Foveal photoreceptor atrophy, persistent fetal vasculature, congenital cataracts, and microphthalmia in a pediatric patient with BCOR-associated oculo-facio-cardio-dental (OFCD) syndrome.

Purpose: To report a case of oculo-facio-cardio-dental (OFCD) syndrome secondary to a novel BCOR variant in a pediatric patient with congenital cataracts, microphthalmia, persistent fetal vasculature (PFV), focal chorioretinal hyperpigmentation, peripheral retinal avascularity, and foveal photoreceptor atrophy. Observations: A 3-month-old female patient was referred for bilateral congenital cataracts with microphthalmia. Her past medical history was significant for syndactyly of the toes, left bifid rib, atrial septal defect, patent ductus arteriosus, mitral regurgitation, pulmonary hypertension, anemia of prematurity, vesicoureteral reflux, and duodenal atresia. Examination under anesthesia revealed persistent fetal vasculature (PFV) with peripheral avascularity, foveal photoreceptor atrophy, and focal chorioretinal hyperpigmentation. A bilateral lensectomy with anterior vitrectomy and posterior capsulotomy were performed. Genetic testing identified a novel heterozygous pathogenic variant in the BCOR gene (c.1612C > T (p.Gln538Ter)), confirming a diagnosis of OFCD syndrome. Conclusions and importance: This case describes novel posterior segment findings in a patient with OFCD. A detailed examination of both anterior and posterior segments in combination with multimodal imaging should be performed in patients suspected of having OFCD, as this may be critical in determining visual potential and appropriate surgical management.

Filamentous RPE Hyperplasia in Combined Hamartoma of the Retina and RPE.

This case report describes a diagnosis of combined hamartoma of the retina and retinal pigment epithelium (RPE) with filamentous RPE hyperplasia in a female child with a history of amblyopia, myopia, and exotropia of the affected eye.

Clinical Outcomes in Patients With Traumatic Dehiscence of Penetrating Keratoplasty Grafts.

PURPOSE: The purpose of this study was to report clinical characteristics and outcomes of surgical repair for patients with traumatic dehiscence of penetrating keratoplasty (PKP) grafts. METHODS: Retrospective, consecutive chart review of patients evaluated at Bascom Palmer Eye Institute between 2015 and 2020 with traumatic dehiscence of penetrating keratoplasty grafts. RESULTS: The study cohort consisted of 65 eyes of 65 patients. The mean age at presentation was 72 years (SD 18), with a male predominance (65%). The most common indications for PKP included keratoconus (42%), corneal scar (31%), and Fuchs corneal dystrophy (8%). Dehiscence occurred as a result of blunt trauma in 94% of cases, and the mean wound length was 6.4 clock hours (SD 2.4), with a predominance of inferior dehiscence. The mean presenting visual acuity (VA) was 2.45 logMAR (SD 0.41), and the mean final VA was 2.17 logMAR (SD 0.99). Graft failure occurred in 64% of patients, and 22% underwent repeat PKP. When stratified by indication for corneal transplantation (keratoconus vs. other), there was no significant difference in graft age at the time of rupture, final VA, rate of graft failure, or rate of repeat PKP. CONCLUSIONS: Traumatic dehiscence of corneal grafts remains a rare but serious subtype of ocular trauma with generally poor visual prognoses. Presenting VA along with severity of trauma and posterior segment involvement tend to be the worst prognostic factors in final visual outcome.

Fulgor: a fast and compact k-mer index for large-scale matching and color queries.

The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.

A patient with concurrent Axenfeld-Rieger and Stickler syndromes verified by molecular genetics.

