Using a new artificial intelligence-aided method to assess body composition CT segmentation in colorectal cancer patients

INTRODUCTION

This study aimed to evaluate the accuracy of our own artificial intelligence (AI)-generated model to assess automated segmentation and quantification of body composition-derived computed tomography (CT) slices from the lumber (L3) region in colorectal cancer (CRC) patients.

METHODS

A total of 541 axial CT slices at the L3 vertebra were retrospectively collected from 319 patients with CRC diagnosed during 2012-2019 at a single Australian tertiary institution, Western Health in Melbourne. A two-dimensional U-Net convolutional network was trained on 338 slices to segment muscle, visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). Manual reading of these same slices of muscle, VAT and SAT was created to serve as ground truth data. The Dice similarity coefficient was used to assess the U-Net-based segmentation performance on both a validation dataset (68 slices) and a test dataset (203 slices). The measurement of cross-sectional area and Hounsfield unit (HU) density of muscle, VAT and SAT were compared between two methods.

RESULTS

The segmentation for muscle, VAT and SAT demonstrated excellent performance for both the validation (Dice similarity coefficients >0.98, respectively) and test (Dice similarity coefficients >0.97, respectively) datasets. There was a strong positive correlation between manual and AI segmentation measurements of body composition for both datasets (Spearman's correlation coefficients: 0.944-0.999, P < 0.001).

CONCLUSIONS

Compared to the gold standard, this fully automated segmentation system exhibited a high accuracy for assessing segmentation and quantification of abdominal muscle and adipose tissues of CT slices at the L3 in CRC patients.

Body composition assessment by artificial intelligence can be a predictive tool for short-term postoperative complications in Hartmann's reversals

BACKGROUND

Hartmann's reversal, a complex elective surgery, reverses and closes the colostomy in individuals who previously underwent a Hartmann's procedure due to colonic pathology like cancer or diverticulitis. It demands careful planning and patient optimisation to help reduce postoperative complications. Preoperative evaluation of body composition has been useful in identifying patients at high risk of short-term postoperative outcomes following colorectal cancer surgery. We sought to explore the use of our in-house derived Artificial Intelligence (AI) algorithm to measure body composition within patients undergoing Hartmann's reversal procedure in the prediction of short-term postoperative complications.

METHODS

A retrospective study of all patients who underwent Hartmann's reversal within a single tertiary referral centre (Western) in Melbourne, Australia and who had a preoperative Computerised Tomography (CT) scan performed. Body composition was measured using our previously validated AI algorithm for body segmentation developed by the Department of Surgery, Western Precinct, University of Melbourne. Sarcopenia in our study was defined as a skeletal muscle index (SMI), calculated as Skeletal Muscle Area (SMA) /height2 < 38.5 cm2/m2 in women and < 52.4 cm2/m2 in men.

RESULTS

Between 2010 and 2020, 47 patients (mean age 63.1 ± 12.3 years; male, n = 28 (59.6%) underwent body composition analysis. Twenty-one patients (44.7%) were sarcopenic, and 12 (25.5%) had evidence of sarcopenic obesity. The most common postoperative complication was surgical site infection (SSI) (n = 8, 17%). Sarcopenia (n = 7, 87.5%, p = 0.02) and sarcopenic obesity (n = 5, 62.5%, p = 0.02) were significantly associated with SSIs. The risks of developing an SSI were 8.7 times greater when sarcopenia was present.

CONCLUSION

Sarcopenia and sarcopenic obesity were related to postoperative complications following Hartmann's reversal. Body composition measured by a validated AI algorithm may be a beneficial tool for predicting short-term surgical outcomes for these patients.

Artificial intelligence measured 3D body composition to predict pathological response in rectal cancer patients

BACKGROUND

The treatment of locally advanced rectal cancer (LARC) is moving towards total neoadjuvant therapy and potential organ preservation. Of particular interest are predictors of pathological complete response (pCR) that can guide personalized treatment. There are currently no clinical biomarkers which can accurately predict neoadjuvant therapy (NAT) response but body composition (BC) measures present as an emerging contender. The primary aim of the study was to determine if artificial intelligence (AI) derived body composition variables can predict pCR in patients with LARC.

METHODS

LARC patients who underwent NAT followed by surgery from 2012 to 2023 were identified from the Australian Comprehensive Cancer Outcomes and Research Database registry (ACCORD). A validated in-house pre-trained 3D AI model was used to measure body composition via computed tomography images of the entire Lumbar-3 vertebral level to produce a volumetric measurement of visceral fat (VF), subcutaneous fat (SCF) and skeletal muscle (SM). Multivariate analysis between patient body composition and histological outcomes was performed.

RESULTS

Of 214 LARC patients treated with NAT, 22.4% of patients achieved pCR. SM volume (P = 0.015) and age (P = 0.03) were positively associated with pCR in both male and female patients. SCF volume was associated with decreased likelihood of pCR (P = 0.059).

CONCLUSION

This is the first study in the literature utilizing AI-measured 3D Body composition in LARC patients to assess their impact on pathological response. SM volume and age were positive predictors of pCR disease in both male and female patients following NAT for LARC. Future studies investigating the impact of body composition on clinical outcomes and patients on other neoadjuvant regimens such as TNT are potential avenues for further research.

The association of body composition on chemotherapy toxicities in non-metastatic colorectal cancer patients: a systematic review

BACKGROUND

In recent years, certain body composition measures, assessed by computed tomography (CT), have been found to be associated with chemotherapy toxicities. This review aims to explore available data on the relationship between skeletal muscle and adiposity, including visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), intramuscular and intermuscular adipose tissue and their association with chemotherapy toxicity in non-metastatic colorectal cancer (CRC) patients.

METHODS

A systematic literature search following PRISMA guidelines was conducted in Medline, Embase, Cochrane and Web of Science, for papers published between 2011 and 2023. The search strategy combined keywords and MESH terms relevant to 'body composition', 'chemotherapy toxicities', and 'non-metastatic colorectal cancer'.

RESULTS

Out of 3868 studies identified, six retrospective studies fulfilled the inclusion criteria with 1024 eligible patients. Low skeletal muscle mass was strongly associated with increased incidence of both chemotherapy toxicities and dose-limiting toxicity (DLT). The association of VAT, intramuscular and intermuscular adiposity was heterogeneous and inconclusive. There was no association between SAT and chemotherapy intolerance. No universal definitions or cut-offs for sarcopenia and obesity were noted. All studies utilized 2-dimensional (2D) CT slices for CT body composition assessment with varied selection on the vertebral landmark and inconsistent reporting of tissue-defining Hounsfield unit (HU) measurements.

CONCLUSION

Low skeletal muscle is associated with chemotherapy toxicities in non-metastatic CRC. However, quality evidence on the role of adiposity is limited and heterogeneous. More studies are needed to confirm these associations with an emphasis on a more coherent body composition definition and an approach to its assessment, especially regarding sarcopenia.

Can AI-based body composition assessment outperform body surface area in predicting dose-limiting toxicities for colonic cancer patients on chemotherapy?

PURPOSE

Gold standard chemotherapy dosage is based on body surface area (BSA); however many patients experience dose-limiting toxicities (DLT). We aimed to evaluate the effectiveness of BSA, two-dimensional (2D) and three-dimensional (3D) body composition (BC) measurements derived from Lumbar 3 vertebra (L3) computed tomography (CT) slices, in predicting DLT in colon cancer patients.

METHODS

203 patients (60.87 ± 12.42 years; 97 males, 47.8%) receiving adjuvant chemotherapy (Oxaliplatin and/or 5-Fluorouracil) were retrospectively evaluated. An artificial intelligence segmentation model was used to extract 2D and 3D body composition measurements from each patients' single mid-L3 CT slice as well as multiple-L3 CT scans to produce a 3D BC report. DLT was defined as any incidence of dose reduction or discontinuation due to chemotherapy toxicities. A receiver operating characteristic (ROC) analysis was performed on BSA and individual body composition measurements to demonstrate their predictive performance.

RESULTS

A total of 120 (59.1%) patients experienced DLT. Age and BSA did not vary significantly between DLT and non-DLT group. Females were significantly more likely to experience DLT (p = 4.9 × 10-3). In all patients, the predictive effectiveness of 2D body composition measurements (females: AUC = 0.50-0.54; males: AUC = 0.50-0.61) was equivalent to that of BSA (females: AUC = 0.49; males: AUC = 0.58). The L3 3D skeletal muscle volume was the most predictive indicator of DLT (AUC of 0.66 in females and 0.64 in males).

CONCLUSION

Compared to BSA and 2D body composition measurements, 3D L3 body composition measurements had greater potential to predict DLT in CRC patients receiving chemotherapy and this was sex dependent.

