AAV capsid bioengineering in primary human retina models.

Adeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.

Prevalence of Glaucoma Following Paediatric Cataract Surgery in an Australian Tertiary Referral Centre.

Purpose: Secondary glaucoma following childhood cataract surgery remains the most common complication in the paediatric population. This study aimed to determine the incidence, time to progression and risk factors associated with the development of secondary glaucoma following childhood cataract surgery in a paediatric population. Outcome measures were the detection of secondary glaucoma, postoperative time frame to development of glaucoma and risk factors in its development. Patients and Methods: A retrospective case series was conducted between 2003 and 2017 at a tertiary children's hospital in Sydney. The patient population included those 16 years or less of age who underwent congenital cataract extraction, with or without an intraocular lens implantation and who had been followed up for a minimum of six months following surgery. Patients were excluded if they had cataract aetiology other than congenital idiopathic cataract. Multivariate Cox Regression analysis was used to determine relevant risk factors. Results: A total of 320 eyes in 216 patients were included in the study. Secondary glaucoma developed in 11.9% of eyes. In those that developed secondary glaucoma, the average time to onset from surgery was 3.2 years (median 2.75 years). The mean age of diagnosis of secondary glaucoma was 4.58 years (median 3.5 years, range 2.5 months to 13.23 years). Microcornea was the only adverse characteristic significantly associated with an increased risk of secondary glaucoma (HR 6.30, p 0.003). Conclusion: Despite modern surgical techniques, glaucoma remains a significant long-term sequela in children following cataract surgery.

The health care and societal costs of inherited retinal diseases in Australia: a microsimulation modelling study.

OBJECTIVES: To estimate the health care and societal costs of inherited retinal diseases (IRDs) in Australia. DESIGN, SETTING, PARTICIPANTS: Microsimulation modelling study based on primary data - collected in interviews of people with IRDs who had ophthalmic or genetic consultations at the Children's Hospital at Westmead or the Save Sight Institute (both Sydney) during 1 January 2019 - 31 December 2020, and of their carers and spouses - and linked Medicare Benefits Schedule (MBS) and Pharmaceutical Benefits Schedule (PBS) data. MAIN OUTCOME MEASURES: Annual and lifetime costs for people with IRDs and for their carers and spouses, grouped by payer (Australian government, state governments, individuals, private health insurance) and type (health care costs; societal costs: social support, National Disability Insurance Scheme (NDIS), income and taxation, costs associated with caring for family members with IRDs); estimated annual national cost of IRDs. RESULTS: Ninety-four people (74 adults, 20 people under 18 years; 55 girls and women [59%]) and 30 carers completed study surveys (participation rate: adults, 66%; children, 66%; carers, 63%). Total estimated lifetime cost was $5.2 million per person with an IRD, of which 87% were societal and 13% health care costs. The three highest cost items were lost income for people with IRDs ($1.4 million), lost income for their carers and spouses ($1.1 million), and social spending by the Australian government (excluding NDIS expenses: $1.0 million). Annual costs were twice as high for people who were legally blind as for those with less impaired vision ($83 910 v $41 357 per person). The estimated total annual cost of IRDs in Australia was $781 million to $1.56 billion. CONCLUSION: As the societal costs associated with IRDs are much larger than the health care costs, both contributors should be considered when assessing the cost-effectiveness of interventions for people with IRDs. The increasing loss of income across life reflects the impact of IRDs on employment and career opportunities.

Spectrum of ocular disease in children aged between 0 and 3 years at an Australian paediatric tertiary hospital.