Purpose: To report a case of Axenfeld-Rieger and Stickler Syndrome in a pediatric patient. Observations: A 3-month-old male was referred to the glaucoma clinic after he was noted to have elevated intraocular pressures in both eyes. His family history was notable for infantile glaucoma on his maternal side and retinal detachment on his paternal side. He was found to have anterior segment dysgenesis with iris strands, iridocorneal adhesions, and corectopia, as well as veil-like vitreous in both eyes. He required trabeculotomy, goniotomy, and multiple Baerveldt glaucoma implants in both eyes to achieve intraocular pressure control. Furthermore, the patient later developed macula-involving retinal detachments in both eyes, requiring pars plana vitrectomy with silicone oil tamponade. Genetic analysis confirmed heterozygous pathogenic variants in both the FOXC1 and COL2A1 genes, leading to the concurrent diagnoses of Axenfeld-Rieger and Stickler syndromes. Conclusions and importance: This is a rare case of a patient with concurrent Axenfeld-Rieger and Stickler syndromes. The severity of pathology in both the anterior and posterior segments required a collaborative multidisciplinary approach. In the diagnostic evaluation of congenital eye diseases, if there is strong family history of atypical findings for a given diagnosis, concurrent syndromes should be considered and ruled out. A comprehensive eye genetics panel may be a useful tool in these cases.

Meta-colored compacted de Bruijn graphs.

MOTIVATION: The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods that perform read mapping or alignment, abundance estimation, and subsequent downstream analyses. These applications essentially regard the c-dBG as a map from k-mers to the set of references in which they appear. The c-dBG data structure should retrieve this set -- the color of the k-mer -- efficiently for any given k-mer, while using little memory. To aid retrieval, the colors are stored explicitly in the data structure and take considerable space for large reference collections, even when compressed. Reducing the space of the colors is therefore of utmost importance for large-scale sequence indexing. RESULTS: We describe the meta-colored compacted de Bruijn graph (Mac-dBG) -- a new colored de Bruijn graph data structure where colors are represented holistically, i.e., taking into account their redundancy across the whole collection being indexed, rather than individually as atomic integer lists. This allows the factorization and compression of common sub-patterns across colors. While optimizing the space of our data structure is NP-hard, we propose a simple heuristic algorithm that yields practically good solutions. Results show that the Mac-dBG data structure improves substantially over the best previous space/time trade-off, by providing remarkably better compression effectiveness for the same (or better) query efficiency. This improved space/time trade-off is robust across different datasets and query workloads. Code availability: A C++17 implementation of the Mac-dBG is publicly available on GitHub at: https://github.com/jermp/fulgor.

Fulgor: A fast and compact k-mer index for large-scale matching and color queries.

The problem of sequence identification or matching - determining the subset of references from a given collection that are likely to contain a query nucleotide sequence - is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resourceefficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an index for fast queries. This poses the threefold challenge of designing an index that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe how recent advancements in associative, order-preserving, k-mer dictionaries can be combined with a compressed inverted index to implement a fast and compact colored de Bruijn graph data structure. This index takes full advantage of the fact that unitigs in the colored de Bruijn graph are monochromatic (all k-mers in a unitig have the same set of references of origin, or "color"), leveraging the order-preserving property of its dictionary. In fact, k-mers are kept in unitig order by the dictionary, thereby allowing for the encoding of the map from k-mers to their inverted lists in as little as 1+o(1) bits per unitig. Hence, one inverted list per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for inverted lists, the index achieves very small space. We implement these methods in a tool called Fulgor. Compared to Themisto, the prior state of the art, Fulgor indexes a heterogeneous collection of 30,691 bacterial genomes in 3.8× less space, a collection of 150,000 Salmonella enterica genomes in approximately 2× less space, is at least twice as fast for color queries, and is 2 - 6× faster to construct.

Morgagnian Cataract With Liquified Nuclear Cleft.

This case report discusses a diagnosis of morgagnian cataract with liquified nuclear cleft in a patient in his 60s who presented with gradually decreasing visual acuity.

Peripheral Retinal Nonperfusion in Pediatric Patients with Optic Disc Hypoplasia.