Exploring the contribution of ARMS2 and HTRA1 genetic risk factors in age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of severe irreversible central vision loss in individuals over 65 years old. Genome-wide association studies (GWASs) have shown that the region at chromosome 10q26, where the age-related maculopathy susceptibility (ARMS2/LOC387715) and HtrA serine peptidase 1 (HTRA1) genes are located, represents one of the strongest associated loci for AMD. However, the underlying biological mechanism of this genetic association has remained elusive. In this article, we extensively review the literature by us and others regarding the ARMS2/HTRA1 risk alleles and their functional significance. We also review the literature regarding the presumed function of the ARMS2 protein and the molecular processes of the HTRA1 protein in AMD pathogenesis in vitro and in vivo, including those of transgenic mice overexpressing HtrA1/HTRA1 which developed Bruch's membrane (BM) damage, choroidal neovascularization (CNV), and polypoidal choroidal vasculopathy (PCV), similar to human AMD patients. The elucidation of the molecular mechanisms of the ARMS2 and HTRA1 susceptibility loci has begun to untangle the complex biological pathways underlying AMD pathophysiology, pointing to new testable paradigms for treatment.

Identification of Differences in Body Composition Measures Using 3D-Derived Artificial Intelligence from Multiple CT Scans across the L3 Vertebra Compared to a Single Mid-Point L3 CT Scan

Purpose

Body composition analysis in colorectal cancer (CRC) typically utilises a single 2D-abdominal axial CT slice taken at the mid-L3 level. The use of artificial intelligence (AI) allows for analysis of the entire L3 vertebra (non-mid-L3 and mid-L3). The goal of this study was to determine if the use of an AI approach offered any additional information on capturing body composition measures.

Methods

A total of 2203 axial CT slices of the entire L3 level (4-46 slices were available per patient) were retrospectively collected from 203 CRC patients treated at Western Health, Melbourne (97 males; 47.8%). A pretrained artificial intelligence (AI) model was used to segment muscle, visceral adipose tissue (VAT), and subcutaneous adipose tissue (SAT) on these slices. The difference in body composition measures between mid-L3 and non-mid-L3 scans was compared for each patient, and for males and females separately.

Results

Body composition measures derived from non-mid-L3 scans exhibited a median range of 0.85% to 6.28% (average percent difference) when compared to the use of a single mid-L3 scan. Significant variation in the VAT surface area (p = 0.02) was observed in females compared to males, whereas male patients exhibited a greater variation in SAT surface area (p < 0.001) and radiodensity (p = 0.007).

Conclusion

Significant differences in various body composition measures were observed when comparing non-mid-L3 slices to only the mid-L3 slice. Researchers should be aware that considering only the use of a single midpoint L3 CT scan slice will impact the estimate of body composition measurements.

Can sarcopenia predict survival in locally advanced rectal cancer patients?

BACKGROUND

There is mounting evidence that suggests sarcopenia can be used to predict survival outcomes in patients with colon cancer. However, the effect on locally advanced rectal cancer (LARC) is less clear. We sought to determine the association between sarcopenia on Overall Survival and Recurrence-free Survival (OS and RFS) in patients with LARC undergoing multimodal treatment.

METHODS

A retrospective study was undertaken of all pre-treatment stage 2-3 rectal cancer patients who underwent neo-adjuvant treatment and surgery with curative intent between January 2010 and September 2016 at Western Health. Sarcopenia was measured on pre-treatment staging scans at the third lumbar vertebrae and defined using cohort-derived, sex-specific thresholds. Primary outcomes were OS and RFS.

RESULTS

A total of 132 patients with LARC were analysed. Sarcopenia: Hazard ratio (HR) 3.71; 95% CI, 1.28-10.75, P = 0.016 was independently associated with worse Overall Survival following multivariate analysis. There was no significant relationship between sarcopenia and RFS: Time ratio (TR) 1.67; 95% CI 0.52-5.34, P = 0.386.

CONCLUSION

Sarcopenia was found to be an independent risk factor for worse overall survival, but not recurrence free survival, in patients with locally advanced rectal cancer undergoing neo-adjuvant chemo-radiotherapy and surgery with curative intent.

Keratoconus International Consortium (KIC)- advancing keratoconus research

CLINICAL RELEVANCE

The Keratoconus International Consortium (KIC) will allow better understanding of keratoconus.

BACKGROUND

Keratoconus is a disorder characterised by corneal elevation and thinning, leading to reduced vision. The current gaps in understanding of this disease will be discussed and the need for a multi-pronged and multi-centre engagement to enhance our understanding of keratoconus will be highlighted.

DESIGN

KIC has been established to address the gaps in our understanding of keratoconus with the aim of collecting baseline as well as longitudinal data on several fields.

PARTICIPANTS

Keratoconus and control (no corneal condition) subjects from different sites globally will be recruited in the study.

METHODS

KIC collects data using an online, secure database, which enables standardised data collection at member sites. Data fields collected include medical history, clinical features, quality of life and economic burden questionnaires and possible genetic sample collection from patients of different ethnicities across different geographical locations.

RESULTS

There are currently 40 Australian and international clinics or hospital departments who have joined the KIC. Baseline data has so far been collected on 1130 keratoconus patients and indicates a median age of 29.70 years with 61% being male. A total of 15.3% report a positive family history of keratoconus and 57.7% self-report a history of frequent eye rubbing.

CONCLUSION

The strength of this consortium is its international, collaborative design and use of a common data collection tool. Inclusion and analyses of cross-sectional and longitudinal data will help answer many questions that remain in keratoconus, including factors affecting progression and treatment outcomes.

Comparison of CT derived body composition at the thoracic T4 and T12 with lumbar L3 vertebral levels and their utility in patients with rectal cancer

BACKGROUND

Computed tomography (CT) derived body composition measurements of sarcopenia are an emerging form of prognostication in many disease processes. Although the L3 vertebral level is commonly used to measure skeletal muscle mass, other studies have suggested the utilisation of other segments. This study was performed to assess the variation and reproducibility of skeletal muscle mass at vertebral levels T4, T12 and L3 in pre-operative rectal cancer patients. If thoracic measurements were equivalent to those at L3, it will allow for body composition comparisons in a larger range of cancers where lumbar CT images are not routinely measured.

RESEARCH METHODS

Patients with stage I - III rectal cancer, undergoing curative resection from 2010 - 2014, were assessed. CT based quantification of skeletal muscle was used to determine skeletal muscle cross sectional area (CSA) and skeletal muscle index (SMI). Systematic differences between the measurements at L3 with T4 and T12 vertebral levels were evaluated by percentile rank differences to assess distribution of differences and ordinary least product regression (OLP) to detect and distinguish fixed and proportional bias.

RESULTS

Eighty eligible adult patients were included. Distribution of differences between T12 SMI and L3 SMI were more marked than differences between T4 SMI and L3 SMI. There was no fix or proportional bias with T4 SMI, but proportional bias was detected with T12 SMI measurements. T4 CSA duplicate measurements had higher test-retest reliability: coefficient of repeatability was 34.10 cm² for T4 CSA vs 76.00 cm² for T12 CSA. Annotation time (minutes) with L3 as reference, the median difference was 0.85 for T4 measurements and -0.03 for T12 measurements. Thirty-seven patients (46%) had evidence of sarcopenia at the L3 vertebral level, with males exhibiting higher rates of sarcopenia. However, there was no association between sarcopenia and post-operative complications, recurrence or hospital LOS (length of stay) in patients undergoing curative resection.

CONCLUSIONS

Quantifying skeletal muscle mass at the T4 vertebral level is comparable to measures achieved at L3 in patients with rectal cancer, notwithstanding annotation time for T4 measurements are longer.

Vision-Related Quality of Life and Ocular Parameters in End-Stage Renal Disease Patients Undergoing Hemodialysis

Purpose

To evaluate the vision-related quality of life (VRQoL) of patients receiving hemodialysis through the assessment of the impact of vision impairment (IVI) questionnaire and ocular parameters, including best-corrected visual acuity (BCVA), intraocular pressure (IOP), and refraction as calculated by spherical equivalent (SE) of each eye.

Methods

Fifty-one patients with end-stage renal disease undergoing hemodialysis at a single center were recruited, and a total of 77 eyes were evaluated. BCVA, IOP, and SE were evaluated before and after hemodialysis (within 30 min).

Results

Of the 51 patients recruited, 13 (25%) were female, 37 (73%) were male, and one (2%) chose not to specify gender. The mean age was 61.85 ± 32 years. The mobility IVI score was correlated significantly with the presence of hypertension (P = 0.01), eye drop usage (P = 0.04), and gender (P = 0.04). Emotional IVI scores were correlated significantly with diabetes (P = 0.03) and hypertension (P < 0.01). IOP significantly correlated with the IVI overall score (P = 0.02), including the reading IVI subscale and the emotional IVI subscale. Several factors were associated with posthemodialysis ocular parameters, including predialysis ocular parameters, age, and hypertension (P < 0.05 for all).

