, in most severe cases, total blindness. The aim of our study was to identify the underlying gene defect leading to severe RCD in a 60‐year‐old woman. The patient's DNA was investigated by targeted next generation sequencing followed by whole exome sequencing. A novel nonsense variant, c.267G>A p.(Trp89*), was identified at a homozygous state in the proband in REEP6 gene, recently reported mutated in 7 unrelated families with RCD. Further functional studies will help to understand the physiopathology associated with REEP6 mutations that may be linked to a protein trafficking defect. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

41. Mutations in IMPG1 Cause Vitelliform Macular Dystrophies

Author

Manes, G., Meunier, I., Avila-Fernandez, A., Banfi, S., Meur, G. Le, Zanlonghi, X., Corton, M., Simonelli, F., Brabet, P., Labesse, G., Audo, I., Mohand-Said, S., Zeitz, C., Sahel, J.A., Weber, M., Dollfus, H., Dhaenens, C.M., Allorge, D., Baere, E. de, Koenekoop, R.K., Kohl, S., Cremers, F.P.M., Hollyfield, J.G., Senechal, A., Hebrard, M., Bocquet, B., Garcia, C.A., Hamel, C.P., Manes, G., Meunier, I., Avila-Fernandez, A., Banfi, S., Meur, G. Le, Zanlonghi, X., Corton, M., Simonelli, F., Brabet, P., Labesse, G., Audo, I., Mohand-Said, S., Zeitz, C., Sahel, J.A., Weber, M., Dollfus, H., Dhaenens, C.M., Allorge, D., Baere, E. de, Koenekoop, R.K., Kohl, S., Cremers, F.P.M., Hollyfield, J.G., Senechal, A., Hebrard, M., Bocquet, B., Garcia, C.A., and Hamel, C.P.

Abstract

Item does not contain fulltext, Vitelliform macular dystrophies (VMD) are inherited retinal dystrophies characterized by yellow, round deposits visible upon fundus examination and encountered in individuals with juvenile Best macular dystrophy (BMD) or adult-onset vitelliform macular dystrophy (AVMD). Although many BMD and some AVMD cases harbor mutations in BEST1 or PRPH2, the underlying genetic cause remains unknown for many affected individuals. In a large family with autosomal-dominant VMD, gene mapping and whole-exome sequencing led to the identification of a c.713T>G (p.Leu238Arg) IMPG1 mutation, which was subsequently found in two other families with autosomal-dominant VMD and the same phenotype. IMPG1 encodes the SPACR protein, a component of the rod and cone photoreceptor extracellular matrix domains. Structural modeling indicates that the p.Leu238Arg substitution destabilizes the conserved SEA1 domain of SPACR. Screening of 144 probands who had various forms of macular dystrophy revealed three other IMPG1 mutations. Two individuals from one family affected by autosomal-recessive VMD were homozygous for the splice-site mutation c.807+1G>T, and two from another family were compound heterozygous for the mutations c.461T>C (p.Leu154Pro) and c.1519C>T (p.Arg507( *)). Most cases had a normal or moderately decreased electrooculogram Arden ratio. We conclude that IMPG1 mutations cause both autosomal-dominant and -recessive forms of VMD, thus indicating that impairment of the interphotoreceptor matrix might be a general cause of VMD.

