Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations.

PURPOSE: Current sequencing strategies can genetically solve 55-60% of inherited retinal degeneration (IRD) cases, despite recent progress in sequencing. This can partially be attributed to elusive pathogenic variants (PVs) in known IRD genes, including copy-number variations (CNVs), which have been shown as major contributors to unsolved IRD cases. METHODS: Five hundred IRD patients were analyzed with targeted next-generation sequencing (NGS). The NGS data were used to detect CNVs with ExomeDepth and gCNV and the results were compared with CNV detection with a single-nucleotide polymorphism (SNP) array. Likely causal CNV predictions were validated by quantitative polymerase chain reaction (qPCR). RESULTS: Likely disease-causing single-nucleotide variants (SNVs) and small indels were found in 55.6% of subjects. PVs in USH2A (11.6%), RPGR (4%), and EYS (4%) were the most common. Likely causal CNVs were found in an additional 8.8% of patients. Of the three CNV detection methods, gCNV showed the highest accuracy. Approximately 30% of unsolved subjects had a single likely PV in a recessive IRD gene. CONCLUSION: CNV detection using NGS-based algorithms is a reliable method that greatly increases the genetic diagnostic rate of IRDs. Experimentally validating CNVs helps estimate the rate at which IRDs might be solved by a CNV plus a more elusive variant.

Contribution of noncoding pathogenic variants to RPGRIP1-mediated inherited retinal degeneration.

PURPOSE: With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision-making. Yet the genetic cause of disease cannot be identified using exon-based sequencing for a significant portion of patients. We hypothesized that noncoding pathogenic variants contribute significantly to the genetic causality of IRDs and evaluated patients with single coding pathogenic variants in RPGRIP1 to test this hypothesis. METHODS: IRD families underwent targeted panel sequencing. Unsolved cases were explored by exome and genome sequencing looking for additional pathogenic variants. Candidate pathogenic variants were then validated by Sanger sequencing, quantitative polymerase chain reaction, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing. RESULTS: Among 1722 families, 3 had biallelic loss-of-function pathogenic variants in RPGRIP1 while 7 had a single disruptive coding pathogenic variants. Exome and genome sequencing revealed potential noncoding pathogenic variants in these 7 families. In 6, the noncoding pathogenic variants were shown to lead to loss of function in vitro. CONCLUSION: Noncoding pathogenic variants were identified in 6 of 7 families with single coding pathogenic variants in RPGRIP1. The results suggest that noncoding pathogenic variants contribute significantly to the genetic causality of IRDs and RPGRIP1-mediated IRDs are more common than previously thought.

The genomic landscape of epithelioid sarcoma cell lines and tumours.

We carried out whole genome and transcriptome sequencing on four tumour/normal pairs of epithelioid sarcoma. These index cases were supplemented with whole transcriptome sequencing of three additional tumours and three cell lines. Unlike rhabdoid tumour (the other major group of SMARCB1-negative cancers), epithelioid sarcoma shows a complex genome with a higher mutational rate, comparable to that of ovarian carcinoma. Despite this mutational burden, SMARCB1 mutations remain the most frequently recurring event and are probably critical drivers of tumour formation. Several cases show heterozygous SMARCB1 mutations without inactivation of the second allele, and we explore this further in vitro. Finding CDKN2A deletions in our discovery cohort, we evaluated CDKN2A protein expression in a tissue microarray. Six out of 16 cases had lost CDKN2A in greater than or equal to 90% of cells, while the remaining cases had retained the protein. Expression analysis of epithelioid sarcoma cell lines by transcriptome sequencing shows a unique profile that does not cluster with any particular tissue type or with other SWI/SNF-aberrant lines. Evaluation of the levels of members of the SWI/SNF complex other than SMARCB1 revealed that these proteins are expressed as part of a residual complex, similarly to previously studied rhabdoid tumour lines. This residual SWI/SNF is susceptible to synthetic lethality and may therefore indicate a therapeutic opportunity.

Diagnostic value of next-generation sequencing in an unusual sphenoid tumor.