Conclusions

IOP significantly correlated with VRQoL in hemodialysis patients. Demographic variables such as diabetes status, hypertension, eye drop usage, and gender also significantly correlated with subsections of the IVI questionnaire. This study investigated the relationship between ocular parameters and VRQoL in hemodialysis patients, and future longitudinal research is needed to further elucidate the mechanisms.

The extracellular microenvironment in immune dysregulation and inflammation in retinal disorders

Inherited retinal dystrophies (IRDs) as well as genetically complex retinal phenotypes represent a heterogenous group of ocular diseases, both on account of their phenotypic and genotypic characteristics. Therefore, overlaps in clinical features often complicate or even impede their correct clinical diagnosis. Deciphering the molecular basis of retinal diseases has not only aided in their disease classification but also helped in our understanding of how different molecular pathologies may share common pathomechanisms. In particular, these relate to dysregulation of two key processes that contribute to cellular integrity, namely extracellular matrix (ECM) homeostasis and inflammation. Pathological changes in the ECM of Bruch's membrane have been described in both monogenic IRDs, such as Sorsby fundus dystrophy (SFD) and Doyne honeycomb retinal dystrophy (DHRD), as well as in the genetically complex age-related macular degeneration (AMD) or diabetic retinopathy (DR). Additionally, complement system dysfunction and distorted immune regulation may also represent a common connection between some IRDs and complex retinal degenerations. Through highlighting such overlaps in molecular pathology, this review aims to illuminate how inflammatory processes and ECM homeostasis are linked in the healthy retina and how their interplay may be disturbed in aging as well as in disease.

Non-genetic risk factors for keratoconus

Keratoconus is a complex and multifactorial disease and its exact aetiology remains unknown. This current study examined the important environmental risk factors and their association with keratoconus. This study was registered in the PROSPERO International Prospective Register of systematic reviews under registration number CRD42021256792 in 2021. Scopus, Web of Science, PubMed, and Cochrane CENTRAL databases were searched for all relevant articles published from 1 January 1900 to 31 July 2021. National Institutes of Health Quality Assessment Tool was used to assess the methodological quality of the studies. The assessment for statistical heterogeneity was assessed using the Z-statistics on RevMan v5.4. P-value of <0.05 was considered as statistically significant and I² < 25% as homogenous. Thirty studies were included in this meta-analysis. Pooled odds ratio was calculated with 95% CI. The pooled odds ratio (OR) of eye rubbing, atopy, asthma, and eczema was 3.64 (95% CI, 2.02, 6.57), 1.90 (95% CI, 1.22, 2.94), 1.36 (95% CI, 1.15, 1.61) and 1.90 (95% CI, 1.22, 2.94), respectively. The OR for diabetes was 0.86 (95% CI 0.73, 1.02), and use of sunglasses, contact lens, allergic conjunctivitis, side sleep position and prone sleep position was 0.40 (95% CI, 0.16, 0.99), 1.68 (0.70, 4.00), 2.24 (95% CI, 0.68, 7.36), 3.81 (95% CI, 0.31, 46.23), 12.76 (95% CI, 0.27, 598.58), respectively. Twenty studies were considered to be of high quality, nine to be moderate and one to be low. Environmental risk factors have been identified to play a role in the susceptibility of keratoconus. However, further large-scale longitudinal studies are needed to understand the mechanisms between environmental risk factors and keratoconus.

Examining Corneal Tissue Exportation Fee and Its Impact on Equitable Allocation

METHODS

We conducted grounded theory semistructured interviews, purposively inviting participants until themed saturation was met. Sentiment analysis was used to determine opinion.

RESULTS

We interviewed n = 92 global eye tissue and eye bank professionals. We determined that corneal tissue, which is exported, costs between US $100 and US $6000 or is provided as gratis. Collectively, interviewees indicated that, globally, there were no fixed fee structures in place, and the fee was influenced by multiple factors on both export and import sides. They indicated that ultimately corneas were allocated based on the importers' ability to pay the price determined by the exporting eye bank.

DISCUSSION

Allocation of corneal tissue, which is exported, is influenced by the fees charged by the exporters to meet their bottom line and the funds available to importers. Therefore, export allocation is not equitable, with those who can pay a higher fee, prioritized. Steps to guide and support exporters with the development of fee structures that promote equitable allocation are essential. This will assist both export and import eye bank development, corneal tissue access development, and those awaiting a corneal transplant.

Accuracy of Machine Learning Assisted Detection of Keratoconus: A Systematic Review and Meta-Analysis

(1) Background: The objective of this review was to synthesize available data on the use of machine learning to evaluate its accuracy (as determined by pooled sensitivity and specificity) in detecting keratoconus (KC), and measure reporting completeness of machine learning models in KC based on TRIPOD (the transparent reporting of multivariable prediction models for individual prognosis or diagnosis) statement. (2) Methods: Two independent reviewers searched the electronic databases for all potential articles on machine learning and KC published prior to 2021. The TRIPOD 29-item checklist was used to evaluate the adherence to reporting guidelines of the studies, and the adherence rate to each item was computed. We conducted a meta-analysis to determine the pooled sensitivity and specificity of machine learning models for detecting KC. (3) Results: Thirty-five studies were included in this review. Thirty studies evaluated machine learning models for detecting KC eyes from controls and 14 studies evaluated machine learning models for detecting early KC eyes from controls. The pooled sensitivity for detecting KC was 0.970 (95% CI 0.949–0.982), with a pooled specificity of 0.985 (95% CI 0.971–0.993), whereas the pooled sensitivity of detecting early KC was 0.882 (95% CI 0.822–0.923), with a pooled specificity of 0.947 (95% CI 0.914–0.967). Between 3% and 48% of TRIPOD items were adhered to in studies, and the average (median) adherence rate for a single TRIPOD item was 23% across all studies. (4) Conclusions: Application of machine learning model has the potential to make the diagnosis and monitoring of KC more efficient, resulting in reduced vision loss to the patients. This review provides current information on the machine learning models that have been developed for detecting KC and early KC. Presently, the machine learning models performed poorly in identifying early KC from control eyes and many of these research studies did not follow established reporting standards, thus resulting in the failure of these clinical translation of these machine learning models. We present possible approaches for future studies for improvement in studies related to both KC and early KC models to more efficiently and widely utilize machine learning models for diagnostic process.

Machine learning with a reduced dimensionality representation of comprehensive Pentacam tomography parameters to identify subclinical keratoconus

PURPOSE

To investigate the performance of a machine learning model based on a reduced dimensionality parameter space derived from complete Pentacam parameters to identify subclinical keratoconus (KC).

METHODS

All 1692 available parameters were obtained from the Pentacam imaging machine on 145 subclinical KC and 122 control eyes. We applied a principal component analysis (PCA) to the complete Pentacam dataset to reduce its parameter dimensionality. Subsequently, we investigated machine learning performance of the random forest algorithm with increasing numbers of components to identify their optimal number for detecting subclinical KC from control eyes.

RESULTS

The dimensionality of the complete set of 1692 Pentacam parameters was reduced to 267 principal components using PCA. Subsequent selection of 15 of these principal components explained over 85% of the variance of the original Pentacam-derived parameters and input to train a random forest machine learning model to achieve the best accuracy of 98% in detecting subclinical KC eyes. The model established also reached a high sensitivity of 97% in identification of subclinical KC and a specificity of 98% in recognizing control eyes.

CONCLUSIONS

A random forest-based model trained using a modest number of components derived from a reduced dimensionality representation of complete Pentacam system parameters allowed for high accuracy of subclinical KC identification.

Supply and Demand of Domestic Corneal Tissue and Its Implications on Export Potential-Using Australia as an Example

PURPOSE

Corneal tissue importation is only possible if another country is able to export corneas without impacting its own domestic demand. Currently, there is little evidence to indicate whether export nations have such surplus capacity and in a position to export. To explore this concept, we examined our nation, Australia, which is reported to routinely decline donations because of its ability to meet domestic corneal transplant demand. Our research offers insights and opportunities for Australia and other nations to evaluate their domestic and international supply and allocation of corneal tissue in this space.

METHOD

We collated 12 months of data on collected and noncollected donations, through participating Australian Eye Banks. The explanation of why some known donors were declined or not pursued indicated if demand was met and potential surplus-for-export levels.