Published
2013

42. Seven new loci associated with age-related macular degeneration

Author

Fritsche, LG, Chen, W, Schu, M, Yaspan, BL, Yu, Y, Thorleifsson, G, Zack, DJ, Arakawa, S, Cipriani, V, Ripke, S, Igo, RP, Buitendijk, GHS, Sim, X, Weeks, DE, Guymer, RH, Merriam, JE, Francis, PJ, Hannum, G, Agarwal, A, Armbrecht, AM, Audo, I, Aung, T, Barile, GR, Benchaboune, M, Bird, AC, Bishop, PN, Branham, KE, Brooks, M, Brucker, AJ, Cade, WH, Cain, MS, Campochiaroll, PA, Chan, C-C, Cheng, C-Y, Chew, EY, Chin, KA, Chowers, I, Clayton, DG, Cojocaru, R, Conley, YP, Cornes, BK, Daly, MJ, Dhillon, B, Edwards, A, Evangelou, E, Fagemess, J, Ferreyra, HA, Friedman, JS, Geirsdottir, A, George, RJ, Gieger, C, Gupta, N, Hagstrom, SA, Harding, SP, Haritoglou, C, Heckenlively, JR, Hoz, FG, Hughes, G, Ioannidis, JPA, Ishibashi, T, Joseph, P, Jun, G, Kamatani, Y, Katsanis, N, Keilhauer, CN, Khan, JC, Kim, IK, Kiyohara, Y, Klein, BEK, Klein, R, Kovach, JL, Kozak, I, Lee, CJ, Lee, KE, Lichtner, P, Lotery, AJ, Meitinger, T, Mitchell, P, Mohand-Saied, S, Moore, AT, Morgan, DJ, Morrison, MA, Myers, CE, Naj, AC, Nakamura, Y, Okada, Y, Orlin, A, Ortube, MC, Othman, MI, Pappas, C, Park, KH, Pauer, GJT, Peachey, NS, Poch, O, Priya, RR, Reynolds, R, Richardson, AJ, Ripp, R, Rudolph, G, Ryu, E, Sahel, J-A, Schaumberg, DA, Scholl, HPN, Schwartz, SG, Scott, WK, Shahid, H, Sigurdsson, H, Silvestri, G, Sivakumaran, TA, Smith, RT, Sobrin, L, Souied, EH, Stambolian, DE, Stefansson, H, Sturgill-Short, GM, Takahashi, A, Tosakulwong, N, Truitt, BJ, Tsironi, EE, Uitterlinden, AG, van Duijn, CM, Vijaya, L, Vingerling, JR, Vithana, EN, Webster, AR, Wichmann, H-E, Winkler, TW, Wong, TY, Wright, AF, Zelenika, D, Zhang, M, Zhao, L, Zhang, K, Klein, ML, Hageman, GS, Lathrop, GM, Stefansson, K, Allikmets, R, Baird, PN, Gorin, MB, Wang, JJ, Klaver, CCW, Seddon, JM, Pericak-Vance, MA, Iyengar, SK, Yates, JRW, Swaroop, A, Weber, BHF, Kubo, M, DeAngelis, MM, Leveillard, T, Thorsteinsdottir, U, Haines, JL, Farrer, LA, Heid, IM, Abecasis, GR, Fritsche, LG, Chen, W, Schu, M, Yaspan, BL, Yu, Y, Thorleifsson, G, Zack, DJ, Arakawa, S, Cipriani, V, Ripke, S, Igo, RP, Buitendijk, GHS, Sim, X, Weeks, DE, Guymer, RH, Merriam, JE, Francis, PJ, Hannum, G, Agarwal, A, Armbrecht, AM, Audo, I, Aung, T, Barile, GR, Benchaboune, M, Bird, AC, Bishop, PN, Branham, KE, Brooks, M, Brucker, AJ, Cade, WH, Cain, MS, Campochiaroll, PA, Chan, C-C, Cheng, C-Y, Chew, EY, Chin, KA, Chowers, I, Clayton, DG, Cojocaru, R, Conley, YP, Cornes, BK, Daly, MJ, Dhillon, B, Edwards, A, Evangelou, E, Fagemess, J, Ferreyra, HA, Friedman, JS, Geirsdottir, A, George, RJ, Gieger, C, Gupta, N, Hagstrom, SA, Harding, SP, Haritoglou, C, Heckenlively, JR, Hoz, FG, Hughes, G, Ioannidis, JPA, Ishibashi, T, Joseph, P, Jun, G, Kamatani, Y, Katsanis, N, Keilhauer, CN, Khan, JC, Kim, IK, Kiyohara, Y, Klein, BEK, Klein, R, Kovach, JL, Kozak, I, Lee, CJ, Lee, KE, Lichtner, P, Lotery, AJ, Meitinger, T, Mitchell, P, Mohand-Saied, S, Moore, AT, Morgan, DJ, Morrison, MA, Myers, CE, Naj, AC, Nakamura, Y, Okada, Y, Orlin, A, Ortube, MC, Othman, MI, Pappas, C, Park, KH, Pauer, GJT, Peachey, NS, Poch, O, Priya, RR, Reynolds, R, Richardson, AJ, Ripp, R, Rudolph, G, Ryu, E, Sahel, J-A, Schaumberg, DA, Scholl, HPN, Schwartz, SG, Scott, WK, Shahid, H, Sigurdsson, H, Silvestri, G, Sivakumaran, TA, Smith, RT, Sobrin, L, Souied, EH, Stambolian, DE, Stefansson, H, Sturgill-Short, GM, Takahashi, A, Tosakulwong, N, Truitt, BJ, Tsironi, EE, Uitterlinden, AG, van Duijn, CM, Vijaya, L, Vingerling, JR, Vithana, EN, Webster, AR, Wichmann, H-E, Winkler, TW, Wong, TY, Wright, AF, Zelenika, D, Zhang, M, Zhao, L, Zhang, K, Klein, ML, Hageman, GS, Lathrop, GM, Stefansson, K, Allikmets, R, Baird, PN, Gorin, MB, Wang, JJ, Klaver, CCW, Seddon, JM, Pericak-Vance, MA, Iyengar, SK, Yates, JRW, Swaroop, A, Weber, BHF, Kubo, M, DeAngelis, MM, Leveillard, T, Thorsteinsdottir, U, Haines, JL, Farrer, LA, Heid, IM, and Abecasis, GR

