Discovery and genotyping of structural variation from long-read haploid genome sequence data

In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that &gt;89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF &gt; 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.</jats:p

Characterization of Errors in Retinopathy of Prematurity Diagnosis by Ophthalmologists-in-Training in the United States and Canada

PURPOSE: To identify the prominent factors that lead to misdiagnosis of retinopathy of prematurity (ROP) by ophthalmologists-in-training in the United States and Canada. METHODS: This prospective cohort study included 32 ophthalmologists-in-training at six ophthalmology training programs in the United States and Canada. Twenty web-based cases of ROP using wide-field retinal images were presented, and ophthalmologists-in-training were asked to diagnose plus disease, zone, stage, and category for each eye. Responses were compared to a consensus reference standard diagnosis for accuracy, which was established by combining the clinical diagnosis and the image-based diagnosis by multiple experts. The types of diagnostic errors that occurred were analyzed with descriptive and chi-squared analysis. Main outcome measures were frequency of types (category, zone, stage, plus disease) of diagnostic errors; association of errors in zone, stage, and plus disease diagnosis with incorrectly identified category; and performance of ophthalmologists-in-training across postgraduate years. RESULTS: Category of ROP was misdiagnosed at a rate of 48%. Errors in classification of plus disease were most commonly associated with misdiagnosis of treatment-requiring (plus error rate = 16% when treatment-requiring was correctly diagnosed vs 81% when underdiagnosed as type 2 or pre-plus; mean difference: 64.3; 95% CI: 51.9 to 76.7; CONCLUSIONS: Ophthalmologists-in-training in the United States and Canada misdiagnosed ROP nearly half of the time, with incorrect identification of plus disease as a leading cause. Integration of structured learning for ROP in residency education may improve diagnostic competency

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Telemedical Diagnosis of Stage 4 and Stage 5 Retinopathy of Prematurity

To determine the accuracy of image-based diagnosis for stage 4 or worse retinopathy of prematurity (ROP) disease. Prospective cohort study. We prospectively obtained data, from 8 major ROP centers, for 1220 eye examinations from 230 infants. An ophthalmologist at each center provided a clinical diagnosis using indirect ophthalmoscopy. Wide-angle retinal images (RetCam; Clarity Medical Systems, Pleasanton, CA) were then obtained, and these were independently read by 2 ROP experts using a web-based system for an image-based diagnosis. Sensitivity and specificity of image-based diagnosis from the ROP experts were calculated using the clinical diagnosis as the reference standard. Of 1220 examinations, 28 (2%) had a clinical diagnosis of stage 4 or worse. Sensitivity and specificity for stage 4 or worse disease were 75% and 99% for expert 1, and 86% and 99% for expert 2. Sensitivity and specificity for the detection of stage 5 disease were 69% and 99% for both experts. There are inconsistencies in the accuracy of image-based diagnosis of stage 4 and stage 5 ROP when compared with the clinical diagnosis

Accuracy and Reliability of Eye-Based vs Quadrant-Based Diagnosis of Plus Disease in Retinopathy of Prematurity

This multicenter cohort study compares eye-based vs quadrant-based diagnosis of plus disease in infants with retinopathy of prematurity and provides insight for ophthalmologists about the diagnostic process

Automated Fundus Image Quality Assessment in Retinopathy of Prematurity Using Deep Convolutional Neural Networks

Accurate image-based ophthalmic diagnosis relies on fundus image clarity. This has important implications for the quality of ophthalmic diagnoses and for emerging methods such as telemedicine and computer-based image analysis. The purpose of this study was to implement a deep convolutional neural network (CNN) for automated assessment of fundus image quality in retinopathy of prematurity (ROP). Experimental study. Retinal fundus images were collected from preterm infants during routine ROP screenings. Six thousand one hundred thirty-nine retinal fundus images were collected from 9 academic institutions. Each image was graded for quality (acceptable quality [AQ], possibly acceptable quality [PAQ], or not acceptable quality [NAQ]) by 3 independent experts. Quality was defined as the ability to assess an image confidently for the presence of ROP. Of the 6139 images, NAQ, PAQ, and AQ images represented 5.6%, 43.6%, and 50.8% of the image set, respectively. Because of low representation of NAQ images in the data set, images labeled NAQ were grouped into the PAQ category, and a binary CNN classifier was trained using 5-fold cross-validation on 4000 images. A test set of 2109 images was held out for final model evaluation. Additionally, 30 images were ranked from worst to best quality by 6 experts via pairwise comparisons, and the CNN's ability to rank quality, regardless of quality classification, was assessed. The CNN performance was evaluated using area under the receiver operating characteristic curve (AUC). A Spearman's rank correlation was calculated to evaluate the overall ability of the CNN to rank images from worst to best quality as compared with experts. The mean AUC for 5-fold cross-validation was 0.958 (standard deviation, 0.005) for the diagnosis of AQ versus PAQ images. The AUC was 0.965 for the test set. The Spearman's rank correlation coefficient on the set of 30 images was 0.90 as compared with the overall expert consensus ranking. This model accurately assessed retinal fundus image quality in a comparable manner with that of experts. This fully automated model has potential for application in clinical settings, telemedicine, and computer-based image analysis in ROP and for generalizability to other ophthalmic diseases

Assessment of a Tele-education System to Enhance Retinopathy of Prematurity Training by International Ophthalmologists-in-Training in Mexico

To evaluate a tele-education system developed to improve diagnostic competency in retinopathy of prematurity (ROP) by ophthalmologists-in-training in Mexico. Prospective, randomized cohort study. Fifty-eight ophthalmology residents and fellows from a training program in Mexico consented to participate. Twenty-nine of 58 trainees (50%) were randomized to the educational intervention (pretest, ROP tutorial, ROP educational chapters, and posttest), and 29 of 58 trainees (50%) were randomized to a control group (pretest and posttest only). A secure web-based educational system was created using clinical cases (20 pretest, 20 posttest, and 25 training chapter-based) developed from a repository of over 2500 unique image sets of ROP. For each image set used, a reference standard ROP diagnosis was established by combining the clinical diagnosis by indirect ophthalmoscope examination and image-based diagnosis by multiple experts. Trainees were presented with image-based clinical cases of ROP during a pretest, posttest, and training chapters. The accuracy of ROP diagnosis (e.g., plus disease, zone, stage, category) was determined using sensitivity and specificity calculations from the pretest and posttest results of the educational intervention group versus control group. The unweighted kappa statistic was used to analyze the intragrader agreement for ROP diagnosis by the ophthalmologists-in-training during the pretest and posttest for both groups. Trainees completing the tele-education system had statistically significant improvements (P < 0.01) in the accuracy of ROP diagnosis for plus disease, zone, stage, category, and aggressive posterior ROP (AP-ROP). Compared with the control group, trainees who completed the ROP tele-education system performed better on the posttest for accurately diagnosing plus disease (67% vs. 48%; P = 0.04) and the presence of ROP (96% vs. 91%; P < 0.01). The specificity for diagnosing AP-ROP (94% vs. 78%; P < 0.01), type 2 ROP or worse (92% vs. 84%; P = 0.04), and ROP requiring treatment (89% vs. 79%; P < 0.01) was better for the trainees completing the tele-education system compared with the control group. Intragrader agreement improved for identification of plus disease, zone, stage, and category of ROP after completion of the educational intervention. A tele-education system for ROP education was effective in improving the diagnostic accuracy of ROP by ophthalmologists-in-training in Mexico. This system has the potential to increase competency in ROP diagnosis and management for ophthalmologists-in-training from middle-income nations