RESULTS

There were 7.5% (n = 11,889) of deaths in Australia that were notified to Australian Eye Banks during our reporting period. Of those, 9.3% (n = 1106/11,889) were recovered and allocated, 15.7% (n = 1863/11,889) were known but declined, and 75% (n = 8920/11,889) were not pursued. Of those that were declined, 64.3% (n = 1197/1863) were declined because of limitations with service/manpower at the eye bank, whereas 35.7% (n = 666/1863) were declined because demand was met.

CONCLUSIONS

Australia did not meet demand all the time, during our data period. There were adequate quantities of potential donors to support increasing recovery for domestic allocation and provide for exportation without hindrance to Australian demand. Further examination of domestic supply and demand cycles and the export process is required before routine exportation.

Identification of novel loci influencing refractive error in East Asian populations using an extreme phenotype design

The global "myopia boom" has raised significant international concerns. Despite a higher myopia prevalence in Asia, previous large-scale genome-wide association studies (GWASs) were mostly based on European descendants. Here, we report a GWAS of spherical equivalent (SE) in 1852 Chinese Han individuals with extreme SE from Guangzhou (631 < -6D and 574 > 0D) and Wenzhou (593 < -6D and 54 > -1.75 D), followed by a replication study in two independent cohorts with totaling 3538 East Asian individuals. The discovery GWAS and meta-analysis identify three novel loci which show genome-wide significant associations with SE, including 1q25.2 FAM163A, 10p11.22 NRP1/PRAD3, and 10p11.21 ANKRD30A/MTRNR2L7, together explaining 3.34% of SE variance. 10p11.21 was successfully replicated. The allele frequencies of all three loci show significant differences between major continental groups (P < 0.001). The SE reducing (more myopic) allele of rs10913877 (1q25.2 FAM163A) demonstrates the highest frequency in East Asians and much lower frequencies in Europeans and Africans (EAS = 0.60, EUR = 0.20, AFR = 0.18). The gene-based analysis additionally identifies three novel genes associated with SE, including EI24, LHX5 and ARPP19. These results provide new insights into myopia pathogenesis, and indicate the role of genetic heterogeneity in myopia epidemiology among different ethnicities.

Corneal supply and the use of technology to reduce its demand: A review

Recovery and access to end-of-life corneal tissue for corneal transplantation, training and research is globally maldistributed. The reasons for the maldistribution are complex and multifaceted, and not well defined or understood. Currently there are few solutions available to effectively address these issues. This review provides an overview of the system, key issues impacting recovery and allocation and emphasises how end-user ophthalmologists and researchers, with support from administrators and the wider sector, can assist in increasing access long-term through sustaining eye banks nationally and globally. We posit that prevention measures and improved surgical techniques, together with the development of novel therapies will play a significant role in reducing demand and enhance the equitable allocation of corneas.

Do Eye Bank Models and Competitive Practice Affect International Cornea Allocation?

PURPOSE

International export and import of corneas is dependent on the stakeholders involved in the process and how those organizations engage to move corneas from one point to another. Our article presents the pathway of corneal donation from the export nation until its use in the import nation. It presents opinion on how aspects, such as competition and promotional behaviors, the use of online systems, and third-party engagement may influence allocation.

METHODS

We interviewed n = 92 international eye tissue and eye bank (EB) professionals to garner their opinion. We used saturation and sentiment methods to extract and consolidate group opinion.

RESULTS

Interviewees indicated that competition and promotional behaviors existed in some EB nations-although it was not universal. They indicated that the behavioral approach used by the individual EB, rather than the act of information sharing, influenced allocation. They also indicated that organizational models and allocation systems (eg, online ordering) and engagement with nonstate actors were important in allocation practice and decision making.

CONCLUSION

We mapped the pathways for corneas involved in export and import from the point of recovery to their point of transplantation. Although generalist in nature and limited by the paucity of the existing literature, our article outlines that different business models, partnerships, and applied methods influence corneal export and import.

Deep Learning Applied to Automated Segmentation of Geographic Atrophy in Fundus Autofluorescence Images

Purpose

This study describes the development of a deep learning algorithm based on the U-Net architecture for automated segmentation of geographic atrophy (GA) lesions in fundus autofluorescence (FAF) images.

Methods

Image preprocessing and normalization by modified adaptive histogram equalization were used for image standardization to improve effectiveness of deep learning. A U-Net-based deep learning algorithm was developed and trained and tested by fivefold cross-validation using FAF images from clinical datasets. The following metrics were used for evaluating the performance for lesion segmentation in GA: dice similarity coefficient (DSC), DSC loss, sensitivity, specificity, mean absolute error (MAE), accuracy, recall, and precision.

Results

In total, 702 FAF images from 51 patients were analyzed. After fivefold cross-validation for lesion segmentation, the average training and validation scores were found for the most important metric, DSC (0.9874 and 0.9779), for accuracy (0.9912 and 0.9815), for sensitivity (0.9955 and 0.9928), and for specificity (0.8686 and 0.7261). Scores for testing were all similar to the validation scores. The algorithm segmented GA lesions six times more quickly than human performance.

Conclusions

The deep learning algorithm can be implemented using clinical data with a very high level of performance for lesion segmentation. Automation of diagnostics for GA assessment has the potential to provide savings with respect to patient visit duration, operational cost and measurement reliability in routine GA assessments.

Translational Relevance

A deep learning algorithm based on the U-Net architecture and image preprocessing appears to be suitable for automated segmentation of GA lesions on clinical data, producing fast and accurate results.

Model Structure Uncertainty in the Characterization and Growth of Geographic Atrophy

Purpose

To identify the most suitable model for assessing the rate of growth of total geographic atrophy (GA) by analysis of model structure uncertainty.

Methods

Model structure uncertainty refers to unexplained variability arising from the choice of mathematical model and represents an example of epistemic uncertainty. In this study, we quantified this uncertainty to help identify a model most representative of GA progression. Fundus autofluorescence (FAF) images and GA progression data (i.e., total GA area estimation at each presentation) were acquired using Spectralis HRA+OCT instrumentation and RegionFinder software. Six regression models were evaluated. Models were compared using various statistical tests, [i.e., coefficient of determination (r²), uncertainty metric (U), and test of significance for the correlation coefficient, r], as well as adherence to expected physical and clinical assumptions of GA growth.

Results

Analysis was carried out for 81 GA-affected eyes, 531 FAF images (range: 3–17 images per eye), over median of 57 months (IQR: 42, 74), with a mean baseline lesion size of 2.62 ± 4.49 mm² (range: 0.11–20.69 mm²). The linear model proved to be the most representative of total GA growth, with lowest average uncertainty (original scale: U = 0.025, square root scale: U = 0.014), high average r² (original scale: 0.92, square root scale: 0.93), and applicability of the model was supported by a high correlation coefficient, r, with statistical significance (P = 0.01).

Conclusions

Statistical analysis of uncertainty suggests that the linear model provides an effective and practical representation of the rate and progression of total GA growth based on data from patient presentations in clinical settings.

Translational Relevance

Identification of correct model structure to characterize rate of growth of total GA in the retina using FAF images provides an objective metric for comparing interventions and charting GA progression in clinical presentations.

Should Donors Consent to Export Their Corneas? Examination of Eye Tissue and Eye Care Sector Opinion

PURPOSE

Corneal tissue international activity is only possible because of the willingness of export populations to donate their corneas on their death. Current predonation public education campaigns and at-the-point-of-donation consent practice generally includes consent for transplantation, research, and/or training. It is unclear whether a consent-for-export step is universally included in the consent process or, indeed, whether it should. We interviewed eye tissue and eye care professionals from around the world, who exported, imported, or did neither to understand current consent-for-export awareness and determine opinion on future practice.

METHOD

During wider qualitative grounded-theory semistructured interviews with sector experts, to determine whether Australia should export, we captured sector opinion on consent-for-export. We used saturation and sentiment methods to determine opinion and χ2 correlation coefficients to examine association, using an α of P = 0.05.

RESULTS

We interviewed 92 individuals, 83 of whom discussed consent-for-export. Of those, 51% (42/83) demonstrated some awareness of the practice; however, there were contradictions between interviewees from the same location. Regardless of current awareness, 57% (41/72) believed donors should be informed or consented for export. Their approval did not extend to donor-directed decisions, which would allow donors to decide which nation their donation should be sent, with 62.5% (45/72) opposing that notion.

CONCLUSIONS

Our research indicates that the consent-for-export practice is not universally applied by exporting nations and that eye tissue and eye care professionals have limited awareness of the practice. Universally implementing a consent-for-export step within general consent practice would improve awareness, reduce confusion, and support donor wishes.

A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus

Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.

