Validating Variational Bayes Linear Regression Method With Multi-Central Datasets.

PurposeTo validate the prediction accuracy of variational Bayes linear regression (VBLR) with two datasets external to the training dataset.MethodThe training dataset consisted of 7268 eyes of 4278 subjects from the University of Tokyo Hospital. The Japanese Archive of Multicentral Databases in Glaucoma (JAMDIG) dataset consisted of 271 eyes of 177 patients, and the Diagnostic Innovations in Glaucoma Study (DIGS) dataset includes 248 eyes of 173 patients, which were used for validation. Prediction accuracy was compared between the VBLR and ordinary least squared linear regression (OLSLR). First, OLSLR and VBLR were carried out using total deviation (TD) values at each of the 52 test points from the second to fourth visual fields (VFs) (VF2-4) to 2nd to 10th VF (VF2-10) of each patient in JAMDIG and DIGS datasets, and the TD values of the 11th VF test were predicted every time. The predictive accuracy of each method was compared through the root mean squared error (RMSE) statistic.ResultsOLSLR RMSEs with the JAMDIG and DIGS datasets were between 31 and 4.3 dB, and between 19.5 and 3.9 dB. On the other hand, VBLR RMSEs with JAMDIG and DIGS datasets were between 5.0 and 3.7, and between 4.6 and 3.6 dB. There was statistically significant difference between VBLR and OLSLR for both datasets at every series (VF2-4 to VF2-10) (P < 0.01 for all tests). However, there was no statistically significant difference in VBLR RMSEs between JAMDIG and DIGS datasets at any series of VFs (VF2-2 to VF2-10) (P > 0.05).ConclusionsVBLR outperformed OLSLR to predict future VF progression, and the VBLR has a potential to be a helpful tool at clinical settings

Diagnosis of choroidal disease with deep learning-based image enhancement and volumetric quantification of optical coherence tomography

Purpose: The purpose of this study was to quantify choroidal vessels (CVs) in pathological eyes in three dimensions (3D) using optical coherence tomography (OCT) and a deep-learning analysis. Methods: A single-center retrospective study including 34 eyes of 34 patients (7 women and 27 men) with treatment-naïve central serous chorioretinopathy (CSC) and 33 eyes of 17 patients (7 women and 10 men) with Vogt-Koyanagi-Harada disease (VKH) or sympathetic ophthalmitis (SO) were imaged consecutively between October 2012 and May 2019 with a swept source OCT. Seventy-seven eyes of 39 age-matched volunteers (26 women and 13 men) with no sign of ocular pathology were imaged for comparison. Deep-learning-based image enhancement pipeline enabled CV segmentation and visualization in 3D, after which quantitative vessel volume maps were acquired to compare normal and diseased eyes and to track the clinical course of eyes in the disease group. Region-based vessel volumes and vessel indices were utilized for disease diagnosis. Results: OCT-based CV volume maps disclose regional CV changes in patients with CSC, VKH, or SO. Three metrics, (i) choroidal volume, (ii) CV volume, and (iii) CV index, exhibit high sensitivity and specificity in discriminating pathological choroids from healthy ones. Conclusions: The deep-learning analysis of OCT images described here provides a 3D visualization of the choroid, and allows quantification of features in the datasets to identify choroidal disease and distinguish between different diseases. Translational Relevance: This novel analysis can be applied retrospectively to existing OCT datasets, and it represents a significant advance toward the automated diagnosis of choroidal pathologies based on observations and quantifications of the vasculature

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Defects of the lamina cribrosa in eyes with localized retinal nerve fiber layer loss.

