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Francis JH, Arcila ME, Sigler A, Bossert DF, Abramson DH, Diamond EL. Plasma-Derived Cell-Free DNA for the Diagnosis of Ocular-Involving Histiocytosis. OPHTHALMOLOGY SCIENCE 2024; 4:100530. [PMID: 39071917 PMCID: PMC11283146 DOI: 10.1016/j.xops.2024.100530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 07/30/2024]
Abstract
Purpose Circulating tumor DNA (ctDNA) is released into the plasma by many cancers and offers clinical applications including noninvasive diagnostics. Histiocytosis results from myelogenous clonal expansion of histiocytes, predominantly driven by mutations in the mitogen-activated protein kinase pathway that are potentially detectable by ctDNA-based sequencing assays. However, ocular-involving histiocytosis is often a diagnostic challenge leading to delayed diagnosis and the need for invasive biopsy of sensitive ocular structures. The purpose of this study is to determine whether sequencing of plasma-derived ctDNA can noninvasively diagnose ocular-involving histiocytosis. Design Single tertiary cancer referral center. Participants Twenty-four adult patients with ocular-involving histiocytosis and ctDNA sequencing. Methods Circulating tumor DNA was analyzed (via digital droplet polymerase chain reaction for BRAF V600E, and/or next-generation sequencing) and variant allele frequency was measured at initial presentation to our center. Patient demographics, clinical characteristics, and oncogenic mutations identified from tumor-based sequencing were recorded. Main Outcome Measures Plasma-derived ctDNA detectability of pertinent driver mutations of histiocytosis. Results At the initial presentation of 14 patients with ocular-involving histiocytosis, sequencing of plasma-derived ctDNA detected driver mutations for histiocytosis (BRAF V600E [10], KRAS [2], ARAF [1], and concurrent MAP2K1/KRAS [1]). Mutations found in circulating cell-free DNA were 100% concordant in 11 of 11 patients with mutations identified by solid tumor sequencing. Of 10 patients without driver mutation detected in ctDNA, 3 patients had alterations (CBL mutation or kinase fusion) not captured in the ctDNA sequencing assay, 3 were wildtype even by tumor sequencing; in 4 patients, tumor-based sequencing identified mutations (BRAF [2], MAP2K1 [2]) not detected in ctDNA. Detectable mutations in ctDNA were significantly more likely in patients with uveal infiltration (P = 0.036). Conclusions In this cohort, plasma-derived ctDNA was detectable and diagnostic in the majority of patients with ocular-involving histiocytosis. This suggests that if ocular histiocytosis is suspected (particularly if involving the uvea), noninvasive plasma-derived ctDNA analysis is a helpful diagnostic tool that may obviate the need to invasively biopsy sensitive ocular structures. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Jasmine H. Francis
- Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allison Sigler
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dana F. Bossert
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H. Abramson
- Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Eli L. Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York
- Early Drug Development Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Sirivolu S, Peng CC, Neviani P, Xu BY, Berry JL, Xu L. Comparative Single Vesicle Analysis of Aqueous Humor Extracellular Vesicles before and after Radiation in Uveal Melanoma Eyes. Int J Mol Sci 2024; 25:6035. [PMID: 38892225 PMCID: PMC11172950 DOI: 10.3390/ijms25116035] [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: 04/10/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Small extracellular vesicles (sEVs) have been shown to promote tumorigenesis, treatment resistance, and metastasis in multiple cancer types; however, sEVs in the aqueous humor (AH) of uveal melanoma (UM) patients have never previously been profiled. In this study, we used single particle analysis to characterize sEV subpopulations in the AH of UM patients by quantifying their size, concentration, and phenotypes based on cell surface markers, specifically the tetraspanin co-expression patterns of CD9, CD63, and CD81. sEVs were analyzed from paired pre- and post-treatment (brachytherapy, a form of radiation) AH samples collected from 19 UM patients. In post-brachytherapy samples, two subpopulations, CD63/81+ and CD9/63/81+ sEVs, were significantly increased. These trends existed even when stratified by tumor location and GEP class 1 and class 2 (albeit not significant for GEP class 2). In this initial report of single vesicle profiling of sEVs in the AH of UM patients, we demonstrated that sEVs can be detected in the AH. We further identified two subpopulations that were increased post-brachytherapy, which may suggest radiation-induced release of these particles, potentially from tumor cells. Further study of the cargo carried by these sEV subpopulations may uncover important biomarkers and insights into tumorigenesis for UM.
