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Automated 3-D Retinal Layer Segmentation of Macular Optical Coherence Tomography Images with Serous Pigment Epithelial Detachments.
IEEE Trans Med Imaging. 2014 Sep 24;
Authors: Shi F, Chen X, Zhao H, Zhu W, Xiang D, Gao E, Sonka M, Chen H
Automated retinal layer segmentation of optical coherence tomography (OCT) images has been successful for normal eyes but becomes challenging for eyes with retinal diseases if the retinal morphology experiences critical changes. We pro-pose a method to automatically segment the retinal layers in 3-D OCT data with serous retinal pigment epithelial detachments (PED), which is a prominent feature of many chorioretinal disease processes. The proposed framework consists of the following steps: fast denoising and B-scan alignment, multi-resolution graph search based surface detection, PED region detection and surface correction above the PED region. The proposed technique was evaluated on a dataset with OCT images from 20 subjects diag-nosed with PED. The experimental results showed that: (1) the overall mean unsigned border positioning error for layer seg-mentation is 7.87±3.36 μm, and is comparable to the mean in-ter-observer variability (7.81±2.56 μm). (2) the true positive vo-lume fraction (TPVF), false positive volume fraction (FPVF) and positive predicative value (PPV) for PED volume segmentation are 87.1%, 0.37% and 81.2%, respectively; (3) the average run-ning time is 220s for OCT data of 512×64×480 voxels.
PMID: 25265605 [PubMed - as supplied by publisher]
Normative Databases for Imaging Instrumentation.
J Glaucoma. 2014 Sep 26;
Authors: Realini T, Zangwill LM, Flanagan JG, Garway-Heath D, Patella VM, Johnson CA, Artes PH, Gaddie IB, Fingeret M
PURPOSE:: To describe the process by which imaging devices undergo reference database development and regulatory clearance. The limitations and potential improvements of reference (normative) data sets for ophthalmic imaging devices will be discussed.
METHOD:: A symposium was held in July 2013 in which a series of speakers discussed issues related to the development of reference databases for imaging devices.
RESULTS:: Automated imaging has become widely accepted and used in glaucoma management. The ability of such instruments to discriminate healthy from glaucomatous optic nerves, and to detect glaucomatous progression over time is limited by the quality of reference databases associated with the available commercial devices. In the absence of standardized rules governing the development of reference databases, each manufacturer's database differs in size, eligibility criteria, and ethnic make-up, among other key features.
CONCLUSIONS:: The process for development of imaging reference databases may be improved by standardizing eligibility requirements and data collection protocols. Such standardization may also improve the degree to which results may be compared between commercial instruments.
PMID: 25265003 [PubMed - as supplied by publisher]
Utilizing Ethnic-Specific Differences in Minor Allele Frequency to Recategorize Reported Pathogenic Deafness Variants.
Am J Hum Genet. 2014 Sep 24;
Authors: Shearer AE, Eppsteiner RW, Booth KT, Ephraim SS, Gurrola J, Simpson A, Black-Ziegelbein EA, Joshi S, Ravi H, Giuffre AC, Happe S, Hildebrand MS, Azaiez H, Bayazit YA, Erdal ME, Lopez-Escamez JA, Gazquez I, Tamayo ML, Gelvez NY, Leal GL, Jalas C, Ekstein J, Yang T, Usami SI, Kahrizi K, Bazazzadegan N, Najmabadi H, Scheetz TE, Braun TA, Casavant TL, LeProust EM, Smith RJ
Ethnic-specific differences in minor allele frequency impact variant categorization for genetic screening of nonsyndromic hearing loss (NSHL) and other genetic disorders. We sought to evaluate all previously reported pathogenic NSHL variants in the context of a large number of controls from ethnically distinct populations sequenced with orthogonal massively parallel sequencing methods. We used HGMD, ClinVar, and dbSNP to generate a comprehensive list of reported pathogenic NSHL variants and re-evaluated these variants in the context of 8,595 individuals from 12 populations and 6 ethnically distinct major human evolutionary phylogenetic groups from three sources (Exome Variant Server, 1000 Genomes project, and a control set of individuals created for this study, the OtoDB). Of the 2,197 reported pathogenic deafness variants, 325 (14.8%) were present in at least one of the 8,595 controls, indicating a minor allele frequency (MAF) >0.00006. MAFs ranged as high as 0.72, a level incompatible with pathogenicity for a fully penetrant disease like NSHL. Based on these data, we established MAF thresholds of 0.005 for autosomal-recessive variants (excluding specific variants in GJB2) and 0.0005 for autosomal-dominant variants. Using these thresholds, we recategorized 93 (4.2%) of reported pathogenic variants as benign. Our data show that evaluation of reported pathogenic deafness variants using variant MAFs from multiple distinct ethnicities and sequenced by orthogonal methods provides a powerful filter for determining pathogenicity. The proposed MAF thresholds will facilitate clinical interpretation of variants identified in genetic testing for NSHL. All data are publicly available to facilitate interpretation of genetic variants causing deafness.
PMID: 25262649 [PubMed - as supplied by publisher]