Determining the willingness of Australians to export their corneas on death

Background

12.7 million people await a corneal transplant, but 53% are without access to corneal tissue. Sharing corneal tissue across nations can provide some access, however the willingness of export populations, like Australians, to export their donation on death, has never been evaluated. Our research samples the Australian population, determining their willingness to export.

Materials and method

We conducted e-surveys. N = 1044 Australians participated. The sample represented the Australian population, based on population demographics. Chi-Square and bivariate correlation coefficients examined associations between categorical variables, with a sample size of N = 1044, power of 0.80, and alpha of p = 0.05. Outcome measures were based on population sampling, by exploring willingness export, through the e-survey method.

Results

38% (n = 397) of respondents said yes to exportation, 23.8% (n = 248) said no, and 38.2% (n = 399) were undecided. We found no relationship between willingness to export and general demographics, though those registered on the Donatelife Register (p = < .001), and those already willing to donate their eyes (p = < .001) were significantly more willing to export.

Discussion

More Australians are willing to export their corneas than not, though a significant portion remain undecided. The Donatelife Register, and donation awareness, are key components of respondent decision making. Therefore, the provision of information about exportation prior to, and at the point-of-donation, is essential for assisting Australian’s to decide to export or not. Further examination and development of consent-for-export systems are necessary before routine exportation is undertaken.

Eye rubbing in the aetiology of keratoconus: a systematic review and meta-analysis

PURPOSE

Keratoconus is a potentially blinding condition that slowly deforms the cornea in young people. Despite the increasing prevalence of keratoconus, the exact aetiology of the condition is unknown. This first systematic review examines the evidence of eye rubbing and its association with keratoconus and presents the findings of the meta-analysis.

METHODS

Two independent reviewers searched the electronic databases for all potential articles published from 1st of January 1900 to 31st of July 2020 on eye rubbing and keratoconus. The researchers assessed the methodological quality of the studies using the Newcastle-Ottawa scale for observational studies. The assessment for statistical heterogeneity was estimated using chi-square and I-square (I²) tests. A p value of < 0.05 was considered as statistically significant and I² < 30% as homogenous. Begg funnel plot was used to interpret the asymmetry or small study effects.

RESULTS

Eight case-control studies were included in this systematic review. Two studies assessed eye rubbing without odds ratios and thus were excluded. The pooled odds ratios for the six remaining studies included in the meta-analysis was 6.46 (95% CI 4.12-10.1). The study results were heterogenous (I² = 71.69 [95% CI 35.14-87.88]). All the studies scored moderate quality methodology on the Newcastle-Ottawa scale. Begg funnel plot showed asymmetry supporting heterogeneity.

CONCLUSION

Eye rubbing showed consistent association with keratoconus. However, the current evidence is limited to only a small number of case-control studies which present as heterogeneous and of sub-optimal methodological quality. Additionally, the cause-effect temporal relationship cannot be determined. Further studies are needed to address this intricate relationship of eye rubbing and its induction, ongoing progression, and severity of keratoconus.

Binding of Gtf2i-β/δ transcription factors to the ARMS2 gene leads to increased circulating HTRA1 in AMD patients and in vitro

The disease-initiating molecular events for age-related macular degeneration (AMD), a multifactorial retinal disease affecting many millions of elderly individuals worldwide, are still unknown. Of the over 30 risk and protective loci so far associated with AMD through whole genome-wide association studies (GWAS), the Age-Related Maculopathy Susceptibility 2 (ARMS2) gene locus represents one of the most highly associated risk regions for AMD. A unique insertion/deletion (in/del) sequence located immediately upstream of the High Temperature Requirement A1 (HTRA1) gene in this region confers high risk for AMD. Using electrophoretic mobility shift assay (EMSA), we identified that two Gtf2i-β/δ transcription factor isoforms bind to the cis-element 5'- ATTAATAACC-3' contained in this in/del sequence. The binding of these transcription factors leads to enhanced upregulation of transcription of the secretory serine protease HTRA1 in transfected cells and AMD patient-derived induced pluripotent stem cells (iPSCs). Overexpression of Htra1 in mice using a CAG-promoter demonstrated increased blood concentration of Htra1 protein, caused upregulation of vascular endothelial growth factor (VEGF), and produced a choroidal neovascularization (CNV)-like phenotype. Finally, a comparison of 478 AMD patients to 481 healthy, age-matched controls from Japan, India, Australia, and the USA showed a statistically increased level of secreted HTRA1 blood concentration in AMD patients compared with age-matched controls. Taken together, these results suggest a common mechanism across ethnicities whereby increased systemic blood circulation of secreted serine protease HTRA1 leads to subsequent degradation of Bruch's membrane and eventual CNV in AMD.

Association of Genetic Variation With Keratoconus

Importance

Keratoconus is a condition in which the cornea progressively thins and protrudes in a conical shape, severely affecting refraction and vision. It is a major indication for corneal transplant. To discover new genetic loci associated with keratoconus and better understand the causative mechanism of this disease, we performed a genome-wide association study on patients with keratoconus.

Objective

To identify genetic susceptibility regions for keratoconus in the human genome.

Design, Setting, and Participants

This study was conducted with data from eye clinics in Australia, the United States, and Northern Ireland. The discovery cohort of individuals with keratoconus and control participants from Australia was genotyped using the Illumina HumanCoreExome single-nucleotide polymorphism array. After quality control and data cleaning, genotypes were imputed against the 1000 Genomes Project reference panel (phase III; version 5), and association analyses were completed using PLINK version 1.90. Single-nucleotide polymorphisms with P < 1.00 × 10-6 were assessed for replication in 3 additional cohorts. Control participants were drawn from the cohorts of the Blue Mountains Eye Study and a previous study of glaucoma. Replication cohorts were from a previous keratoconus genome-wide association study data set from the United States, a cohort of affected and control participants from Australia and Northern Ireland, and a case-control cohort from Victoria, Australia. Data were collected from January 2006 to March 2019.

Main Outcomes and Measures

Associations between keratoconus and 6 252 612 genetic variants were estimated using logistic regression after adjusting for ancestry using the first 3 principal components.

Results

The discovery cohort included 522 affected individuals and 655 control participants, while the replication cohorts included 818 affected individuals (222 from the United States, 331 from Australia and Northern Ireland, and 265 from Victoria, Australia) and 3858 control participants (2927 from the United States, 229 from Australia and Northern Ireland, and 702 from Victoria, Australia). Two novel loci reached genome-wide significance (defined as P < 5.00 × 10-8), with a P value of 7.46 × 10-9 at rs61876744 in patatin-like phospholipase domain-containing 2 gene (PNPLA2) on chromosome 11 and a P value of 6.35 × 10-12 at rs138380, 2.2 kb upstream of casein kinase I isoform epsilon gene (CSNK1E) on chromosome 22. One additional locus was identified with a P value less than 1.00 × 10-6 in mastermind-like transcriptional coactivator 2 (MAML2) on chromosome 11 (P = 3.91 × 10-7). The novel locus in PNPLA2 reached genome-wide significance in an analysis of all 4 cohorts (P = 2.45 × 10-8).

Conclusions and Relevance

In this relatively large keratoconus genome-wide association study, we identified a genome-wide significant locus for keratoconus in the region of PNPLA2 on chromosome 11.

Risk factors and association with severity of keratoconus: the Australian study of Keratoconus

SIGNIFICANCE

Our results show that asthmatic patients tend to have more severe KC and thus close monitoring for disease progression would be advised, and appropriate treatment strategies may be actioned stabilise the condition that may reduce the need for future corneal transplantation.

PURPOSE

To explore a wide range of risk factors associated with the severity of keratoconus (KC).

METHODS

A cross-sectional study of KC patients was undertaken in Melbourne, Australia. A questionnaire addressing age, gender, educational background, ocular and medical history, smoking and alcohol consumption, and physical examination comprising anthropometric measurements was collected; eye examination was undertaken. The associations between a range of risk factors and the severity of KC were determined using univariate and multivariable linear regression analyses.

RESULTS

A total of 260 KC subjects were included in this study. Mean age of subject was 35.5 (SD = 14.8) years and the majority of the subjects were European 171 (68.2%). Initial univariate regression analysis identified the following risk factors at the p < 0.1 level with KC: higher body mass index, smoking cigarettes, diabetes, rheumatoid arthritis and asthma were associated with increased severity of KC, whereas eczema was associated with less severe KC. Following multivariable regression analysis, only asthma remained as a significant risk factor associated with 2.2 diopters (D) steeper average mean keratometry compared to KC subjects having no asthma [p = 0.03; β = 2.18; 95% confidence intervals: 1.22, 4.14].