BACKGROUND: Childhood ocular disease can be a significant health burden to the child, family and society. Previous studies have examined the spectrum of paediatric ocular disease presenting to tertiary hospitals; however, these studies have broader age ranges, smaller sample sizes, and are largely based in developing countries. This study aims to assess the spectrum of ocular disease in the first 3 years of life presenting to the eye department of an Australian tertiary paediatric hospital. METHODS: The records of 3337 children who had their initial presentation at the eye clinic between the age of 0 and 36 months were reviewed, spanning 6.5 years from 1st July 2012 to 31st December 2018. RESULTS: The most common primary diagnoses overall were strabismic amblyopia (6.0%), retinopathy of prematurity (5.0%) and nasolacrimal duct obstruction (4.5%). Bilateral visual impairment was more common in younger children, while unilateral visual impairment was more common in older children. The proportion of all children presenting with visual impairment was 10.3%, with 5.7% of all children presenting with bilateral visual impairment and 4.6% presenting with unilateral visual impairment. In children with visual impairment, the most common sites of primary abnormality were lens (21.4%), retina (17.3%), and cerebral and visual pathways (12.1%). The most common primary diagnoses in children with visual impairment were cataract (21.4%), strabismic amblyopia (9.3%) and retinoblastoma (6.5%). CONCLUSIONS: The spectrum of eye disease and vision impairment presenting in the first 3 years of life facilitates health care planning, greater community education about vision impairment and importance of early intervention, and guidance for appropriate resource allocation. Health systems can apply these findings to aid in early identification and intervention to reduce preventable blindness and institute appropriate rehabilitation services.

Electronegative electroretinogram in the modern multimodal imaging era.

BACKGROUND: The electronegative electroretinogram (ERG) reflecting inner retinal dysfunction can assist as a diagnostic tool to determine the anatomical location in eye disease. The aim of this study is to determine the frequency and aetiology of electronegative ERG in a tertiary ophthalmology centre and to develop a clinical algorithm to assist patient management. METHODS: Retrospective review of ERGs performed at the Save Sight Institute from January 2011 to December 2020. ERGs were performed according to ISCEV standard. The b:a ratio was analysed in dark adapted (DA) 3.0 or 12.0 recordings. Patients with ratio of ≤1.0 were included. RESULTS: A total of 4421 patients had ERGs performed during study period, of which 139 patients (3.1%) had electronegative ERG. The electronegative ERG patients' median age at referral time was 37 (0.7-90.6) years. The causative aetiologies were photoreceptor dystrophy (48, 34.5%), Congenital Stationary Night Blindness (CSNB) (33, 23.7%), retinal ischemia (18, 12.9%), retinoschisis (15, 10.8%), paraneoplastic autoimmune retinopathy (PAIR) and nonPAIR (14, 10.1%), batten disease (4, 2.9%), and inflammatory retinopathy (4, 2.9%). There were three patients with an unclassified diagnosis. Thirty-two patients (23%) had good vision and a normal fundus appearance. Eleven patients (7.9%) had good vision and normal results in all multimodal imaging. CONCLUSIONS: The frequency of electronegative ERG in our referral centre was 3.1% with photoreceptor dystrophy as the main aetiology. A significant number of the cases had good vision with normal fundus or normal multimodal imaging. This further highlights the value of an ERG in this modern multimodal imaging era.

MERTK retinopathy: biomarkers assessing vision loss.

