Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads.

Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.

Autologous internal limiting membrane transplantation achieves anatomic closure and functional improvement in the treatment of large, persistent macular holes.

PURPOSE: To evaluate the clinical outcome of subretinal autologous internal limiting membrane (ILM) transplantation during pars-plana vitrectomy for persistent full-thickness macular hole (FTMH) repair. METHODS: Retrospective, consecutive case series of 13 eyes (13 patients) undergoing small-incision vitrectomy with ILM transplantation and air tamponade for large persistent FTMH after prior unsuccessful vitrectomy with posterior hyaloid detachment and ILM peeling. MAIN OUTCOME MEASUREMENTS: For all eyes, high-definition spectral domain optical coherence tomography scans (SD-OCT Spectralis, Heidelberg Engineering GmbH, Germany) of the macula were routinely performed before surgery, 1 and 4 weeks after surgery, and at the final follow-up visit. Additionally, age, gender, axial length, macular hole diameter, biomicroscopic fundus evaluation and best-corrected visual acuity (BCVA) at baseline, 1 and 4 weeks after surgery, and at the final follow-up visit were analyzed. RESULTS: Anatomic closure was achieved in all 13 cases (100% success rate). Closure pattern was classified in accordance with to Rossi et al. (Graefe's Arch Clin Exp Ophthalmol 258(12):2629-2638, 2020). Mean baseline BCVA logMAR was 0.93, mean postoperative BCVA logMAR was 0.66 with a mean postoperative follow-up period of 11.4 months. No re-opening occurred during the observation period. CONCLUSIONS: Placing an autologous ILM-transplant in the subretinal space beneath the margin of the FTMH can support anatomic restauration and functional improvement in large, persistent FTMHs.

Relaxing radial retinal incisions for the treatment of persistent macular holes.

PURPOSE: Various surgical techniques have been described for managing persistent macular holes after an unsuccessful vitrectomy with internal limiting membrane (ILM) peeling. However, the closure and functional improvement rates after these procedures are limited. Therefore, the aim of this study was to evaluate the usefulness of radial retinal incisions (retinotomies) in eyes with persistent large macula holes despite previous vitrectomy with ILM peeling. DESIGN: In a retrospective case series, closure rate and best-corrected visual acuity (BCVA) were evaluated in eyes with persistent macular holes after an unsuccessful vitrectomy that included posterior vitreous detachment and ILM peeling. SUBJECTS: 22 eyes of 22 patients (10 men and 12 women) underwent re-vitrectomy with radial retinal incisions. All the patients had undergone an unsuccessful surgery before. METHODS: Small-incision re-vitrectomy with radial retinal incisions (retinotomies) and air tamponade was performed. MAIN OUTCOME MEASUREMENTS: For all eyes, high-definition SD-OCT scans (SD-OCT Spectralis, Heidelberg Engineering GmbH, Germany) of the macula were routinely performed before surgery; 1 week and 1 month after surgery; and at final follow-up. Additionally, age, gender, axial length, macular hole diameter, biomicroscopic fundus evaluation and best-corrected visual acuity (BCVA) in logMAR and Snellen at baseline, 1 and 4 months after operation, and at the final follow-up visit were analyzed. RESULTS: The mean baseline macular hole diameter was 668.5 ± 226.8 µm. At the final examination, 16 (72.72%) of the 22 macula holes were closed. Visual acuity increased in 17 eyes, was stable in 3 eyes, and decreased in 2 eyes owing to central retinal atrophy in both. The mean BCVA increased from logMAR 1.04 ± 0.29 at baseline to 0.57 ± 0.31 (Snellen 0.11 ± 0.05 to 0.33 ± 0.18). In all successful cases, macula hole closure was attained after 3 days, and none of the eyes showed macula hole recurrence. CONCLUSION: The results of this limited case series suggest that radial retinal incisions of the rim in persistent macula holes after initial surgery with ILM peeling increase the success rate of macula hole closure and results in a relevant increase in BCVA. However, as the number of eyes included in this series is limited, the results must be confirmed in a study with a larger sample size.

Endpoints for clinical trials in ophthalmology.

With the identification of novel targets, the number of interventional clinical trials in ophthalmology has increased. Visual acuity has for a long time been considered the gold standard endpoint for clinical trials, but in the recent years it became evident that other endpoints are required for many indications including geographic atrophy and inherited retinal disease. In glaucoma the currently available drugs were approved based on their IOP lowering capacity. Some recent findings do, however, indicate that at the same level of IOP reduction, not all drugs have the same effect on visual field progression. For neuroprotection trials in glaucoma, novel surrogate endpoints are required, which may either include functional or structural parameters or a combination of both. A number of potential surrogate endpoints for ophthalmology clinical trials have been identified, but their validation is complicated and requires solid scientific evidence. In this article we summarize candidates for clinical endpoints in ophthalmology with a focus on retinal disease and glaucoma. Functional and structural biomarkers, as well as quality of life measures are discussed, and their potential to serve as endpoints in pivotal trials is critically evaluated.

Strabismus Surgery of Consecutive Exotropia.

PURPOSE: The purpose of this study was to determine the surgical outcome, dose-effect (DE), and degree of binocularity in patients undergoing surgery for consecutive exotropia following initial surgery of esotropia. PATIENTS/METHODS: Twenty-one patients were identified. We analyzed the mean angle of deviation pre- and postoperatively as measured with the alternate prism cover test, DE, and binocularity. RESULTS: All patients had had previous strabismus surgery. The surgery for consecutive exotropia had been performed at a mean age of 35.92 ± 18.26 years. In 19 of these patients, surgery of consecutive exotropia involved at least one previously operated extraocular muscle, and the mean interval to the previous surgery was 25.67 ± 16.14 years. The mean angle of deviation (DE) at distance and in the primary position was - 33.43 ± 12.75 prism diopters (PD) preoperatively, + 0.76 ± 7.91 PD 1 week after surgery, and - 7.24 ± 12.14 PD 3 months after surgery. The mean DE was 3.58 ± 1.53 mm/PD at 1 week and 2.70 ± 1.78 mm/PD at 3 months post-surgery. Postoperatively, 62% patients had a binocularity of at least Bagolini positive, 33% had either a positive TNO or Titmus Test, and 24% were Lang I positive (550″). CONCLUSION: Performing strabismus surgery with consecutive exotropia results in restoration of some binocularity in a large number of patients, even in adults, and should be considered as a possibility. The dose-effect is comparable to conventional surgery of exotropia.