PURPOSE: This study aims to report the association of optic nerve hypoplasia (ONH), peripheral retinal nonperfusion, and secondary complications in pediatric patients. DESIGN: Retrospective case series. METHODS: The study was conducted between January 2015 and January 2022 at the Bascom Palmer Eye Institute. Inclusion criteria were clinical diagnosis of optic disc hypoplasia, age <18 years, and a fluorescein angiography (FA) of acceptable quality. RESULTS: Seven patients (11 eyes) met inclusion criteria. Average age at presentation was 3.5 years (range 1 month-8 years) and the mean follow-up time was 34.28 months (range 2-87 months). Four patients (57.14%) showed bilateral optic disc hypoplasia. All eyes exhibited peripheral retina nonperfusion on FA, in which mild severity was found in 7 eyes (63.63%), moderate in 2 eyes (18.18%), severe in 1 eye (9.09%) and extreme in 1 eye (9.09%). Eight eyes (72.72%) showed evidence of 360 degrees of retinal nonperfusion. Two patients (18.18%) were diagnosed with concurrent retinal detachment that were deemed inoperable at the time of diagnosis. All cases were observed without intervention. None of the patients were observed to have complications during follow-up. CONCLUSION: Among pediatric patients with ONH, there appears to be a high rate of concurrent retinal nonperfusion. In these cases, FA is a helpful tool to detect peripheral nonperfusion. Retinal findings are subtle in some cases and may not be detectable in children with suboptimal imaging performed without examination under anesthesia.

Evolving Use of Regional versus General Anesthesia for the Surgical Repair of Open Globe Injuries.

PURPOSE: The purpose of the current study is to report outcomes with the evolving use of regional anesthesia with monitored anesthesia care (RA-MAC) vs general anesthesia (GA) in the repair of open globe injuries. DESIGN: Retrospective, consecutive, comparative, nonrandomized clinical study. METHODS: The study includes 507 eyes of 507 patients with open globe injuries treated with either RA-MAC or GA at a tertiary referral center between 2015 and 2020. There was no predetermined protocol for selection of anesthesia method. However, based on experience and findings of prior research by this group, regional anesthesia with monitored anesthesia care was typically selected initially and changed to general anesthesia if warranted after evaluation of the patient and discussion with the surgeon. The main outcome measure was visual acuity at last follow-up. Results were compared to previously published study groups between 1995 and 2014. RESULTS: Primary closure of open globe injury was performed under RA-MAC anesthesia in 462 patients (91%) and under GA in 45 patients (9%). Zone 1, 2, and 3 injuries were recorded in 251, 170, and 86 patients, respectively. Zone 1 (96%, 240 of 251 patients) or zone 2 (92%, 156 of 170 patients) (P < .001) were more likely to be repaired under RA-MAC vs zone 3 injuries (76%, 65 of 86 patients). The improvement from presenting visual acuity was similar for the 2 anesthesia groups, 0.52 logMAR and 0.46 logMAR for RA-MAC and GA, respectively (P = .68, CI -0.3 to 0.2). The use of RA-MAC anesthesia for open globe injuries has increased at our institution from 64% in 1995-1999 to 91% in the present study, 2015-2020 (P < .00001). CONCLUSION: The current study demonstrates that with anesthesiologists experienced in ophthalmic regional anesthesia techniques, and appropriate case selection, RA-MAC can be safely used as an alternative to general anesthesia for open globe repair. Considerations when employing RA-MAC include a patient's ability to cooperate, position, and communicate for the duration of the globe repair.

ACUTE- AND DELAYED-ONSET ENDOPHTHALMITIS AFTER OPEN GLOBE INJURIES: Clinical Features and Visual Acuity Outcomes.

PURPOSE: The purpose of the study was to report the clinical features and best-corrected visual acuity outcomes in patients with acute- and delayed-onset endophthalmitis after open globe injuries. METHODS: The study included a retrospective, comparative, consecutive case series of patients with endophthalmitis after open globe injury between January 2016 and October 2020 at the Bascom Palmer Eye Institute. RESULTS: Acute-onset endophthalmitis accounted for 16 of 20 cases (80%), and all cases were diagnosed at the initial examination. Delayed-onset endophthalmitis cases, occurring more than 2 weeks after injury, accounted for 4 of 20 cases (20%) and were because of Zone 1 wound leaks and infections. Factors associated with endophthalmitis included presence of a retained intraocular foreign body (11/20 [55%]) and delay of presentation >24 hours (15/20 [75%]) ( P < 0.001 and 0.002, respectively). The mean presenting best-corrected visual acuity was logMAR 1.64 (20/800), and the mean best-corrected visual acuity at the last follow-up was logMAR 1.22 (20/300). CONCLUSION: In patients with open globe injury-related endophthalmitis, visual acuity outcomes are generally poor. Despite intravitreal antibiotics at primary closure, delayed-onset endophthalmitis cases may develop in the setting of compromised Zone 1 wound integrity.