PURPOSE: Mer tyrosine kinase-retinitis pigmentosa (MERTK-RP) causes a primary defect in the retinal pigment epithelium, which subsequently affects rod and cone photoreceptors. The study aims to identify the most appropriate MERTK-RP biomarkers to measure disease progression for deciding the optimum therapeutic trial intervention time. MATERIALS AND METHODS: Patients' data from baseline (BL) and last follow-up (LFU) were reviewed. Best corrected visual acuity (BCVA), spectral domain-optical coherence tomography (SD-OCT), ultra-widefield fundus autofluorescence (UWF-FAF) patterns, kinetic perimetry (KP), and electroretinography (ERG) parameters were analyzed. RESULTS: Five patients were included with the mean age of 17.7 ± 14.4 years old (6.7-42.3) at BL and mean BCVA follow-up of 8.4 ± 5.1 years. Mean BCVA at BL and LFU were 0.84 ± 0.86 LogMAR and 1.14 ± 0.86 LogMAR, respectively. The BCVA decline rate was 0.05 ± 0.03 LogMAR units/year. Ellipzoid zones (EZ) were measurable in eight eyes with mean BL length of 1293.75 ± 421.07 µm and reduction of 140.95 ± 69.28 µm/year and mean BL CMT of 174.2 ± 37.52 µm with the rate of 11.2 ± 12.77 µm declining/year. Full-field ERG (ffERG) and pattern ERG (pERG) were barely recordable. UWF-FAF showed central macular hyper-autofluorescence (hyperAF). KP (III4e and V4e) was normal in two eyes, restricted nasally in four eyes, superior wedge defect in two eyes and undetectable in two eyes. The four restricted nasally KPs became worse, while the others stayed almost unchanged. CONCLUSIONS: This cohort showed early visual loss, moderately rapid EZ reduction and macular hyperAF. EZ, CMT, and BCVA were consistently reduced. Relative rapid decline in these biomarkers reflecting visual function suggests an early and narrow timespan for intervention.

Heterozygous COL9A3 variants cause severe peripheral vitreoretinal degeneration and retinal detachment.

The COL9A3 gene encodes one of the three alpha chains of Type IX collagen, with heterozygous variants reported to cause multiple epiphyseal dysplasia, and suggested as contributory in some cases of sensorineural hearing loss. Patients with homozygous variants have midface hypoplasia, myopia, sensorineural hearing loss, epiphyseal changes and carry a diagnosis of Stickler syndrome. Variants in COL9A3 have not previously been reported to cause vitreoretinal degeneration and/or retinal detachments. This report describes two families with autosomal dominant inheritance and predominant features of peripheral vitreoretinal lattice degeneration and retinal detachment. Genomic sequencing revealed a heterozygous splice variant in COL9A3 [NG_016353.1(NM_001853.4):c.1107 + 1G>C, NC_000020.10(NM_001853.4):c.1107 + 1G>C, LRG1253t1] in Family 1, and a heterozygous missense variant [NG_016353.1(NM_001853.4):c.388G>A p.(Gly130Ser)] in Family 2, each segregating with disease. cDNA studies of the splice variant demonstrated an in-frame deletion in the COL2 domain, and the missense variant occurred in the COL3 domain, both indicating the critical role of Type IX collagen in the vitreous base of the eye.

Surgical Treatment for SWS Glaucoma: Experience From a Tertiary Referral Pediatric Hospital.

PRECIS: Glaucoma associated with Sturge-Weber syndrome (SWS) often requires surgical intervention. Our study shows that trabeculectomy is efficacious in treating this condition. PURPOSE: The purpose of this study was to describe the surgical outcomes of glaucoma associated with SWS in children presenting to the tertiary Paediatric Ophthalmology Department at The Children's Hospital at Westmead. MATERIALS AND METHODS: A retrospective study of patients with SWS referred to the Department of Ophthalmology at The Children's Hospital at Westmead between 2003 and 2016 with at least 2 years of follow-up were identified, and information was collected from the clinical notes of all subjects. RESULTS: A total of 27 patients with SWS were evaluated for glaucoma in which 8 were excluded due to inadequate follow-up. In total, 19 patients with SWS were included in this study in which glaucoma was diagnosed in 15 patients and 19 eyes, of which 13 eyes required glaucoma surgery. A total of 21 surgical procedures were performed with a median follow-up of 85 months. A primary trabeculotomy was performed in 5 eyes of which 4 required re-do trabeculotomy, and 3 of these eyes underwent a Baerveldt tube (BVT) shunt as a third procedure. One eye with a primary trabeculotomy underwent a BVT as a secondary procedure. A BVT was inserted in a total of 6 eyes in which it was a primary procedure in 2 eyes. Of the 6 eyes undergoing a BVT insertion, 5 achieved success (2 complete and 3 qualified), and 1 failed. One case underwent intraluminal stent removal. Six eyes underwent a primary trabeculectomy and needed no further surgical intervention. In the trabeculectomy group, 4 eyes achieved complete success and 2 eyes achieved qualified success. CONCLUSIONS: Glaucoma affects a significant proportion of patients with SWS and is associated with the presence of an ipsilateral port-wine stain in most cases. In our study, trabeculectomy was the most efficacious procedure for controlling intraocular pressure and reducing the burden of ongoing treatment in SWS-associated glaucoma.