Abstract

Age-related macular degeneration (AMD) is a common cause of blindness in older individuals. To accelerate the understanding of AMD biology and help design new therapies, we executed a collaborative genome-wide association study, including >17,100 advanced AMD cases and >60,000 controls of European and Asian ancestry. We identified 19 loci associated at P < 5 × 10(-8). These loci show enrichment for genes involved in the regulation of complement activity, lipid metabolism, extracellular matrix remodeling and angiogenesis. Our results include seven loci with associations reaching P < 5 × 10(-8) for the first time, near the genes COL8A1-FILIP1L, IER3-DDR1, SLC16A8, TGFBR1, RAD51B, ADAMTS9 and B3GALTL. A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD.

Published
2013

44. Genotyping microarray for CSNB-associated genes.

Author

Zeitz, C., Labs, S., Lorenz, B., Forster, U., Uksti, J., Kroes, H.Y., Baere, E. de, Leroy, B.P., Cremers, F.P.M., Wittmer, M., Genderen, M. van, Sahel, J.A., Audo, I., Poloschek, C.M., Mohand-Said, S., Fleischhauer, J.C., Huffmeier, U., Moskova-Doumanova, V., Levin, A.V., Hamel, C.P., Leifert, D., Munier, F.L., Schorderet, D.F., Zrenner, E., Friedburg, C., Wissinger, B., Kohl, S., Berger, W., Zeitz, C., Labs, S., Lorenz, B., Forster, U., Uksti, J., Kroes, H.Y., Baere, E. de, Leroy, B.P., Cremers, F.P.M., Wittmer, M., Genderen, M. van, Sahel, J.A., Audo, I., Poloschek, C.M., Mohand-Said, S., Fleischhauer, J.C., Huffmeier, U., Moskova-Doumanova, V., Levin, A.V., Hamel, C.P., Leifert, D., Munier, F.L., Schorderet, D.F., Zrenner, E., Friedburg, C., Wissinger, B., Kohl, S., and Berger, W.