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Affiliation(s)
- Shreya Sirivolu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.); (C.-C.P.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chen-Ching Peng
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.); (C.-C.P.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Paolo Neviani
- Extracellular Vesicle Core, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Benjamin Y. Xu
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jesse L. Berry
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.); (C.-C.P.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The Saban Research Institute, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (S.S.); (C.-C.P.)
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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de Bruyn DP, van Poppelen NM, Brands T, van den Boom SC, Eikenboom E, Wagner A, van Veghel-Plandsoen MM, Geeven G, Beverloo B, van Rij CM, Verdijk RM, Naus NC, Bagger MM, Kiilgaard JF, de Klein A, Brosens E, Kiliç E. Evaluation of Circulating Tumor DNA as a Liquid Biomarker in Uveal Melanoma. Invest Ophthalmol Vis Sci 2024; 65:11. [PMID: 38319670 PMCID: PMC10854420 DOI: 10.1167/iovs.65.2.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/14/2023] [Indexed: 02/07/2024] Open
Abstract
Purpose Uveal melanoma (UM) has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations (CNVs), but limited primary tumor tissue is available for molecular characterization due to eye-sparing irradiation treatment. This study aimed to assess the rise in circulating tumor DNA (ctDNA) levels in UM and evaluate its efficacy for CNV-profiling of patients with UM. Methods In a pilot study, we assessed ctDNA levels in the blood of patients with UM (n = 18) at various time points, including the time of diagnosis (n = 13), during fractionated stereotactic radiotherapy (fSRT) treatment (n = 6), and upon detection of metastatic disease (n = 13). Shallow whole-genome sequencing (sWGS) combined with in silico size-selection was used to identify prognostically relevant CNVs in patients with UM (n = 26) from peripheral blood retrieved at the time of diagnosis (n = 9), during fSRT (n = 5), during post-treatment follow-up (n = 4), metastasis detection (n = 6), and metastasis follow-up (n = 4). Results A total of 34 patients had blood analyzed for ctDNA detection (n = 18) and/or CNV analysis (n = 26) at various time points. At the time of diagnosis, 5 of 13 patients (38%) had detectable ctDNA (median = 0 copies/mL). Upon detection of metastatic disease, ctDNA was detected in 10 of 13 patients (77%) and showed increased ctDNA levels (median = 24 copies/mL, P < 0.01). Among the six patients analyzed during fSRT, three (50%) patients had detectable ctDNA at baseline and three of six (50%) patients had undetectable levels of ctDNA. During the fSRT regimen, ctDNA levels remained unchanged (P > 0.05). The ctDNA fractions were undetectable to low in localized disease, and sWGS did not elucidate chromosome 3 status from blood samples. However, in 7 of 10 (70%) patients with metastases, the detection of chromosome 3 loss corresponded to the high metastatic-risk class. Conclusions The rise in ctDNA levels observed in patients with UM harboring metastases suggests its potential utility for CNV profiling. These findings highlight the potential of using ctDNA for metastasis detection and patient inclusion in therapeutic studies targeting metastatic UM.
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Affiliation(s)
- Daniel P. de Bruyn
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Natasha M. van Poppelen
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Tom Brands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Ellis Eikenboom
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Geert Geeven
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Berna Beverloo
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Caroline M. van Rij
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pathology, LUMC, Leiden, The Netherlands
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Mette M. Bagger
- Department of Ophthalmology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Jens F. Kiilgaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
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Spiliopoulou P, Holanda Lopes CD, Spreafico A. Promising and Minimally Invasive Biomarkers: Targeting Melanoma. Cells 2023; 13:19. [PMID: 38201222 PMCID: PMC10777980 DOI: 10.3390/cells13010019] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
The therapeutic landscape of malignant melanoma has been radically reformed in recent years, with novel treatments emerging in both the field of cancer immunotherapy and signalling pathway inhibition. Large-scale tumour genomic characterization has accurately classified malignant melanoma into four different genomic subtypes so far. Despite this, only somatic mutations in BRAF oncogene, as assessed in tumour biopsies, has so far become a validated predictive biomarker of treatment with small molecule inhibitors. The biology of tumour evolution and heterogeneity has uncovered the current limitations associated with decoding genomic drivers based only on a single-site tumour biopsy. There is an urgent need to develop minimally invasive biomarkers that accurately reflect the real-time evolution of melanoma and that allow for streamlined collection, analysis, and interpretation. These will enable us to face challenges with tumour tissue attainment and process and will fulfil the vision of utilizing "liquid biopsy" to guide clinical decisions, in a manner akin to how it is used in the management of haematological malignancies. In this review, we will summarize the most recent published evidence on the role of minimally invasive biomarkers in melanoma, commenting on their future potential to lead to practice-changing discoveries.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada;