Revealing hidden genetic diagnoses in the ocular anterior segment disorders.

PURPOSE: Ocular anterior segment disorders (ASDs) are clinically and genetically heterogeneous, and genetic diagnosis often remains elusive. In this study, we demonstrate the value of a combined analysis protocol using phenotypic, genomic, and pedigree structure data to achieve a genetic conclusion. METHODS: We utilized a combination of chromosome microarray, exome sequencing, and genome sequencing with structural variant and trio analysis to investigate a cohort of 41 predominantly sporadic cases. RESULTS: We identified likely causative variants in 54% (22/41) of cases, including 51% (19/37) of sporadic cases and 75% (3/4) of cases initially referred as familial ASD. Two-thirds of sporadic cases were found to have heterozygous variants, which in most cases were de novo. Approximately one-third (7/22) of genetic diagnoses were found in rarely reported or recently identified ASD genes including PXDN, GJA8, COL4A1, ITPR1, CPAMD8, as well as the new phenotypic association of Axenfeld-Rieger anomaly with a homozygous ADAMTS17 variant. The remainder of the variants were in key ASD genes including FOXC1, PITX2, CYP1B1, FOXE3, and PAX6. CONCLUSIONS: We demonstrate the benefit of detailed phenotypic, genomic, variant, and segregation analysis to uncover some of the previously "hidden" heritable answers in several rarely reported and newly identified ocular ASD-related disease genes.

Outcome measures in juvenile X-linked retinoschisis: A systematic review.

X-linked retinoschisis (XLRS) is a leading cause of hereditary juvenile macular degeneration in males resulting in significant vision impairment. Outcome measures to monitor disease progression or therapeutic interventions have evolved with technology. A systematic review was undertaken to evaluate outcome measures for XLRS. Inclusion criteria were all publications examining outcome measures for natural history studies or following an interventional approach for patients with XLRS. Studies which did not present follow-up data were excluded. We searched medical databases including CENTRAL, Ovid Medline, pre-Medline and ahead of Print up to February 2019. Two authors independently assessed the risk of bias. Twelve studies meet the inclusion criteria with four prospective and eight retrospective case series. Five series were natural history observational studies and seven were interventional series using either topical or systemic carbonic anhydrase inhibitors. Visual acuity (VA) declined very slowly in the natural history studies equivalent to 0.22-0.5 letters per year. Five of the six interventional studies showed an improvement in VA and four a reduction in spectral domain optical coherence tomography (SD-OCT) parameters for central macular thickness (CMT). The full-field electroretinogram identified the 30-Hz latency as a further parameter to monitor function. VA was the measure most likely to show a statistically significant outcome. How functionally meaningful this is, requires further evaluation. CMT SD-OCT outcomes are variable depending on cystic changes. More refined measures are required to better correlate structure with function.

Biomarkers in Usher syndrome: ultra-widefield fundus autofluorescence and optical coherence tomography findings and their correlation with visual acuity and electrophysiology findings.

