{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T15:06:25Z","timestamp":1787497585085,"version":"build-2736575974"},"reference-count":35,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:00:00Z","timestamp":1760054400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Congenital eye malformations like microphthalmia\u2013anophthalmia\u2013coloboma (MAC), anterior segment dysgenesis (ASD), primary congenital glaucoma (PCG) and congenital cataracts (CC) are significant causes of childhood visual impairment. Phenotypic heterogeneity often complicates diagnosis. The goal of this study was to optimize the diagnostic strategy for next-generation sequencing (NGS)-based procedures, thereby aiming to identify genetic causes of congenital eye malformations. Forty patients with congenital eye malformations were included. A primary diagnostic testing (PD) of a limited number of genes was followed by multigene panel (MGP) testing, including 186 eye-related genes, and exome sequencing. Causative variants were identified in 17 patients (43%) and clinically relevant variants of uncertain significance (VUS) in 6 patients (15%). PD had a diagnostic yield (DY) of 15%, MGP of 29% and exome sequencing of 4%, leading to a cumulative DY of 43%. Diagnostic rates were highest in CC (75%), bilateral cases (46%), complex ocular phenotypes (78%), patients with extraocular manifestations (55%) and positive family history (70%). Rare and possible new genotype\u2013phenotype correlations and candidate genes (FAT1, POGZ) could be identified. In total, eight (likely) pathogenic variants in six genes (CYP1B1, ADAMTS18, MAB21L2, NHS, MFRP, CRYBB1) were not yet reported. A stepwise genetic testing approach starting with a broad multigene panel followed by exome sequencing provides higher diagnostic yield than limited phenotype-specific testing. Comprehensive genetic diagnosis is essential for prognosis, treatment and genetic counseling, underscoring the need for routine genetic testing and interdisciplinary collaboration in managing congenital eye malformations.<\/jats:p>","DOI":"10.3390\/ijms26209854","type":"journal-article","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:50:16Z","timestamp":1760107816000},"page":"9854","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Next-Generation Sequencing in Congenital Eye Malformations: Identification of Genetic Causes and Comparison of Different Panel-Based Diagnostic Strategies"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-2632-5762","authenticated-orcid":false,"given":"Lukas","family":"Neuhann","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, LMU University Hospital, LMU Munich, 80336 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Laner","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ) M\u00fcnchen, 80335 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5172-2818","authenticated-orcid":false,"given":"Elke","family":"Holinski-Feder","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ) M\u00fcnchen, 80335 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa","family":"Neuhann","sequence":"additional","affiliation":[{"name":"Medizinisch Genetisches Zentrum (MGZ) M\u00fcnchen, 80335 Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3425","DOI":"10.1167\/iovs.10-6747","article-title":"A Novel Locus for Congenital Simple Microphthalmia Family Mapping to 17p12-q12","volume":"52","author":"Hu","year":"2011","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/ejhg.2017.9","article-title":"Diagnostic exome sequencing in 266 Dutch patients with visual impairment","volume":"25","author":"Pfundt","year":"2017","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Sun, W., Xiao, X., Li, S., Guo, X., Zhang, Q., and Leung, Y.F. (2014). Exome Sequencing of 18 Chinese Families with Congenital Cataracts: A New Sight of the NHS Gene. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0100455"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1167\/tvst.8.2.21","article-title":"An Ophthalmic Targeted Exome Sequencing Panel as a Powerful Tool to Identify Causative Mutations in Patients Suspected of Hereditary Eye Diseases","volume":"8","author":"Wang","year":"2019","journal-title":"Transl. Vis. Sci. Technol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/cge.12275","article-title":"Molecular findings and clinical data in a cohort of 150 patients with anophthalmia\/microphthalmia","volume":"86","author":"Chassaing","year":"2013","journal-title":"Clin. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1016\/j.ophtha.2014.06.006","article-title":"Personalized Diagnosis and Management of Congenital Cataract by Next-Generation Sequencing","volume":"121","author":"Gillespie","year":"2014","journal-title":"Ophthalmology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1159\/000360532","article-title":"Late Diagnosis of COL4A1 Mutation and Problematic Vascular Risk Fac-tor Management","volume":"72","author":"Magnin","year":"2014","journal-title":"Eur. Neurol."},{"key":"ref_8","first-page":"2515841420954592","article-title":"Practical guide to genetic screening for inherited eye diseases","volume":"12","author":"Malka","year":"2020","journal-title":"Ther. Adv. Ophthalmol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.ejmg.2013.12.006","article-title":"Molecular genetics of congenital nuclear cataract","volume":"57","author":"Deng","year":"2014","journal-title":"Eur. J. Med. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/j.ophtha.2018.12.050","article-title":"The Oculome Panel Test: Next-Generation Sequencing to Diagnose a Di-verse Range of Genetic Developmental Eye Disorders","volume":"126","author":"Patel","year":"2019","journal-title":"Ophthalmology"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1136\/bjo-2022-321991","article-title":"Real-world clinical and molecular management of 50 prospective patients with microphthalmia, anophthalmia and\/or ocular coloboma","volume":"107","author":"Harding","year":"2022","journal-title":"Br. J. Ophthalmol."