Atypical Presentations of Extraparenchymal Neurocysticercosis.

BACKGROUND: Neurocysticercosis (NCC) is the most common parasitic infection of the central nervous system and is typically diagnosed through visualization of the cysts in the cerebral parenchyma by neuro-imaging. However, neuro-imaging may not detect extraparenchymal neurocysticercosis (EPNCC), which is a rare manifestation of the disease involving the subarachnoid, meningeal, and intraventricular spaces. We report 2 cases of extraparenchymal neurocysticercosis, and discuss the diagnostic challenges and management of this entity. METHODS: Two cases were identified through clinical records. RESULTS: Both patients had an insidious onset with slow progression of disease, and presented with papilledema and cerebrospinal fluid (CSF) eosinophilia. One case was diagnosed with spinal cord biopsy. The other was diagnosed with CSF serology and next-generation sequencing-based pathogen analysis. Both patients were treated with ventriculoperitoneal shunt, systemic antiparasitic agents, and immunosuppression. CONCLUSIONS: EPNCC is less common than parenchymal NCC. A high level of clinical suspicion is required given its rarity, long incubation period, and slow progression. Diagnosis and treatment can be challenging and requires a multidisciplinary approach.

Tree-based differential testing using inferential uncertainty for RNA-Seq.

Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exaggeration of false positives and, if included, may lead to reduced power. For a given set of RNA-Seq samples, TreeTerminus arranges transcripts in a hierarchical tree structure that encodes different layers of resolution for interpretation of the abundance of transcriptional groups, with uncertainty generally decreasing as one ascends the tree from the leaves. We introduce trenDi, which utilizes the tree structure from TreeTerminus for differential testing. The candidate nodes are determined in a data-driven manner to maximize the signal that can be extracted from the data while controlling for the uncertainty associated with estimating the transcript abundances. The identified candidate nodes can include transcripts and inner nodes, with no two nodes having an ancestor/descendant relationship. We evaluated our method on both simulated and experimental datasets, comparing its performance with other tree-based differential methods as well as with uncertainty-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.

Outcomes in Patients with Suprachoroidal Hemorrhage After Anterior Segment Surgery.

Objective: The purpose of the current study is to report outcomes of suprachoroidal hemorrhage (SCH) after anterior segment surgery at a single institution, and to identify clinical features associated with visual prognosis. Methods and Analysis: Retrospective consecutive case series of patients with SCH occurring after anterior segment surgery. Results: The study includes 112 eyes of 112 patients between 2014 and 2020. There were 76 cases of non-appositional SCH versus 36 cases of appositional SCH. The mean presenting visual acuity for patients with non-appositional versus appositional SCH was 2.03 logMAR (SD 0.78) versus 2.39 logMAR (SD 0.43), respectively. Visual acuity outcomes generally remained poor at last follow-up: 64 (58%) patients had a visual acuity (VA) of ≤ 20/200, including 19 (17%) with light perception (LP), and 11 (10%) with no light perception (NLP). Regarding management of non-appositional versus appositional SCH, observation was selected in 46 (61%) vs 12 (33%), delayed drainage in 14 (18%) vs 15 (42%), delayed pars plana vitrectomy in 16 (21%) vs 13 (36%), and VA at last follow-up was 1.2 versus 1.86 logMAR (p=0.002). In patients that were observed, both appositional SCH (p=0.01) and duration of apposition (p=0.04) were correlated with worse outcome. Conclusion: Appositional SCH was associated with poorer visual outcomes compared to non-appositional SCH. Observation remains a reasonable management strategy for non-appositional SCH.

Chemical induction of gut ß-like-cells by combined FoxO1/Notch inhibition as a glucose-lowering treatment for diabetes.