PURPOSE: To investigate the functional and structural biomarkers and their correlation with Usher syndrome (USH). METHODS: Medical records, imaging and electrophysiology test results of USH patients attending the Save Sight Institute between 2012 and 2017 were reviewed. Best corrected visual acuity (BCVA), ultra-widefield autofluorescence (UW-FAF), spectral-domain optical coherence tomography (SD-OCT), full-field electroretinogram and pattern electroretinogram (pERG) were performed. SD-OCT scans assessed central macular thickness (CMT), greatest linear diameter of preserved outer retinal layers-macular island (MI) and presence of cystoid macular edema (CME). UW-FAF images were qualitatively graded to identify hypo/hyperfluorescence patterns in the peripheral fundus. RESULTS: Thirty-six eyes from 18 subjects were included. Mean BCVA was 0.22 ± 0.3 LogMAR. MI extent was significantly associated with better vision (ß = - 0.175 per 1000 µm; R2 = 0.487; P = 0.002; Fig. 4). A higher pERG P50 was associated with a larger macular island (ß = 782 per µV; R2 = 0.238; P = 0.025), while a higher pERG N95 was associated with a smaller macular island (ß = - 499 per µV; R2 = 0.219; P = 0.030). Mean CMT was 271 ± 35 µm and was significantly associated with better vision (ß = - 0.083 per 10 µm; R2 = 0.612; P < 0.001). CME was diagnosed in 47.2% (n = 17) eyes. There was no significant difference in mean BCVA for those with CME (0.19 ± 0.2 LogMAR) and without CME (0.40 ± 0.5; R2 = 0.081; P = 0.17). All patients had abnormal UW-FAF. Four main patterns of change were identified (granular 55%, annular 11%, bone spicule 17% and patchy 17%). Patients with the patchy pattern demonstrated worse BCVA in comparison with those with granular (P < 0.0001) and bone spicule (P = 0.0179) patterns. CONCLUSIONS: Structural changes identified on OCT and UW-FAF correlated with BCVA and pERG in this cohort representing different stages of the disease. These parameters could represent reliable biomarkers in therapeutic clinical trials on USH.

Neurofibromatosis Type 1: Review and Update on Emerging Therapies.

Neurofibromatosis type 1 is an autosomal dominant neurocutaneous disorder affecting 1 in 3000 births. This familial tumor predisposition syndrome is diagnosed clinically and affects the skin, bones, and nervous system. Malignant tumors can arise in childhood or adulthood and are the most common cause of mortality in this population. Early diagnosis and management led by a multidisciplinary team remains the standard of care, particularly in the management of optic pathway glioma. Emerging concepts in the genetic patterns of this condition have led to the introduction of new treatment modalities that target the mitogen-activated protein kinase and the mammalian target of rapamycin pathways. In this review, the role of the ophthalmologist and approach to screening for optic pathway glioma are outlined based on previous recommendations. Updates on choroidal involvement, as a diagnostic criterion, will also be discussed, further highlighting the pivotal role of the ophthalmologist in the diagnosis and management of this complex condition.

Investigation of clinically relevant germline variants detected by next-generation sequencing in patients with childhood cancer: a review of the literature.

Genetic predisposition is an important underlying cause of childhood cancer, although the proportion of patients with childhood cancer carrying predisposing pathogenic germline variants is uncertain. This review considers the pathogenic or likely pathogenic germline variants reported by six studies that used next-generation sequencing to investigate genetic predisposition in selected cohorts of patients with childhood cancer and used incompletely overlapping gene sets for analysis and interpretation. These six studies reported that 8.5%-35.5% of patients with childhood cancer carried clinically relevant germline variants. Analysis of 52 autosomal dominant cancer predisposition genes assumed common to all six studies showed that 5.5%-25.8% of patients with childhood cancer carried pathogenic or likely pathogenic germline variants in at least one of these genes. When only non-central nervous system solid tumours (excluding adrenocortical carcinomas) were considered, 8.5%-10.3% of the patients carried pathogenic or likely pathogenic germline variants in at least one of 52 autosomal dominant cancer predisposition genes. There was a lack of concordance between the genotype and phenotype in 33.3%-57.1% of the patients reported with pathogenic or likely pathogenic germline variants, most of which represented variants in autosomal dominant cancer predisposition genes associated with adult onset cancers. In summary, germline genetic testing in patients with childhood cancer requires clear definition of phenotypes and genes considered for interpretation, with potential to inform and broaden childhood cancer predisposition syndromes.