CONCLUSION

Our study describes the comprehensive assessment of all the known risk factors in a large KC cohort recruited in Australia. Our study has reported asthma as the only risk factor found to be significantly associated with the severity of KC. The results of this study allow us to better understand the aetiology of KC and such knowledge could be useful in instigate systemic management of patients to slow or prevent KC.

Artificial Intelligence Algorithms for Analysis of Geographic Atrophy: A Review and Evaluation

Purpose

The purpose of this study was to summarize and evaluate artificial intelligence (AI) algorithms used in geographic atrophy (GA) diagnostic processes (e.g. isolating lesions or disease progression).

Methods

The search strategy and selection of publications were both conducted in accordance with the Preferred of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. PubMed and Web of Science were used to extract literary data. The algorithms were summarized by objective, performance, and scope of coverage of GA diagnosis (e.g. lesion automation and GA progression).

Results

Twenty-seven studies were identified for this review. A total of 18 publications focused on lesion segmentation only, 2 were designed to detect and classify GA, 2 were designed to predict future overall GA progression, 3 focused on prediction of future spatial GA progression, and 2 focused on prediction of visual function in GA. GA-related algorithms reported sensitivities from 0.47 to 0.98, specificities from 0.73 to 0.99, accuracies from 0.42 to 0.995, and Dice coefficients from 0.66 to 0.89.

Conclusions

Current GA-AI publications have a predominant focus on lesion segmentation and a minor focus on classification and progression analysis. AI could be applied to other facets of GA diagnoses, such as understanding the role of hyperfluorescent areas in GA. Using AI for GA has several advantages, including improved diagnostic accuracy and faster processing speeds.

Translational Relevance

AI can be used to quantify GA lesions and therefore allows one to impute visual function and quality-of-life. However, there is a need for the development of reliable and objective models and software to predict the rate of GA progression and to quantify improvements due to interventions.

Evaluating the Performance of Various Machine Learning Algorithms to Detect Subclinical Keratoconus

Purpose

Keratoconus (KC) represents one of the leading causes of corneal transplantation worldwide. Detecting subclinical KC would lead to better management to avoid the need for corneal grafts, but the condition is clinically challenging to diagnose. We wished to compare eight commonly used machine learning algorithms using a range of parameter combinations by applying them to our KC dataset and build models to better differentiate subclinical KC from non-KC eyes.

Methods

Oculus Pentacam was used to obtain corneal parameters on 49 subclinical KC and 39 control eyes, along with clinical and demographic parameters. Eight machine learning methods were applied to build models to differentiate subclinical KC from control eyes. Dominant algorithms were trained with all combinations of the considered parameters to select important parameter combinations. The performance of each model was evaluated and compared.

Results

Using a total of eleven parameters, random forest, support vector machine and k-nearest neighbors had better performance in detecting subclinical KC. The highest area under the curve of 0.97 for detecting subclinical KC was achieved using five parameters by the random forest method. The highest sensitivity (0.94) and specificity (0.90) were obtained by the support vector machine and the k-nearest neighbor model, respectively.

Conclusions

This study showed machine learning algorithms can be applied to identify subclinical KC using a minimal parameter set that are routinely collected during clinical eye examination.

Translational Relevance

Machine learning algorithms can be built using routinely collected clinical parameters that will assist in the objective detection of subclinical KC.

Do age-related macular degeneration genes show association with keratoconus?

Background

Keratoconus (KC) is a common corneal condition with an unknown gender predominance. Although numerous studies have investigated the genetic component of KC, no specific genes have yet been attributed to the condition. We recently reported posterior segment changes occurring in the eyes of KC patients. However, it is not clear whether these changes are part of KC pathogenesis or reflect changes in anatomical features of the eye manifested by changes at the cornea. Given retinal changes represent the main characteristics observed in age-related macular degeneration (AMD) and that pleiotropy has been demonstrated between different eye diseases, we wished to assess if known AMD associated genes were also associated with KC.

Methods

A total of 248 KC subjects and 366 non-KC (control) subjects were recruited from public and private clinics in Melbourne for this analysis. Nineteen single nucleotide polymorphisms (SNPs) previously associated with AMD, including rs10490924 (ARMS2/HTRA1), rs10737680 (CFH), rs13278062 (TNFRSF10A), rs1864163 (CETP), rs2230199 (C3), rs3130783 (IER3/DDR1), rs334353 (TGFBR1), rs3812111 (COL10A1), rs429608 (C2/CFB), rs4420638 (APOE), rs4698775 (CFI), rs5749482 (TIMP3), rs6795735 (ADAMTS9), rs8017304 (RAD51B), rs8135665 (SLC16A8), rs920915 (LIPC), rs943080 (VEGFA), rs9542236 (B3GALTL) and rs13081855 (COL8A1/FILIP1L), were genotyped in this cohort. Logistic regression was applied to evaluate the association between these SNPs and KC on both genders together, as well as each gender separately. Linear regression was also applied to assess the association between SNPs and corneal curvature. Bonferroni correction was applied to adjust for multiple testing.

Results

Genotyping data were available for 18 SNPs. The SNP, rs6795735 (ADAMTS9) was significantly associated with KC (p = 3.5 × 10^- 4) when both genders were assessed, whereas rs5749482 (TIMP3) was only associated in males (p = 7.7 × 10^- 4) following Bonferroni multiple correction. However, when the covariates of age and gender were included, the associations became non-significant. In addition, none of the SNPs appeared significant for corneal curvature.

Conclusions

Our study suggested a potential association of rs6795735 in the ADAMTS9 gene and rs5749482 in the TIMP3 gene in KC and that different associations may be gender specific. Overall, SNPs initially identified as associated with AMD following multiple correction may be further impacted by other factors such as age or gender and further studies are needed to resolve this issue.

Gene Expression and Pathways Underlying Form Deprivation Myopia in the Guinea Pig Sclera

Purpose

Posterior scleral remodeling accompanies myopia. In guinea pigs developing myopia, the region around the optic nerve (peripapillary zone, PPZ) rapidly expands followed by inhibition in eye size in the periphery. We studied the differential gene expression in the sclera that accompanies these changes.

Methods

Guinea pigs were form-deprived (FD) for 2 weeks to induce myopia, while the fellow eye served as a control. After 2 weeks, the PPZ and the peripheral temporal sclera were isolated in representative animals to extract the RNA. RNA sequencing was undertaken using an Illumina HiSeq 2000, with differential expression analyzed using Voom and pathways analyzed using the Ingenuity Pathway Analysis tool. RNA from additional PPZ and peripheral temporal sclera in FD and fellow eyes was used for validation of gene expression using quantitative real-time PCR (qRT-PCR).

Results

In myopic sclera, 348 genes were differentially expressed between PPZ and the peripheral temporal region (corrected P < 0.05), of which 61 were differentially expressed in the PPZ between myopic and control eyes. Pathway analyses of these gene sets showed the involvement of Gαi signaling along with previously reported gamma-aminobutyric acid (GABA) and glutamate receptors among numerous novel pathways. The expression pattern of three novel genes and two myopia-related genes was validated using qRT-PCR.

Conclusions

Gene expression changes are associated with the rapid elongation that occurs around the optic nerve region during the development of myopia. A prominent change in Gαi signaling, which affects cAMP synthesis and thus collagen levels, may be critical in mediating the regional changes in myopic sclera.

Association of Genetic Variants With Response to Anti-Vascular Endothelial Growth Factor Therapy in Age-Related Macular Degeneration

Importance

Visual acuity (VA) outcomes differ considerably among patients with neovascular age-related macular degeneration (nAMD) treated with anti-vascular endothelial growth factor (VEGF) drugs. Identification of pharmacogenetic associations may help clinicians understand the mechanisms underlying this variability as well as pave the way for personalized treatment in nAMD.

Objective

To identify genetic factors associated with variability in the response to anti-VEGF therapy for patients with nAMD.

Design, Setting, and Participants

In this multicenter genome-wide association study, 678 patients with nAMD with genome-wide genotyping data were included in the discovery phase; 1380 additional patients with nAMD were genotyped for selected common variants in the replication phase. All participants received 3 monthly injections of bevacizumab or ranibizumab. Clinical data were evaluated for inclusion/exclusion criteria from October 2014 to October 2015, followed by data analysis from October 2015 to February 2016. For replication cohort genotyping, clinical data collection and analysis (including meta-analysis) was performed from March 2016 to April 2017.

Main Outcomes and Measures

Change in VA after the loading dose of 3 monthly anti-VEGF injections compared with baseline.