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Beasley AB, de Bruyn DP, Calapre L, Al-Ogaili Z, Isaacs TW, Bentel J, Reid AL, Dwarkasing RS, Pereira MR, Khattak MA, Meniawy TM, Millward M, Brosens E, de Klein A, Chen FK, Kiliҫ E, Gray ES. Detection of metastases using circulating tumour DNA in uveal melanoma. J Cancer Res Clin Oncol 2023; 149:14953-14963. [PMID: 37608028 PMCID: PMC10602949 DOI: 10.1007/s00432-023-05271-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
BACKGROUND Approximately 50% of uveal melanoma (UM) patients will develop metastatic disease depending on the genetic features of the primary tumour. Patients need 3-12 monthly scans, depending on their prognosis, which is costly and often non-specific. Circulating tumour DNA (ctDNA) quantification could serve as a test to detect and monitor patients for early signs of metastasis and therapeutic response. METHODS We assessed ctDNA as a biomarker in three distinct UM cohorts using droplet-digital PCR: (A) a retrospective analysis of primary UM patients to predict metastases; (B) a prospective analysis of UM patients after resolution of their primary tumour for early detection of metastases; and (C) monitoring treatment response in metastatic UM patients. RESULTS Cohort A: ctDNA levels were not associated with the development of metastases. Cohort B: ctDNA was detected in 17/25 (68%) with radiological diagnosis of metastases. ctDNA was the strongest predictor of overall survival in a multivariate analysis (HR = 15.8, 95% CI 1.7-151.2, p = 0.017). Cohort C: ctDNA monitoring of patients undergoing immunotherapy revealed a reduction in the levels of ctDNA in patients with combination immunotherapy. CONCLUSIONS Our proof-of-concept study shows the biomarker feasibility potential of ctDNA monitoring in for the clinical management of uveal melanoma patients.
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Affiliation(s)
- Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
| | - Daniël P de Bruyn
- Department of Ophthalmology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Zeyad Al-Ogaili
- Department of Molecular Imaging and Therapy Service, Fiona Stanley Hospital, Murdoch, WA, 6150, Australia
| | - Timothy W Isaacs
- Perth Retina, Subiaco, WA, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Crawley, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
| | - Jacqueline Bentel
- Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Anna L Reid
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Roy S Dwarkasing
- Department of Radiology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
| | - Michelle R Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Muhammad A Khattak
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Department of Medical Oncology, Fiona Stanley Hospital, Murdoch, WA, Australia
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Tarek M Meniawy
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Michael Millward
- School of Medicine, The University of Western Australia, Crawley, WA, Australia
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Crawley, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Emine Kiliҫ
- Department of Ophthalmology, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus MC, 3000 CA, Rotterdam, The Netherlands
- Erasmus MC Cancer Institute, 3000 CA, Rotterdam, The Netherlands
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
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Kim V, Guberina M, Bechrakis NE, Lohmann DR, Zeschnigk M, Le Guin CHD. Release of Cell-Free Tumor DNA in the Plasma of Uveal Melanoma Patients Under Radiotherapy. Invest Ophthalmol Vis Sci 2023; 64:35. [PMID: 37862025 PMCID: PMC10599159 DOI: 10.1167/iovs.64.13.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose Uveal melanoma (UM) is a tumor of the eye that metastasizes in approximately half of cases. Prognostic testing requires accessibility to tumor tissue, which is usually not available with eye-preserving therapies. Noninvasive approaches to prognostic testing that provide valuable information for patient care are therefore needed. The aim of this study was to evaluate the use of circulating cell-free plasma DNA analysis in UM patients undergoing brachytherapy. Methods The study recruited 26 uveal melanoma patients referred to the department between February and October 2020. Blood samples were collected at various time points before, during, and after treatment, and deep amplicon sequencing was used to identify oncogenic variant alleles of the GNAQ and GNA11 genes, which serve as indicators for the presence of circulating tumor DNA (ctDNA). Results The results showed that all patients were ctDNA negative before brachytherapy. In 31% of patients, ctDNA was detected during therapy. The variant allele fraction of GNAQ or GNA11 alleles in ctDNA positive samples ranged from 0.24% to 2% and correlates with the largest basal diameter and thickness of the tumor. Conclusions The findings suggest that brachytherapy increases the presence of tumor DNA in the plasma of UM patients. Thus ctDNA analysis may offer a noninvasive approach for prognostic testing. However, efforts are still required to lower the limit of detection for tumor-specific genetic alterations.
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Affiliation(s)
- Viktoria Kim
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Maja Guberina
- Department of Radiotherapy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Claudia H D Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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