},{"key":"ref_12","first-page":"1215","article-title":"Screening of CYP1B1 and MYOC in Moroccan families with primary congenital glaucoma: Three novel mutations in CYP1B1","volume":"16","author":"Hilal","year":"2010","journal-title":"Mol. Vis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"732170","DOI":"10.3389\/fgene.2021.732170","article-title":"Heterogeneity of Axenfeld\u2013Rieger Syndrome: Molecular and Clinical Findings in Chinese Patients","volume":"12","author":"Zhang","year":"2021","journal-title":"Front. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1111\/cge.12379","article-title":"Whole exome analysis identifies dominant COL4A1 mutations in patients with complex ocular phenotypes involving microphthalmia","volume":"86","author":"Deml","year":"2014","journal-title":"Clin. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s13023-018-0828-0","article-title":"Clinical and genetic characteristics of Chinese patients with familial or sporadic pe-diatric cataract","volume":"13","author":"Li","year":"2018","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/ng1321","article-title":"Oculofaciocardiodental and Lenz microphthalmia syndromes result from distinct classes of mutations in BCOR","volume":"36","author":"Ng","year":"2004","journal-title":"Nat. Genet."},{"key":"ref_17","first-page":"540","article-title":"A detailed phenotypic assessment of individuals affected by MFRP-related oculopathy","volume":"16","author":"Mukhopadhyay","year":"2010","journal-title":"Mol. Vis."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.ajhg.2014.05.005","article-title":"Monoallelic and Biallelic Mutations in MAB21L2 Cause a Spectrum of Major Eye Malformations","volume":"94","author":"Rainger","year":"2014","journal-title":"Am. J. Hum. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.ajhg.2011.02.006","article-title":"Autosomal-Recessive Posterior Microphthalmos Is Caused by Mutations in PRSS56, a Gene Encoding a Trypsin-Like Serine Protease","volume":"88","author":"Gal","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_20","first-page":"1229","article-title":"Analysis of CYP1B1 in pediatric and adult glaucoma and other ocular pheno-types","volume":"22","author":"Reis","year":"2016","journal-title":"Mol. Vis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1002\/ajmg.a.61380","article-title":"Phenotypic expansion of POGZ-related intellectual disability syndrome (White-Sutton syndrome)","volume":"182","author":"Posey","year":"2020","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e1997","DOI":"10.1002\/mgg3.1997","article-title":"Panel-based next-generation sequencing identifies novel mutations in Bulgarian patients with inherited retinal dystrophies","volume":"10","author":"Kamenarova","year":"2022","journal-title":"Mol. Genet. Genom. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1002\/ajmg.c.31837","article-title":"Molecular diagnostic challenges for non-retinal developmental eye disorders in the United Kingdom","volume":"184","author":"Jackson","year":"2020","journal-title":"Am. J. Med. Genet. C Semin. Med. Genet."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1093\/pch\/pxz005","article-title":"Newborn with bilateral congenital cataracts: Never forget congenital rubella syndrome","volume":"25","author":"Wong","year":"2020","journal-title":"Paediatr. Child Health"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1002\/ajmg.a.33817","article-title":"Trisomy 2 mosaicism with caudal dysgenesis, Hirschsprung disease, and micro-anophthalmia","volume":"155","author":"Prontera","year":"2011","journal-title":"Am. J. Med. Genet. A"},{"key":"ref_26","first-page":"161","article-title":"CYP1B1 Gene and Phenotypic Correlation in Patients From Northeastern Brazil With Primary Congenital Glaucoma","volume":"28","author":"Sena","year":"2019","journal-title":"Eur. J. Gastroenterol. Hepatol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1097\/ICU.0b013e328356893d","article-title":"A new approach to the classification of neonatal corneal opacities","volume":"23","author":"Nischal","year":"2012","journal-title":"Curr. Opin. Ophthalmol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1001\/jamaophthalmol.2014.940","article-title":"Expansion of Ocular Phenotypic Features Associated With Mutations in ADAMTS18","volume":"132","author":"Chandra","year":"2014","journal-title":"JAMA Ophthalmol."},{"key":"ref_29","first-page":"598","article-title":"Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA\u2013protein interaction","volume":"22","author":"Williamson","year":"2019","journal-title":"Anesth. Analg."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1038\/s41467-019-08547-w","article-title":"Homozygous frameshift mutations in FAT1 cause a syndrome characterized by colobomatous-microphthalmia, ptosis, nephropathy and syndactyly","volume":"10","author":"Lahrouchi","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41431-021-00961-3","article-title":"Further delineation of the clinical spectrum of White\u2013Sutton syndrome: 12 new individuals and a review of the literature","volume":"30","author":"Murch","year":"2021","journal-title":"Eur. J. Hum. Genet."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.ejmg.2014.05.002","article-title":"The genetic architecture of microphthalmia, anophthalmia and coloboma","volume":"57","author":"Williamson","year":"2014","journal-title":"Eur. J. Med. Genet."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Moon, D., Park, H.W., Surl, D., Won, D., Lee, S.-T., Shin, S., Choi, J.R., and Han, J. (2021). Precision Medicine through Next-Generation Sequencing in Inherited Eye Diseases in a Korean Cohort. Genes, 13.","DOI":"10.3390\/genes13010027"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1001\/jamaophthalmol.2021.0385","article-title":"Genetic Analysis in a Swiss Cohort of Bilateral Congenital Cataract","volume":"139","author":"Rechsteiner","year":"2021","journal-title":"JAMA Ophthalmol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/20\/9854\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:00:08Z","timestamp":1760108408000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/20\/9854"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,10]]},"references-count":35,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2025,10]]}},"alternative-id":["ijms26209854"],"URL":"https:\/\/doi.org\/10.3390\/ijms26209854","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,10]]}}}