Results

Of the 2058 included patients, 1210 (58.8%) were women, and the mean (SD) age across all cohorts was 78 (7.4) years. Patients included in the discovery cohort and most of the patients in the replication cohorts were of European descent. The mean (SD) baseline VA was 51.3 (20.3) Early Treatment Diabetic Retinopathy Study (ETDRS) score letters, and the mean (SD) change in VA after the loading dose of 3 monthly injections was a gain of 5.1 (13.9) ETDRS score letters (ie, 1-line gain). Genome-wide single-variant analyses of common variants revealed 5 independent loci that reached a P value less than 10 × 10-5. After replication and meta-analysis of the lead variants, rs12138564 located in the CCT3 gene remained nominally associated with a better treatment outcome (ETDRS letter gain, 1.7; β, 0.034; SE, 0.008; P = 1.38 × 10-5). Genome-wide gene-based optimal unified sequence kernel association test of rare variants showed genome-wide significant associations for the C10orf88 (P = 4.22 × 10-7) and UNC93B1 (P = 6.09 × 10-7) genes, in both cases leading to a worse treatment outcome. Patients carrying rare variants in the C10orf88 and UNC93B1 genes lost a mean (SD) VA of 30.6 (17.4) ETDRS score letters (ie, loss of 6.09 lines) and 26.5 (13.8) ETDRS score letters (ie, loss of 5.29 lines), respectively, after 3 months of anti-VEGF treatment.

Conclusions and Relevance

We propose that there is a limited contribution of common genetic variants to variability in nAMD treatment response. Our results suggest that rare protein-altering variants in the C10orf88 and UNC93B1 genes are associated with a worse response to anti-VEGF therapy in patients with nAMD, but these results require further validation in other cohorts.

Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error

Refractive errors, including myopia, are the most frequent eye disorders worldwide and an increasingly common cause of blindness. This genome-wide association meta-analysis in 160,420 participants and replication in 95,505 participants increased the number of established independent signals from 37 to 161 and showed high genetic correlation between Europeans and Asians (>0.78). Expression experiments and comprehensive in silico analyses identified retinal cell physiology and light processing as prominent mechanisms, and also identified functional contributions to refractive-error development in all cell types of the neurosensory retina, retinal pigment epithelium, vascular endothelium and extracellular matrix. Newly identified genes implicate novel mechanisms such as rod-and-cone bipolar synaptic neurotransmission, anterior-segment morphology and angiogenesis. Thirty-one loci resided in or near regions transcribing small RNAs, thus suggesting a role for post-transcriptional regulation. Our results support the notion that refractive errors are caused by a light-dependent retina-to-sclera signaling cascade and delineate potential pathobiological molecular drivers.

Changing vision: a review of pharmacogenetic studies for treatment response in age-related macular degeneration patients

Nonresponsiveness to age-related macular degeneration (AMD) treatments has become a growing concern in ophthalmology. Disparity among publications that have assessed pharmacogenetic (PGx) connections between AMD disease genes and treatments has delayed the implementation of PGx testing in AMD. We assessed all AMD PGx publications to identify the degree of agreement for publications within similar ethnic cohorts and worldwide, and the causes for differences in study outcomes. There are no accepted genotype–phenotype correlations, either within similar ethnic cohorts or worldwide. The diversity of measured outcomes, treatment protocols and statistical methods used may be causing this discrepancy. A universally accepted treatment protocol and the creation of agreed response group classification may bridge the gap between AMD PGx publications.

A genome-wide association study of corneal astigmatism: The CREAM Consortium

Purpose

To identify genes and genetic markers associated with corneal astigmatism.

Methods

A meta-analysis of genome-wide association studies (GWASs) of corneal astigmatism undertaken for 14 European ancestry (n=22,250) and 8 Asian ancestry (n=9,120) cohorts was performed by the Consortium for Refractive Error and Myopia. Cases were defined as having >0.75 diopters of corneal astigmatism. Subsequent gene-based and gene-set analyses of the meta-analyzed results of European ancestry cohorts were performed using VEGAS2 and MAGMA software. Additionally, estimates of single nucleotide polymorphism (SNP)-based heritability for corneal and refractive astigmatism and the spherical equivalent were calculated for Europeans using LD score regression.

Results

The meta-analysis of all cohorts identified a genome-wide significant locus near the platelet-derived growth factor receptor alpha (PDGFRA) gene: top SNP: rs7673984, odds ratio=1.12 (95% CI:1.08-1.16), p=5.55×10^-9. No other genome-wide significant loci were identified in the combined analysis or European/Asian ancestry-specific analyses. Gene-based analysis identified three novel candidate genes for corneal astigmatism in Europeans-claudin-7 (CLDN7), acid phosphatase 2, lysosomal (ACP2), and TNF alpha-induced protein 8 like 3 (TNFAIP8L3).

Conclusions

In addition to replicating a previously identified genome-wide significant locus for corneal astigmatism near the PDGFRA gene, gene-based analysis identified three novel candidate genes, CLDN7, ACP2, and TNFAIP8L3, that warrant further investigation to understand their role in the pathogenesis of corneal astigmatism. The much lower number of genetic variants and genes demonstrating an association with corneal astigmatism compared to published spherical equivalent GWAS analyses suggest a greater influence of rare genetic variants, non-additive genetic effects, or environmental factors in the development of astigmatism.

Joint Analysis of Nuclear and Mitochondrial Variants in Age-Related Macular Degeneration Identifies Novel Loci TRPM1 and ABHD2/RLBP1

Purpose

Presently, 52 independent nuclear single nucleotide polymorphisms (nSNPs) have been associated with age-related macular degeneration (AMD) but their effects do not explain all its variance. Genetic interactions between the nuclear and mitochondrial (mt) genome may unearth additional genetic loci previously unassociated with AMD risk.

Methods

Joint effects of nSNPs and selected mtSNPs were analyzed by two degree of freedom (2df) joint tests of association in the International AMD Genomics Consortium (IAMDGC) dataset (17,832 controls and 16,144 advanced AMD cases of European ancestry). Subjects were genotyped on the Illumina HumanCoreExome array. After imputation using MINIMAC and the 1000 Genomes Project Phase I reference panel, pairwise linkage disequilibrium pruning, and quality control, 3.9 million nSNPs were analyzed for interaction with mtSNPs chosen based on association in this dataset or publications: A4917G, T5004C, G12771A, and C16069T.

Results

Novel locus TRPM1 was identified with genome-wide significant joint effects (P < 5.0 × 10⁻⁸) of two intronic TRPM1 nSNPs and AMD-associated nonsynonymous MT-ND2 mtSNP A4917G. Stratified analysis by mt allele identified an association only in 4917A (major allele) carriers (P = 4.4 × 10⁻⁹, odds ratio [OR] = 0.90, 95% confidence interval [CI] = 0.87–0.93). Intronic and intergenic ABHD2/RLBP1 nSNPs demonstrated genome-wide significant joint effects (2df joint test P values from 1.8 × 10⁻⁸ to 4.9 × 10⁻⁸) and nominally statistically significant interaction effects with MT-ND5 synonymous mtSNP G12771A. Although a positive association was detected in both strata, the association was stronger in 12771A subjects (P = 0.0020, OR = 2.17, 95% CI = 1.34–3.60).

Conclusions

These results show that joint tests of main effects and gene–gene interaction reveal associations at some novel loci that were missed when considering main effects alone.

Loss of Function of P2X7 Receptor Scavenger Activity in Aging Mice: A Novel Model for Investigating the Early Pathogenesis of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a leading cause of irreversible, severe vision loss in Western countries. Recently, we identified a novel pathway involving P2X7 receptor scavenger function expressed on ocular immune cells as a risk factor for advanced AMD. In this study, we investigate the effect of loss of P2X7 receptor function on retinal structure and function during aging. P2X7-null and wild-type C57bl6J mice were investigated at 4, 12, and 18 months of age for macrophage phagocytosis activity, ocular histological changes, and retinal function. Phagocytosis activity of blood-borne macrophages decreased with age at 18 months in the wild-type mouse. Lack of P2X7 receptor function reduced phagocytosis at all ages compared to wild-type mice. At 12 months of age, P2X7-null mice had thickening of Bruchs membrane and retinal pigment epithelium dysfunction. By 18 months of age, P2X7-null mice displayed phenotypic characteristics consistent with early AMD, including Bruchs membrane thickening, retinal pigment epithelium cell loss, retinal functional deficits, and signs of subretinal inflammation. Our present study shows that loss of function of the P2X7 receptor in mice induces retinal changes representing characteristics of early AMD, providing a valuable model for investigating the role of scavenger receptor function and the immune system in the development of this age-related disease.

A decade of age-related macular degeneration risk models: What have we learned from them and where are we going?