Extraordinary advancements in sequencing technology have made what was once a decade-long multi-institutional endeavor into a methodology with the potential for practical use in a clinical setting. We therefore set out to examine the clinical value of next-generation sequencing by enrolling patients with incurable or ambiguous tumors into the Personalized OncoGenomics initiative at the British Columbia Cancer Agency whereby whole genome and transcriptome analyses of tumor/normal tissue pairs are completed with the ultimate goal of directing therapeutics. First, we established that the sequencing, analysis, and communication with oncologists could be completed in less than 5 weeks. Second, we found that cancer diagnostics is an area that can greatly benefit from the comprehensiveness of a whole genome analysis. Here, we present a scenario in which a metastasized sphenoid mass, which was initially thought of as an undifferentiated squamous cell carcinoma, was rediagnosed as an SMARCB1-negative rhabdoid tumor based on the newly acquired finding of homozygous SMARCB1 deletion. The new diagnosis led to a change in chemotherapy and a complete nodal response in the patient. This study also provides additional insight into the mutational landscape of an adult SMARCB1-negative tumor that has not been explored at a whole genome and transcriptome level.

Belzutifan in Individuals with von Hippel-Lindau Retinal Hemangioblastomas: Institutional Experience and Review of the Literature.

Introduction: The systemic HIF-2 alpha inhibitor, belzutifan, has been approved for use in patients with von Hippel-Lindau disease (VHL)-associated renal cell carcinoma, central nervous system (CNS) hemangioblastomas, and pancreatic neuroendocrine tumors. This drug has also shown promise in controlling VHL retinal hemangioblastomas (RHs), but little work has been published on the use of the drug in this setting. Methods: We conducted a retrospective review of patients with VHL-associated RHs followed by the retina service at our institution who were treated with systemic belzutifan. Patient age, gender, genotype, presence of systemic tumors, indication for the drug, initial dose, adjusted dose, side effects, and tumor response were recorded. We also conducted a literature search for all manuscripts describing the effect of belzutifan on VHL-associated ocular tumors. Results: We identified 12 eyes of 7 patients with VHL-associated ocular tumors who were treated with belzutifan at our institution. Of these, 5 eyes of 3 patients had progressing ocular tumors when belzutifan was started. Of the 7 total patients, 2 were treated for renal cell carcinoma, 2 for CNS hemangioblastomas, 2 for RHs, and one for pancreatic neuroendocrine tumors. Initial dose was 120 mg PO daily in 6 patients and 80 mg PO daily in 1 patient. The dose was reduced in all but 1 patient due to side effects. The ocular tumors were controlled in all patients with an average follow-up of 13 months (range 4-24 months). Literature review identified 7 manuscripts that described belzutifan-mediated control of ocular tumors in patients with VHL-associated RHs in 21 patients. Conclusion: The drug belzutifan shows great promise for controlling RHs and preventing vision loss in patients with VHL. Further work needs to address the optimal dose, role of the drug as a neoadjuvant therapy, and long-term efficacy and tolerability of the drug in a larger cohort of patients with ocular tumors.

Scientific overview: CSCI-CITAC annual general meeting and young investigator's forum 2011.

In 2011, members of the Clinician Investigator Trainee Association of Canada - Association des cliniciens-chercheurs en formation du Canada (CITAC-ACCFC) and the Canadian Society for Clinician Investigators (CSCI) held a joint Annual General Meeting (AGM) and Young Investigator Forum (YIF) September 12-14 in Ottawa, ON, Canada. The theme of the meeting was "The Role of Government and Regulatory Organizations in Shaping the Environment of the Clinician Scientist". The meeting was well attended by established clinician scientists and clinician investigator trainees from across Canada. The aim of this scientific overview is to highlight the research presented by trainees at both the oral plenary session as well as the poster presentation sessions of this meeting. This work covers a wide variety of medical disciplines, focusing on translational medicine, from the basic sciences to clinical application.

