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Abstract

We thank Bateman and Maumenee for their comments and are grateful for the opportunity to reply. The eye disorders panel testing we present in our report was developed in the UK at Great Ormond Street Hospital for Children and the University College London Institute of Child Health. It aimed specifically to increase the availability of testing for all genes known to be associated with childhood eye conditions. It was approved for national diagnostic service provision in the UK National Health Service (provided free at the point of delivery) and is provided as part of the UK Genetic Testing Network (www.ukgtn.nhs.uk). In the UK, our genetic diagnostic service applies rigorous variant assessment in accordance with the American College of Medical Genetics and Genomics (ACMG)1Richards S. Aziz N. Bale S. et al.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.Genet Med. 2015; 17: 405-424Abstract Full Text Full Text PDF PubMed Scopus (14601) Google Scholar and The Association for Clinical Genomic Science (ACGS) guidance (www.acgs.uk.com/quality/best-practice-guidelines/). The overall reported diagnostic yield of 68 of 277 samples in our study links partly to inclusion of conditions such as microphthalmia and coloboma and anterior segment developmental anomalies, for which our study indicates incomplete knowledge regarding the genetic etiology, and also to rigor in variant assessment and caution against overinterpretation of findings. We report only definitive diagnoses, that is, class 4 (likely pathogenic) and class 5 (pathogenic) variants. Class 3 variants of unknown significance were also provided as supplementary data; these variants are usually in a relevant eye gene, but without functional or segregation studies, or other evidence to prove pathogenic consequence. Further laboratory research, or additional affected individuals are needed to confirm pathogenicity of such variants. The same challenge, but magnified, applies to interpretation of new variants identified by whole genome sequencing (WGS) in a single affected person’s DNA; more evidence is needed to prove pathogenicity of rare variants identified in genes not previously associated with eye disease. Furthermore, there is not yet any established method for interpreting novel intronic and 5′ untranslated region variants (which could be identified by WGS), even in known disease genes. These factors need to be carefully considered in relation to the comment from Bateman and Maumenee that, “The causative mutation is more likely to be identified as all genes are sequenced,” because the increased diagnostic yield from WGS at the current time, if applying rigorous variant assessment, may not be significant. Nevertheless, the current high value of WGS is to enable research to more completely elucidate novel variants associated with disease through the sharing of genome data resources. In the UK, the 100,000 Genomes Project and Genomics England (genomicsengland.co.uk) is creating such a resource linked with creation of a new genomics medicine service to transform national genetic diagnosis and provide personalized treatments by combining genomic sequence data with medical records. The second point raised by Bateman and Maumenee regarding third-party payers is not relevant in a nationalized health care environment (as we have in the UK), and within which a major consideration is the cost of testing. Decentralized WGS is still not affordable (and certainly was not at the time of inception of the oculome project). The smaller size of the panel testing allows multiplexing of more patients in a sequencing run and ease of data handling. For example, in a run of 64 patients we achieved coverage of 99.5% (>30×) and a mean depth of 363×; to achieve comparable metrics using WGS would require a huge increase in data output per patient. In our new national testing structure in the UK, with decreased costs achieved through scale and technology, all the highly heterogeneous presentations are scheduled to transition from panels to WGS in the future (cataract, retinal, structural eye disease) and diagnostic analysis will first focus on virtual gene panels (as described in our study) to direct the variant Tiering process for the interpretation of genomes (www.panel.app.genomicsengland.co.uk). By sharing data within our Genomics England Clinical interpretation partnerships and with external collaborators outside the UK, over time this open approach is designed to achieve consensus on which new genes have sufficient evidence for diagnostic testing. Re: Patel et al.: The Oculome Panel Test: next-generation sequencing to diagnose a diverse range of genetic developmental eye disorders (Ophthalmology. 2019;126:888–907)OphthalmologyVol. 127Issue 4PreviewThe authors developed a large next-generation DNA sequencing panel assay to screen for coding sequence and copy number variants in genes known to cause developmental eye disorders and inherited eye disease (429 genes); Sanger sequencing confirmed variants.1 They evaluated 277 probands, some of whom had multisystem disorders, using their panel and analyses. Of note, the overall diagnostic yield was relatively low at 68 of 277 samples (<25%). Full-Text PDF