Changing patterns in paediatric optic atrophy aetiology: 1979 to 2015.

BACKGROUND: To evaluate the aetiology of paediatric optic atrophy in an Australian population. DESIGN: Retrospective review of medical records was conducted at The Children's Hospital at Westmead, Sydney, Australia. PARTICIPANTS: Two hundred twenty-seven subjects <16 years who were diagnosed with optic atrophy on fundoscopic examination between 1979 and 2015 were included in the study. METHODS: Subjects were obtained from the hospital database, which codes diagnoses for all admissions, as well as the orthoptic department database, which codes diagnoses for ophthalmology department outpatients. MAIN OUTCOME MEASURES: The predominant cause for optic atrophy was assigned to each patient. Clinical presentation was defined as the principal reason for evaluation. Demographic data included gender, affected eye and age at diagnosis. Data on medical comorbidities (cerebral palsy, developmental delay, microcephaly and seizures) and ocular comorbidities (strabismus and nystagmus) were collected. RESULTS: The mean age at initial eye review was 4.7 ± 4.4 years. There was bilateral optic atrophy in 81.5% of cases. Unilateral optic atrophy was largely due to tumours. When analysing over the three time periods, (1979-1990, 1991-2003 and 2004-2015), perinatal events (3.0%, 22.7% and 22.6%) and neurodegenerative disease (3.0%, 14.9% and 15.1%) are slowly replacing tumours (39.4%, 24.8% and 15.1%) as the top causes for paediatric optic atrophy. The incidence of other causes has remained fairly stable over time, albeit an increase in idiopathic causes. CONCLUSIONS: There has been shift in the etiological profile of optic atrophy. Whilst tumours are still an important cause of paediatric optic atrophy for an Australian population, perinatal events and neurodegenerative disease are becoming more significant.

Sporadic and Familial Congenital Cataracts: Mutational Spectrum and New Diagnoses Using Next-Generation Sequencing.

Congenital cataracts are a significant cause of lifelong visual loss. They may be isolated or associated with microcornea, microphthalmia, anterior segment dysgenesis (ASD) and glaucoma, and there can be syndromic associations. Genetic diagnosis is challenging due to marked genetic heterogeneity. In this study, next-generation sequencing (NGS) of 32 cataract-associated genes was undertaken in 46 apparently nonsyndromic congenital cataract probands, around half sporadic and half familial cases. We identified pathogenic variants in 70% of cases, and over 68% of these were novel. In almost two-thirds (20/33) of these cases, this resulted in new information about the diagnosis and/or inheritance pattern. This included identification of: new syndromic diagnoses due to NHS or BCOR mutations; complex ocular phenotypes due to PAX6 mutations; de novo autosomal-dominant or X-linked mutations in sporadic cases; and mutations in two separate cataract genes in one family. Variants were found in the crystallin and gap junction genes, including the first report of severe microphthalmia and sclerocornea associated with a novel GJA8 mutation. Mutations were also found in rarely reported genes including MAF, VIM, MIP, and BFSP1. Targeted NGS in presumed nonsyndromic congenital cataract patients provided significant diagnostic information in both familial and sporadic cases.

Primary congenital glaucoma outcomes: lessons from 23 years of follow-up.

