Panagiotis I. Sergouniotis

The Human Phenotype Ontology in 2017

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Molecular findings from 537 individuals with inherited retinal disease

Background Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. Methods We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). Results Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. Conclusions Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.

Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases

Background Diagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD. Methods Three read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory. Results We confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques. Conclusion Incorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations.

Panel-Based Clinical Genetic Testing in 85 Children with Inherited Retinal Disease

PURPOSEnTo assess the clinical usefulness of genetic testing in a pediatric population with inherited retinal disease (IRD).nnnDESIGNnSingle-center retrospective case series.nnnPARTICIPANTSnEighty-five unrelated children with a diagnosis of isolated or syndromic IRD who were referred for clinical genetic testing between January 2014 and Julyxa02016.nnnMETHODSnParticipants underwent a detailed ophthalmic examination, accompanied by electrodiagnostic testing (EDT) and dysmorphologic assessment where appropriate. Ocular and extraocular features were recorded using Human Phenotype Ontology terms. Subsequently, multigene panel testing (105 or 177 IRD-associated genes) was performed in an accredited diagnostic laboratory, followed by clinical variant interpretation.nnnMAIN OUTCOME MEASURESnDiagnostic yield and clinical usefulness of genetic testing.nnnRESULTSnOverall, 78.8% of patients (nxa0= 67) received a probable molecular diagnosis; 7.5% (nxa0= 5) of these had autosomal dominant disease, 25.4% (nxa0= 17) had X-linked disease, and 67.2% (nxa0= 45) had autosomal recessive disease. In a further 5.9% of patients (nxa0= 5), a single heterozygous ABCA4 variant was identified; all these participants had a spectrum of clinical features consistent with ABCA4 retinopathy. Most participants (84.7%; nxa0= 72) had undergone EDT and 81.9% (nxa0= 59) of these patients received a probable molecular diagnosis. The genes most frequently mutated in the present cohort were CACNA1F and ABCA4, accounting for 14.9% (nxa0= 10) and 11.9% (nxa0= 8) of diagnoses respectively. Notably, in many cases, genetic testing helped to distinguish stationary from progressive IRD subtypes and to establish a precise diagnosis in a timely fashion.nnnCONCLUSIONSnMultigene panel testing pointed to a molecular diagnosis in 84.7% of children with IRD. Thexa0diagnostic yield in the study population was significantly higher compared with that in previously reported unselected IRD cohorts. Approaches similar to the one described herein are expected to become a standard component of care in pediatric ophthalmology. We propose the introduction of genetic testing early in the diagnostic pathway in children with clinical and/or electrophysiologic findings, suggestive ofxa0IRD.

Variability in the ocular phenotype in mucopolysaccharidosis

Purpose Mucopolysaccharidoses (MPSs) are a heterogeneous group of lysosomal storage disorders. Ocular complications (such as corneal clouding, retinopathy and optic neuropathy) are common. Notably, there is a paucity of data on the effect of genotype and systemic treatments (enzyme replacement therapy or haematopoietic stem cell transplantation) on the ocular phenotype in MPS. We prospectively studied the ocular features of patients with MPSI (Hurler/Hurler-Scheie/Scheie), MPSIV (Morquio) and MPSVI (Maroteaux-Lamy), to evaluate the effect of different therapeutic interventions and to correlate the findings with genetic and biomarker data. Methods Prospective observational cohort study. Study participants underwent detailed ocular examination including visual acuity; assessment of corneal clouding (Iris camera Corneal Opacification Measure score and Pentacam densitometry) and retinal and optic nerve imaging (optical coherence tomography and wide-field fundus imaging). Data on genotype, biomarkers and delivered therapies (type and length of treatment) were also collected for each patient where available. Results Overall, 21 patients with MPSI, 4 patients with MPSIV and 3 patients with MPSVI were recruited. Corneal clouding scores were higher in MPSI compared with MPSIV and MPSVI. Retinopathy was evident in patients with MPSI only. Association was observed between corneal clouding and biomarkers in MPSI, MPSIV and MPSVI. However, no clear association was seen between genotype or treatment type and ocular phenotype. Conclusions The ocular phenotype in MPS is variable, with corneal clouding occurring in MPSI, MPSIV and MPSVI, and retinopathy in MPSI only. There was an association between corneal clouding and efficacy of systemic treatment as measured by biomarkers.

Use of a gene-based case-control association approach in exome sequencing data to elucidate the molecular basis of a mendelian phenotype

Abstract Background Over the past 5 years, exome sequencing and whole-genome sequencing have been extensively used to identify genes underlying rare mendelian disorders. These techniques have accelerated not only discovery but also false-positive reports of causality. To address this issue, we developed a statistical inference framework that evaluates the strength of findings from such studies. This method was applied to exome sequencing data from individuals with a specific retinal dystrophy, aiming to elucidate the genetic basis of their visual impairment. Methods 28 unrelated patients and 1917 controls with no retinal disease underwent exome sequencing. Patients had a progressive retinal dystrophy phenotype with early cone photoreceptor involvement, absence of retinal flecks on fundus autofluorescence imaging, and an unknown molecular diagnosis. Genetic data from cases and controls were analysed with the same bioinformatics pipeline. A gene-based case-control association study was then performed and gene-based p values were derived. Findings The initial analysis focused on rare, presumed loss-of-function variants; the most significant binomial p value (p=2u2008×u200810 −5 ) was obtained for TTLL5 . Closer inspection highlighted biallelic loss-of-function variants in this gene as a probable cause of the studied retinal dystrophy. A second analysis using a recessive model (presence of ≥2 rare, potentially functional variants) was then performed. The most significant binomial p value (p=1u2008×u200810 −4 ) was obtained for DRAM2 , highlighting mutations in this gene as another likely cause of this retinal dystrophy. Validation studies identified additional mutation-positive individuals (four with TTLL5-retinopathy and five with DRAM2-retinopathy in total). Overall, a molecular diagnosis was identified in 15 of the 28 patients. Interpretation Using a phenotype-driven cluster analysis, we have identified two previously unreported disease-associated genes. The success of our method highlights the key role of precise phenotyping in enhancing the utility of genomic investigations. Additionally, we have described a robust genome-wide statistical framework for objectively assigning probability of causation to new candidate genes and variants. This approach is broadly applicable to the study of rare mendelian disorders. Funding National Institute for Health Research, Macular Society UK, RP Fighting Blindness, Fight For Sight, National Eye Research Centre, Wellcome Trust.

Genome sequencing identifies a non-coding variant in the MCDR1 locus as a cause of macular dystrophy

North Carolina macular dystrophy (NCMD) is an uncommon condition characterized by central macular abnormalities that are present at birth but rarely progress. It is inherited in an autosomal dominant manner, and many affected families link to a locus on 6q16.2 (MCDR1). There are 10 genes in this locus, and although these have been extensively interrogated for over 20years, the genetic cause underpinning NCMD was only recently discovered: Small and colleagues identified non-protein-coding variants affecting the regulation of the PRDM13 gene in 12 NCMD families. Here, we report clinical and genomic data for an additional family with NCMD, providing further evidence for the role of PRDM13 regulatory variants in NCMD. The proband is a 34-year-old female who reports having poor central vision from early life and was diagnosed with a retinal dystrophy at 4years of age. Examination at age of 34years revealed visual acuity of 0.54 logMAR in the right eye and 0.48 logMAR in the left eye. Fundoscopy and optical coherence tomography were consistent with a central macular caldera although there was a degree of interocular asymmetry (Fig. 1a). Autofluorescence imaging revealed hyperautofluorescent flecks surrounding the