The genomic revolution has revealed the complexity of multifactorial diseases, making the development of effective diagnostics extremely challenging. In turn, the prospect of precision medicine as applied through targeted therapeutic treatments continues to remain largely elusive. Age-related macular degeneration (AMD) as a complex disease falls under this category, despite it being one of the most well characterized multifactorial diseases. This reflects both the extent of identified genetic components and known environmental risk factors. Additional considerations in dissecting out the roles played by genetic and non-genetic risk factors arise through the rapid increase in prevalence of AMD with age and the varying time periods over which disease progression can occur, complicating efforts to discriminate between "progressors" and non-"progressors." As a consequence, extensive research into the aetiology of AMD is yet to realize a clinically acceptable predictive test. This review covers the current climate of risk models in late AMD but will focus mainly on genetic risk factors as well as the types of models that have currently been employed in the AMD modelling literature.

GWAS study using DNA pooling strategy identifies association of variant rs4910623 in OR52B4 gene with anti-VEGF treatment response in age-related macular degeneration

Pooled DNA based GWAS to determine genetic association of SNPs with visual acuity (VA) outcome in anti-vascular endothelial growth factor (anti-VEGF) treated neovascular age-related macular degeneration (nAMD) patients. We performed pooled DNA based GWAS on 285 anti-VEGF treated nAMD patients using high density Illumina 4.3 M array. Primary outcome was change in VA in Early Treatment Diabetic Retinopathy Study (ETDRS) letters after 6 months of anti-VEGF treatment (patients who lost ≥5 ETDRS letters classified as non-responders and all remaining classified as responders). GWAS analysis identified 44 SNPs of interest: 37 with strong evidence of association (p < 9 × 10⁻⁸), 2 in drug resistance genes (p < 5 × 10⁻⁶) and 5 nonsynonymous changes (p < 1 × 10⁻⁴). In the validation phase, individual genotyping of 44 variants showed three SNPs (rs4910623 p = 5.6 × 10⁻⁵, rs323085 p = 6.5 × 10⁻⁴ and rs10198937 p = 1.30 × 10⁻³) remained associated with VA response at 6 months. SNP rs4910623 also associated with treatment response at 3 months (p = 1.5 × 10⁻³). Replication of these three SNPs in 376 patients revealed association of rs4910623 with poor VA response after 3 and 6 months of treatment (p = 2.4 × 10⁻³ and p = 3.5 × 10⁻², respectively). Meta-analysis of both cohorts (673 samples) confirmed association of rs4910623 with poor VA response after 3 months (p = 1.2 × 10⁻⁵) and 6 months (p = 9.3 × 10⁻⁶) of treatment in nAMD patients.

Pooled genome wide association detects association upstream of FCRL3 with Graves' disease

Background

Graves’ disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves’ disease and it is therefore likely that these can be identified by genome wide association studies. This study aimed to determine if a genome wide association study, using a pooling methodology, could detect genomic loci associated with Graves’ disease.

Results

Nineteen of the top ranking single nucleotide polymorphisms including HLA-DQA1 and C6orf10, were clustered within the Major Histo-compatibility Complex region on chromosome 6p21, with rs1613056 reaching genome wide significance (p = 5 × 10⁻⁸). Technical validation of top ranking non-Major Histo-compatablity complex single nucleotide polymorphisms with individual genotyping in the discovery cohort revealed four single nucleotide polymorphisms with p ≤ 10⁻⁴. Rs17676303 on chromosome 1q23.1, located upstream of FCRL3, showed evidence of association with Graves’ disease across the discovery, replication and combined cohorts. A second single nucleotide polymorphism rs9644119 downstream of DPYSL2 showed some evidence of association supported by finding in the replication cohort that warrants further study.

Conclusions

Pooled genome wide association study identified a genetic variant upstream of FCRL3 as a susceptibility locus for Graves’ disease in addition to those identified in the Major Histo-compatibility Complex. A second locus downstream of DPYSL2 is potentially a novel genetic variant in Graves’ disease that requires further confirmation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3276-z) contains supplementary material, which is available to authorized users.

Meta-analysis of gene-environment-wide association scans accounting for education level identifies additional loci for refractive error

Myopia is the most common human eye disorder and it results from complex genetic and environmental causes. The rapidly increasing prevalence of myopia poses a major public health challenge. Here, the CREAM consortium performs a joint meta-analysis to test single-nucleotide polymorphism (SNP) main effects and SNP × education interaction effects on refractive error in 40,036 adults from 25 studies of European ancestry and 10,315 adults from 9 studies of Asian ancestry. In European ancestry individuals, we identify six novel loci (FAM150B-ACP1, LINC00340, FBN1, DIS3L-MAP2K1, ARID2-SNAT1 and SLC14A2) associated with refractive error. In Asian populations, three genome-wide significant loci AREG, GABRR1 and PDE10A also exhibit strong interactions with education (P<8.5 × 10(-5)), whereas the interactions are less evident in Europeans. The discovery of these loci represents an important advance in understanding how gene and environment interactions contribute to the heterogeneity of myopia.

Reticular Pseudodrusen and Their Association with Age-Related Macular Degeneration: The Melbourne Collaborative Cohort Study

PURPOSE

To determine the prevalence of reticular pseudodrusen (RPD) and its association with age-related macular degeneration (AMD) and AMD risk factors in a large sample.

DESIGN

Community-based cohort study in Melbourne, Victoria, Australia.

PARTICIPANTS

A total of 21,130 participants 48 to 86 years of age available for ophthalmic assessment at follow-up from 2003 through 2007.

METHODS

Lifestyle, diet, and anthropometric measurements were obtained at baseline and follow-up. At follow-up, digital macular color photographs were graded for early, intermediate, and late AMD as well as the presence of RPD. Data were analyzed using multinomial logistic regression controlling for age, gender, smoking, country of birth, and diet.

MAIN OUTCOME MEASURES

Detection of RPD based on color fundus photographs.

RESULTS

Prevalence of RPD was 0.41% (87 of 21,130 participants), with 51% having bilateral RPD. Patients with RPD were older compared with patients with large drusen (>125 μm; 76±4 vs. 68±9 years; P < 0.001). Increasing age, female gender, being a current smoker, as well as focal pigmentary abnormalities and large drusen (>125 μm) were associated with a higher prevalence of RPD. Presence of geographic atrophy (GA) was associated with the highest odds of having RPD (odds ratio [OR], 153; 95% confidence interval [CI], 53-442), followed by choroidal neovascularization (CNV; OR, 90; 95% CI, 26-310), intermediate AMD (OR, 33; 95% CI, 14-77), and early AMD (OR, 12; 95% CI, 5-31) compared with those with no AMD. The ARMS2 single nucleotide polymorphism (SNP) rs10490924, HTRA1 SNPs rs11200638 and rs3793917, and CFH SNPs rs393955, rs1061170, and rs2274700 were associated with increased prevalence of RPD (all P < 0.05).

CONCLUSIONS

Reticular pseudodrusen are highly concurrent with AMD and have similar associations with known AMD risk factors such as age, gender, smoking, and genetic risk factors. Reticular pseudodrusen are associated more strongly with GA than with CNV. Although RPD are not specific to AMD, they are likely to be a strong risk factor for progression to late-stage AMD, similar to focal pigmentary abnormalities and large drusen.

Association Study of Mannose-Binding Lectin Levels and Genetic Variants in Lectin Pathway Proteins with Susceptibility to Age-Related Macular Degeneration: A Case-Control Study

BACKGROUND

In age-related macular degeneration (AMD) the complement system is thought to be activated by chronic oxidative damage with genetic variants identified in the alternative pathway as susceptibility factors. However, the involvement of the lectin pathway of complement, a key mediator of oxidative damage, is controversial. This study investigated whether mannose-binding lectin (MBL) levels and genetic variants in lectin pathway proteins, are associated with the predisposition to and severity of AMD.

METHODS

MBL levels and single nucleotide polymorphisms (SNPs) in the MBL2 and the ficolin-2 (FCN2) gene were determined in 109 patients with AMD and 109 age- and sex-matched controls.

RESULTS

MBL expression levels were equally distributed in both cases (early and late AMD) and controls (p>0.05). However, there was a trend towards higher median MBL levels in cases with late AMD compared to cases with early AMD (1.0 vs. 0.4 μg/ml, p = 0.09) and MBL deficiency (<0.5 μg/ml) was encountered less frequently in the late AMD group (35% vs 56%, p = 0.03). FCN2 and MBL2 allele frequencies were similarly distributed in early and late AMD cases compared with controls (p>0.05 for all analyses) as were MBL2 genotypes. Similarly, there was no significant difference in allele frequencies in any SNPs in either the MBL2 or FCN2 gene in cases with early vs. late AMD.

CONCLUSIONS

SNPs of lectin pathway proteins investigated in this study were not associated with AMD or AMD severity. However, MBL levels deserve further study in a larger cohort of early vs. late AMD patients to elucidate any real effect on AMD severity.