The effect of ocular rinse volume on surface irritation after povidone-iodine preparation for intravitreal injections: a randomized controlled trial.

PURPOSE: To evaluate whether the volume of wash out rinse after povidone iodine (PI) application for intravitreal injections (IVI) affects patients' ocular surface irritation. METHODS: This was a prospective, single-masked, randomized-controlled trial consisting of 142 subjects. A total of 51, 45, and 46 patients received 3-mL, 10-mL, and 15-mL of ocular rinse respectively. Reductions in the Ocular Surface Disease Index (OSDI) and the Standardized Patient Evaluation of Eye Dryness II (SPEED II) surveys, conducted before and at 24-72 h post-injection, were analyzed. RESULTS: There was no statistical difference in objective dry eye findings of Schirmer test (p-value = 0.788), tear break-up time (p-value = 0.403), Oxford fluorescein grade (p-value = 0.424) between the study groups prior to injections. Dry eye symptoms as measured by reductions in the OSDI and SPEEDII scores were not different between the study groups (p-value = 0.0690 and 0.6227, respectively). CONCLUSION: There is no difference in patients' ocular surface irritation between 3-mL, 10-mL, and 15-mL post injection rinse. Given the large number of IVIs performed, modification of practice patterns based on these findings could lead to significant reduction in global cost burden for IVIs.

Utility of No-Charge Panel Genetic Testing for Inherited Retinal Diseases in a Real-World Clinical Setting.

Purpose: To show the utility of genetic testing in inherited retinal disease (IRD) patients. Methods: This retrospective cohort study was performed at a single academic center and comprised 59 patients clinically diagnosed with IRD who had testing via the Invitae IRD Panel (Invitae Corp). Samples were collected from August 2019 to April 2021. The rates of genetic diagnosis and disease-category specific results (ie, positive, undetermined, negative) were assessed. Results: Testing results were returned a mean of 20 days (range, 14-28 days) after submission. Of the samples, 50.8% (30/59) had a diagnostic yield. By disease category, the yield was 46.4% (13/28) nonsyndromic retinitis pigmentosa (RP), 50.0% (4/8) syndromic RP, 46.2% (6/13) macular dystrophies, 75.0% (3/4) cone or cone-rod dystrophies, and 80.0% (4/5) other retinopathies; there were no cases of rod dystrophies. The results were undetermined in 47.5% of patients (28/59) because of identification of only 1 recessive mutation (5.1%; 3/59), 1 recessive mutation and at least 1 variant of uncertain significance (VUS) (13.6%; 8/59), or VUS only (28.8%; 17/59). One patient (1.7%) received negative testing results with no mutations or VUS identified. Conclusions: Open-access, no-charge panel testing offers a reasonable diagnostic yield. Accurate clinical diagnosis of IRD before testing and acknowledgment of the limitations of panel testing are critical. The results add to the current estimates of the value of genetic testing for retina specialists in the management of IRD.

Migration of a Dexamethasone Intravitreal Implant to the Anterior Chamber in a Patient with a Intra-Scleral Haptic Fixated Intraocular Lens.

PURPOSE: To report a case of posterior to anterior migration of a dexamethasone (Ozurdex) implant in a case of scleral-fixated intraocular lens (SFIOL) via Yamane technique. METHODS/PATIENTS: Single case report. RESULTS: Dexamethasone implant was successfully removed in the operating room. The patient had improved confrontational visual field and did not develop corneal edema nor intraocular pressure elevation. CONCLUSION: In the presence of a stable SFIOL via Yamane technique, posterior chamber implants may migrate to the anterior chamber. Clinicians may wish to exercise additional caution in injecting posterior chamber steroid implants in this patient population.

Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR.