OBJECTIVE: Lifelong insulin replacement remains the mainstay of type 1 diabetes treatment. Genetic FoxO1 ablation promotes enteroendocrine cell (EECs) conversion into glucose-responsive ß-like cells. Here, we tested whether chemical FoxO1 inhibitors can generate ß-like gut cells. METHODS: We used Ngn3-or Villin-driven FoxO1 ablation to capture the distinctive developmental effects of FoxO1 on EEC pool. We combined FoxO1 ablation with Notch inhibition to enhance the expansion of EEC pool. We tested the ability of an orally available small molecule of FoxO1 inhibitor, Cpd10, to phenocopy genetic ablation of FoxO1. We evaluated the therapeutic impact of genetic ablation or chemical inhibition of FoxO1 on insulin-deficient diabetes in Ins2Akita/+ mice. RESULTS: Pan-intestinal epithelial FoxO1 ablation expanded the EEC pool, induced ß-like cells, and improved glucose tolerance in Ins2Akita/+ mice. This genetic effect was phenocopied by Cpd10. Cpd10 induced ß-like cells that released insulin in response to glucose in gut organoids, and this effect was enhanced by the Notch inhibitor, DBZ. In Ins2Akita/+ mice, a five-day course of either Cpd10 or DBZ induced intestinal insulin-immunoreactive ß-like cells, lowered glycemia, and increased plasma insulin levels without apparent adverse effects. CONCLUSION: These results provide proof of principle of gut cell conversion into ß-like cells by a small molecule FoxO1 inhibitor, paving the way for clinical applications.

Pharmacological conversion of gut epithelial cells into insulin-producing cells lowers glycemia in diabetic animals.

As a highly regenerative organ, the intestine is a promising source for cellular reprogramming for replacing lost pancreatic ß cells in diabetes. Gut enterochromaffin cells can be converted to insulin-producing cells by forkhead box O1 (FoxO1) ablation, but their numbers are limited. In this study, we report that insulin-immunoreactive cells with Paneth/goblet cell features are present in human fetal intestine. Accordingly, lineage-tracing experiments show that, upon genetic or pharmacologic FoxO1 ablation, the Paneth/goblet lineage can also undergo conversion to the insulin lineage. We designed a screening platform in gut organoids to accurately quantitate ß-like cell reprogramming and fine-tune a combination treatment to increase the efficiency of the conversion process in mice and human adult intestinal organoids. We identified a triple blockade of FOXO1, Notch, and TGF-ß that, when tested in insulin-deficient streptozotocin (STZ) or NOD diabetic animals, resulted in near normalization of glucose levels, associated with the generation of intestinal insulin-producing cells. The findings illustrate a therapeutic approach for replacing insulin treatment in diabetes.

Plasma-first: accelerating lung cancer diagnosis and molecular profiling through liquid biopsy.

Introduction: Molecular profiling of tumor tissue is the gold standard for treatment decision-making in advanced non-small cell lung cancer (NSCLC). Results may be delayed or unavailable due to insufficient tissue, prolonged wait times for biopsy, pathology assessment and testing. We piloted the use of plasma testing in the initial diagnostic workup for patients with suspected advanced lung cancer. Methods: Patients with ⩽15 pack-year smoking history and suspected advanced lung cancer referred to the lung cancer rapid diagnostic program underwent plasma circulating-tumor DNA testing using a DNA-based mutation panel. Tissue testing was performed per standard of care, including comprehensive next-generation sequencing (NGS). The primary endpoint was time from diagnostic program referral to cancer treatment in stage IV NSCLC patients (Cohort A) compared to a contemporary cohort not enrolled in the study (Cohort B) and an historical pre-COVID cohort referred to the program between 2018 and 2019 (Cohort C). Results: From January to June 2021, 20 patients were enrolled in Cohort A; median age was 70.5 years (range 33-87), 70% were female, 55% Caucasian, 85% never smokers, and 75% were diagnosed with NSCLC. Seven had actionable alterations detected in plasma or tissue (4/7 concordant). Fusions, not tested in plasma, were identified by immunohistochemistry for three patients. Mean result turnaround time was 17.8 days for plasma NGS and 23.6 days for tissue (p = 0.10). Mean time from referral to treatment initiation was significantly shorter in cohort A at 32.6 days (SD 13.1) versus 62.2 days (SD 31.2) in cohort B and 61.5 days (SD 29.1) in cohort C, both p < 0.0001. Conclusion: Liquid biopsy in the initial diagnostic workup of patients with suspected advanced NSCLC can lead to faster molecular results and shorten time to treatment even with smaller DNA panels. An expansion study using comprehensive NGS plasma testing with faster turnaround time is ongoing (NCT04862924).