PURPOSE: To determine in primary congenital glaucoma whether age of presentation influences surgical success, the degrees of angle surgery needed to achieve glaucoma control, and whether there are critical ages where glaucoma progresses, requiring further surgical management. DESIGN: Retrospective cohort study. METHODS: The medical records of patients with primary congenital glaucoma over a 23-year period were reviewed: 192 procedures were performed on 117 eyes (70 patients). The number and age of angle procedures and final visual acuity was analyzed. Surgical success was defined as stable intraocular pressure and optic disc appearance. RESULTS: Procedures involving 83 of the 110 eyes (75.5%) undergoing angle surgery were successful, with 2-, 4-, 6-, and 10-year success rates of 92%, 86%, 84%, and 75%, respectively. Subgroup analysis (<3 months; 3-6 months; >6 months) comparing age of diagnosis to visual outcome (<20/200, 20/200-20/40, >20/40) was significant (P = .04). The age at first operation (P = .94), the number of angle operations (P = .43), and their effect on angle surgery success was not significant. Seven of 192 operations were performed after the age of 8 years (3.6%). After the initial angle surgeries within the first year of life, the third procedure occurred at a median age of 2.4 years (interquartile ratio [IQR] 0.6-3.8 years) and the fourth procedure occurred at a median age of 5.3 years (IQR 2.5-6.1 years). CONCLUSIONS: Children diagnosed at <3 months of age had a visual outcome of <20/200 despite successful glaucoma control. Age of presentation did not affect surgical success. A total of 78.9% of cases undergoing primary trabeculotomy were controlled with 1 operation: 4 clock hours of angle (120 degrees). Analysis of glaucoma progression suggests critical ages where further glaucoma surgery is required at around 2 and 5 years of age.

Advantage of Whole Exome Sequencing over Allele-Specific and Targeted Segment Sequencing in Detection of Novel TULP1 Mutation in Leber Congenital Amaurosis.

BACKGROUND: Leber congenital amaurosis (LCA) is a severe form of retinal dystrophy with marked underlying genetic heterogeneity. Until recently, allele-specific assays and Sanger sequencing of targeted segments were the only available approaches for attempted genetic diagnosis in this condition. A broader next-generation sequencing (NGS) strategy, such as whole exome sequencing, provides an improved molecular genetic diagnostic capacity for patients with these conditions. MATERIALS AND METHODS: In a child with LCA, an allele-specific assay analyzing 135 known LCA-causing variations, followed by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and SnpEff to annotate the variants. RESULTS: No disease-causing variants were found using the allele-specific or targeted segment Sanger sequencing assays. Analysis of variants in the exome sequence data revealed a novel homozygous nonsense mutation (c.1081C > T, p.Arg361*) in TULP1, a gene with roles in photoreceptor function where mutations were previously shown to cause LCA and retinitis pigmentosa. The identified homozygous variant was the top candidate using both bioinformatic pipelines. CONCLUSIONS: This study highlights the value of the broad sequencing strategy of exome sequencing for disease gene identification in LCA, over other existing methods. NGS is particularly beneficial in LCA where there are a large number of causative disease genes, few distinguishing clinical features for precise candidate disease gene selection, and few mutation hotspots in any of the known disease genes.

Detection of chromosomal breakpoints in patients with developmental delay and speech disorders.

Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7-11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).

Exome sequencing in developmental eye disease leads to identification of causal variants in GJA8, CRYGC, PAX6 and CYP1B1.

Developmental eye diseases, including cataract/microcornea, Peters anomaly and coloboma/microphthalmia/anophthalmia, are caused by mutations encoding many different signalling and structural proteins in the developing eye. All modes of Mendelian inheritance occur and many are sporadic cases, so provision of accurate recurrence risk information for families and affected individuals is highly challenging. Extreme genetic heterogeneity renders testing for all known disease genes clinically unavailable with traditional methods. We used whole-exome sequencing in 11 unrelated developmental eye disease patients, as it provides a strategy for assessment of multiple disease genes simultaneously. We identified five causative variants in four patients in four different disease genes, GJA8, CRYGC, PAX6 and CYP1B1. This detection rate (36%) is high for a group of patients where clinical testing is frequently not undertaken due to lack of availability and cost. The results affected clinical management in all cases. These variants were detected in the cataract/microcornea and Peters anomaly patients. In two patients with coloboma/microphthalmia, variants in ABCB6 and GDF3 were identified with incomplete penetrance, highlighting the complex inheritance pattern associated with this phenotype. In the coloboma/microphthalmia patients, four other variants were identified in CYP1B1, and CYP1B1 emerged as a candidate gene to be considered as a modifier in coloboma/microphthalmia.