Pseudomonas aeruginosa exhibits swarming motility on semisolid surfaces (0.5 to 0.7% agar). Swarming is a more than just a form of locomotion and represents a complex adaptation resulting in changes in virulence gene expression and antibiotic resistance. In this study, we used a comprehensive P. aeruginosa PA14 transposon mutant library to investigate how the complex swarming adaptation process is regulated. A total of 233 P. aeruginosa PA14 transposon mutants were verified to have alterations in swarming motility. The swarming-associated genes functioned not only in flagellar or type IV pilus biosynthesis but also in processes as diverse as transport, secretion, and metabolism. Thirty-three swarming-deficient and two hyperswarming mutants had transposon insertions in transcriptional regulator genes, including genes encoding two-component sensors and response regulators; 27 of these insertions were newly identified. Of the 25 regulatory mutants whose swarming motility was highly impaired (79 to 97%), only 1 (a PA1458 mutant) had a major defect in swimming, suggesting that this regulator might influence flagellar synthesis or function. Twitching motility, which requires type IV pili, was strongly affected in only two regulatory mutants (pilH and PA2571 mutants) and was moderately affected in three other mutants (algR, ntrB, and nosR mutants). Microarray analyses were performed to compare the gene expression profile of a swarming-deficient PA3587 mutant to that of the wild-type PA14 strain under swarming conditions. PA3587 showed 63% homology to metR, which encodes a regulator of methionine biosynthesis in Escherichia coli. The observed dysregulation in the metR mutant of nine different genes required for swarming motility provided a possible explanation for the swarming-deficient phenotype of this mutant.

Comparison of Sulfur Hexafluoride (SF6) and Air Tamponade in Noniridectomized Descemet Membrane Endothelial Keratoplasty.

PURPOSE: To compare the efficacy and safety of 20% sulfur hexafluoride gas (SF6) and air tamponade in patients who underwent noniridectomized Descemet membrane endothelial keratoplasty (DMEK). METHODS: A retrospective chart review of patients who underwent DMEK with either air or SF6 tamponade: 41 eyes received air tamponade (group 1) and 41 received SF6 tamponade (group 2). Best spectacle-corrected visual acuity, endothelial cell density, and complications including graft detachment and elevated intraocular pressure were compared. RESULTS: The mean follow-up time was 8 ± 4 months in group 1 and 3 ± 2 months in group 2. Mean best spectacle-corrected visual acuity improved from 1.12 ± 0.88 to 0.64 ± 0.78 logarithm of the minimum angle of resolution (logMAR) in group 1 (P = 0.009) and from 1.00 ± 0.78 to 0.62 ± 0.53 logMAR in group 2 (P = 0.006). The graft detachment rate was 39% (16 eyes) in group 1 and 42% (17 eyes) in group 2 (P = 0.822). The rate of graft detachment larger than one third of the graft area was 17% in group 1 and 20% in group 2 (P = 0.775). Rebubbling was performed in 26.8% and 20% of eyes in group 1 and 2, respectively (P = 0.43). Average endothelial cell loss was 32% in group 1 and 33% in group 2 (P = 0.83). In the immediate postoperative period, elevated intraocular pressure was observed in 2 eyes (5%) in group 1 and in 4 eyes (10%) in group 2 (P = 0.4). There was 1 primary graft failure in each group. CONCLUSIONS: Use of air with it being readily available and short acting is a good method of Descemet membrane tamponade in noniridectomized DMEK.

The driver landscape of sporadic chordoma.

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma.

Cancer genomics: why rare is valuable.

Rare conditions are sometimes ignored in biomedical research because of difficulties in obtaining specimens and limited interest from fund raisers. However, the study of rare diseases such as unusual cancers has again and again led to breakthroughs in our understanding of more common diseases. It is therefore unsurprising that with the development and accessibility of next-generation sequencing, much has been learnt from studying cancers that are rare and in particular those with uniform biological and clinical behavior. Herein, we describe how shotgun sequencing of cancers such as granulosa cell tumor, endometrial stromal sarcoma, epithelioid hemangioendothelioma, ameloblastoma, small-cell carcinoma of the ovary, clear-cell carcinoma of the ovary, nonepithelial ovarian tumors, chondroblastoma, and giant cell tumor of the bone has led to rapidly translatable discoveries in diagnostics and tumor taxonomies, as well as providing insights into cancer biology.