ObjectiveTo determine whether focal abnormalities of the lamina cribrosa (LC) are present in glaucomatous eyes with localized retinal nerve fiber layer (RNFL) defects.DesignCross-sectional, observational study.ParticipantsWe analyzed 20 eyes of 14 subjects with localized RNFL defects detected by masked grading of stereophotographs and 40 eyes of 25 age-matched healthy subjects recruited from the Diagnostic Innovations in Glaucoma Study at the University of California, San Diego.MethodsAll eyes had stereoscopic optic disc photography and in vivo LC imaging using enhanced depth imaging optical coherence tomography (EDI-OCT). Two masked graders identified focal LC defects defined by a standardized protocol using 48 radial scan EDI-OCT images. The kappa coefficient was calculated as a measure of the reliability of interobserver agreement.Main outcome measuresThe number of focal LC defects and the relationship between the location of LC defects and the location of localized RNFL defects.ResultsOf 20 eyes with a localized RNFL defect, 15 (75%) had ≥1 LC defect compared with only 1 of 40 healthy eyes (3%). There were 13 eyes with localized RNFL defects that had 1 LC defect, 1 eye with 2 LC defects, and 1eye with 3 LC defects. The largest area LC defect was present in a radial line EDI-OCT scan corresponding with a localized RNFL defect in 13 of 15 eyes (87%). There was good agreement between graders as to whether an eye had an LC defect (kappa = 0.87; 95% confidence interval [CI], 0.73-1.00; P<0.001) and the location of the largest defect (kappa = 0.72; 95% CI, 0.44-1.00; P<0.001).ConclusionsFocal defects of the LC were frequently visible in glaucomatous eyes with localized RNFL defects. Focal abnormalities of the LC may be associated with focal retinal nerve fiber damage

Birefringence-derived artifact in optical coherence tomography imaging of the lamina cribrosa in eyes with glaucoma

Abstract We investigated birefringence-derived artifacts that potentially mimic focal defects of the lamina cribrosa (focal LC defects) in optical coherence tomography (OCT) imaging of eyes with glaucoma. This study included 74 eyes of 48 patients with glaucoma. Five horizontal line B-scan images of the optic disc were obtained using commercial swept-source OCT. From a dataset of prototype swept-source polarization-diversity OCT, we calculated the following types of OCT images: polarization-dependent, polarization-dependent attenuation-coefficient, polarization-independent, and polarization-independent attenuation-coefficient. We assessed the commercial OCT images for the presence of birefringence-derived artifacts by comparison with the polarization-diversity OCT images. Commercial OCT showed suggestive findings of focal LC defects in 17 of 74 eyes. Reevaluation using polarization-independent OCT revealed that the focal LC defects in one of 17 eyes (5.9%) were actually birefringence-derived artifacts. This study demonstrated the existence of birefringence-derived artifacts mimicking focal LC defects in commercial OCT imaging and indicated that polarization-diversity OCT is an effective tool to evaluate the presence of these artifacts

Defects of the lamina cribrosa in eyes with localized retinal nerve fiber layer loss.

ObjectiveTo determine whether focal abnormalities of the lamina cribrosa (LC) are present in glaucomatous eyes with localized retinal nerve fiber layer (RNFL) defects.DesignCross-sectional, observational study.ParticipantsWe analyzed 20 eyes of 14 subjects with localized RNFL defects detected by masked grading of stereophotographs and 40 eyes of 25 age-matched healthy subjects recruited from the Diagnostic Innovations in Glaucoma Study at the University of California, San Diego.MethodsAll eyes had stereoscopic optic disc photography and in vivo LC imaging using enhanced depth imaging optical coherence tomography (EDI-OCT). Two masked graders identified focal LC defects defined by a standardized protocol using 48 radial scan EDI-OCT images. The kappa coefficient was calculated as a measure of the reliability of interobserver agreement.Main outcome measuresThe number of focal LC defects and the relationship between the location of LC defects and the location of localized RNFL defects.ResultsOf 20 eyes with a localized RNFL defect, 15 (75%) had ≥1 LC defect compared with only 1 of 40 healthy eyes (3%). There were 13 eyes with localized RNFL defects that had 1 LC defect, 1 eye with 2 LC defects, and 1eye with 3 LC defects. The largest area LC defect was present in a radial line EDI-OCT scan corresponding with a localized RNFL defect in 13 of 15 eyes (87%). There was good agreement between graders as to whether an eye had an LC defect (kappa = 0.87; 95% confidence interval [CI], 0.73-1.00; P<0.001) and the location of the largest defect (kappa = 0.72; 95% CI, 0.44-1.00; P<0.001).ConclusionsFocal defects of the LC were frequently visible in glaucomatous eyes with localized RNFL defects. Focal abnormalities of the LC may be associated with focal retinal nerve fiber damage