Abstract

Contains fulltext : 80582.pdf (publisher's version ) (Closed access), PURPOSE: Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disease. Although electroretinographic (ERG) measurements can discriminate clinical subgroups, the identification of the underlying genetic defects has been complicated for CSNB because of genetic heterogeneity, the uncertainty about the mode of inheritance, and time-consuming and costly mutation scanning and direct sequencing approaches. METHODS: To overcome these challenges and to generate a time- and cost-efficient mutation screening tool, the authors developed a CSNB genotyping microarray with arrayed primer extension (APEX) technology. To cover as many mutations as possible, a comprehensive literature search was performed, and DNA samples from a cohort of patients with CSNB were first sequenced directly in known CSNB genes. Subsequently, oligonucleotides were designed representing 126 sequence variations in RHO, CABP4, CACNA1F, CACNA2D4, GNAT1, GRM6, NYX, PDE6B, and SAG and spotted on the chip. RESULTS: Direct sequencing of genes known to be associated with CSNB in the study cohort revealed 21 mutations (12 novel and 9 previously reported). The resultant microarray containing oligonucleotides, which allow to detect 126 known and novel mutations, was 100% effective in determining the expected sequence changes in all known samples assessed. In addition, investigation of 34 patients with CSNB who were previously not genotyped revealed sequence variants in 18%, of which 15% are thought to be disease-causing mutations. CONCLUSIONS: This relatively inexpensive first-pass genetic testing device for patients with a diagnosis of CSNB will improve molecular diagnostics and genetic counseling of patients and their families and gives the opportunity to analyze whether, for example, more progressive disorders such as cone or cone-rod dystrophies underlie the same gene defects.

Published
2009

45. Genotyping Microarray for CSNB-Associated Genes

Author

Zeitz, C, Labs, S, Lorenz, B, Forster, U, Üksti, J, Kroes, H Y, De Baere, E, Leroy, B P, Cremers, F P M, Wittmer, M, van Genderen, M M, Sahel, J A, Audo, I, Poloschek, C M, Mohand-Said, S, Fleischhauer, J C, Hüffmeier, U, Moskova-Doumanova, V, Levin, A V, Hamel, C P, Leifert, D, Munier, F L, Schorderet, D F, Zrenner, E, Friedburg, C, Wissinger, B, Kohl, S, Berger, W, Zeitz, C, Labs, S, Lorenz, B, Forster, U, Üksti, J, Kroes, H Y, De Baere, E, Leroy, B P, Cremers, F P M, Wittmer, M, van Genderen, M M, Sahel, J A, Audo, I, Poloschek, C M, Mohand-Said, S, Fleischhauer, J C, Hüffmeier, U, Moskova-Doumanova, V, Levin, A V, Hamel, C P, Leifert, D, Munier, F L, Schorderet, D F, Zrenner, E, Friedburg, C, Wissinger, B, Kohl, S, and Berger, W

Abstract

PURPOSE. Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disease. Although electroretinographic (ERG) measurements can discriminate clinical subgroups, the identification of the underlying genetic defects has been complicated for CSNB because ofgenetic heterogeneity, the uncertainty about the mode of inheritance, and time-consuming and costly mutation scanning and direct sequencing approaches. METHODS. To overcome these challenges and to generate a time- and cost-efficient mutation screening tool, the authors developed a CSNB genotyping microarray with arrayed primer extension (APEX) technology. To cover as many mutations as possible, a comprehensive literature search was performed, and DNA samples from a cohort of patients with CSNB were first sequenced directly in known CSNB genes. Subsequently, oligonucleotides were designed representing 126 sequence variations in RHO, CABP4, CACNA1F, CACNA2D4, GNAT1,GRM6, NYX, PDE6B, and SAG and spotted on the chip. RESULTS. Direct sequencing of genes known to be associated with CSNB in the study cohort revealed 21 mutations (12 novel and 9 previously reported). The resultant microarray containing oligonucleotides, which allow to detect 126 known and novel mutations, was 100% effective in determining the expected sequence changes in all known samples assessed. In addition, investigation of 34 patients with CSNB who were previously not genotyped revealed sequence variants in 18%, of which 15% are thought to be disease-causing mutations. CONCLUSIONS. This relatively inexpensive first-pass genetic testing device for patients with a diagnosis of CSNB will improve molecular diagnostics and genetic counseling of patients and their families and gives the opportunity to analyze whether, for example, more progressive disorders such as cone or cone–rod dystrophies underlie the same gene defects.

Published
2009

Catalog

Books, media, physical & digital resources
See catalog results