Wavelet-based denoising for 3D OCT images

Optical coherence tomography produces high resolution medical images based on spatial and temporal coherence of the optical waves backscattered from the scanned tissue. However, the same coherence introduces speckle noise as well; this degrades the quality of acquired images. In this paper we propose a technique for noise reduction of 3D OCT images, where the 3D volume is considered as a sequence of 2D images, i.e., 2D slices in depth-lateral projection plane. In the proposed method we first perform recursive temporal filtering through the estimated motion trajectory between the 2D slices using noise-robust motion estimation/compensation scheme previously proposed for video denoising. The temporal filtering scheme reduces the noise level and adapts the motion compensation on it. Subsequently, we apply a spatial filter for speckle reduction in order to remove the remainder of noise in the 2D slices. In this scheme the spatial (2D) speckle-nature of noise in OCT is modeled and used for spatially adaptive denoising. Both the temporal and the spatial filter are wavelet-based techniques, where for the temporal filter two resolution scales are used and for the spatial one four resolution scales. The evaluation of the proposed denoising approach is done on demodulated 3D OCT images on different sources and of different resolution. For optimizing the parameters for best denoising performance fantom OCT images were used. The denoising performance of the proposed method was measured in terms of SNR, edge sharpness preservation and contrast-to-noise ratio. A comparison was made to the state-of-the-art methods for noise reduction in 2D OCT images, where the proposed approach showed to be advantageous in terms of both objective and subjective quality measures

Multiresolution denoising for optical coherence tomography: A review and evaluation

Abstract: Recently emerging non-invasive imaging modality- optical coherence tomography (OCT) – is becoming an increasingly important diagnostic tool in various medical applications. One of its main limitations is the presence of speckle noise which obscures small and low-intensity features. The use of multiresolution techniques has been recently reported by several authors with promising results. These approaches take into account the signal and noise properties in different ways. Approaches that take into account the global orientation properties of OCT images apply accordingly different level of smoothing in different orientation subbands. Other approaches take into account local signal and noise covariance's. So far it was unclear how these different approaches compare to each other and to the best available single-resolution despeckling techniques. The clinical relevance of the denoising results also remains to be determined. In this paper we review systematically recent multiresolution OCT speckle filters and we report the results of a comparative experimental study. We use 15 different OCT images extracted from five different three-dimensional volumes, and we also generate a software phantom with real OCT noise. These test images are processed with different filters and the results are evaluated both visually and in terms of different performance measures. The results indicate significant differences in the performance of the analyzed methods. Wavelet techniques perform much better than the single resolution ones and some of the wavelet methods improve remarkably the quality of OCT images

Multiresolution Denoising for Optical Coherence Tomography: A Review and Evaluation

Recently emerging non-invasive imaging modality- optical coherence tomography (OCT) – is becoming an increasingly important diagnostic tool in various medical applications. One of its main limitations is the presence of speckle noise which obscures small and low-intensity features. The use of multiresolution techniques has been recently reported by several authors with promising results. These approaches take into account the signal and noise properties in different ways. Approaches that take into account the global orientation properties of OCT images apply accordingly different level of smoothing in different orientation subbands. Other approaches take into account local signal and noise covariance's. So far it was unclear how these different approaches compare to each other and to the best available single-resolution despeckling techniques. The clinical relevance of the denoising results also remains to be determined. In this paper we review systematically recent multiresolution OCT speckle filters and we report the results of a comparative experimental study. We use 15 different OCT images extracted from five different three-dimensional volumes, and we also generate a software phantom with real OCT noise. These test images are processed with different filters and the results are evaluated both visually and in terms of different performance measures. The results indicate significant differences in the performance of the analyzed methods. Wavelet techniques perform much better than the single resolution ones and some of the wavelet methods improve remarkably the quality of OCT images

Stargardt disease-associated in-frame ABCA4 exon 17 skipping results in significant ABCA4 function

Abstract Background ABCA4, the gene implicated in Stargardt disease (STGD1), contains 50 exons, of which 17 contain multiples of three nucleotides. The impact of in-frame exon skipping is yet to be determined. Antisense oligonucleotides (AONs) have been investigated in Usher syndrome-associated genes to induce skipping of in-frame exons carrying severe variants and mitigate their disease-linked effect. Upon the identification of a STGD1 proband carrying a novel exon 17 canonical splice site variant, the activity of ABCA4 lacking 22 amino acids encoded by exon 17 was examined, followed by design of AONs able to induce exon 17 skipping. Methods A STGD1 proband was compound heterozygous for the splice variant c.2653+1G>A, that was predicted to result in in-frame skipping of exon 17, and a null variant [c.735T>G, p.(Tyr245*)]. Clinical characteristics of this proband were studied using multi-modal imaging and complete ophthalmological examination. The aberrant splicing of c.2653+1G>A was investigated in vitro in HEK293T cells with wild-type and mutant midigenes. The residual activity of the mutant ABCA4 protein lacking Asp864-Gly885 encoded by exon 17 was analyzed with all-trans-retinal-activated ATPase activity assay, along with its subcellular localization. To induce exon 17 skipping, the effect of 40 AONs was examined in vitro in WT WERI-Rb-1 cells and 3D human retinal organoids. Results Late onset STGD1 in the proband suggests that c.2653+1G>A does not have a fully deleterious effect. The in vitro splice assay confirmed that this variant leads to ABCA4 transcripts without exon 17. ABCA4 Asp864_Gly863del was stable and retained 58% all-trans-retinal-activated ATPase activity compared to WT ABCA4. This sequence is located in an unstructured linker region between transmembrane domain 6 and nucleotide-binding domain-1 of ABCA4. AONs were designed to possibly reduce pathogenicity of severe variants harbored in exon 17. The best AON achieved 59% of exon 17 skipping in retinal organoids. Conclusions Exon 17 deletion in ABCA4 does not result in the absence of protein activity and does not cause a severe STGD1 phenotype when in trans with a null allele. By applying AONs, the effect of severe variants in exon 17 can potentially be ameliorated by exon skipping, thus generating partial ABCA4 activity in STGD1 patients. Graphical abstrac

Personalized genetic counseling for Stargardt disease: Offspring risk estimates based on variant severity

Recurrence risk calculations in autosomal recessive diseases are complicated when the effect of genetic variants and their population frequencies and penetrances are unknown. An example of this is Stargardt disease (STGD1), a frequent recessive retinal disease caused by bi-allelic pathogenic variants in ABCA4. In this cross-sectional study, 1,619 ABCA4 variants from 5,579 individuals with STGD1 were collected and categorized by (1) severity based on statistical comparisons of their frequencies in STGD1-affected individuals versus the general population, (2) their observed versus expected homozygous occurrence in STGD1-affected individuals, (3) their occurrence in combination with established mild alleles in STGD1-affected individuals, and (4) previous functional and clinical studies. We used the sum allele frequencies of these severity categories to estimate recurrence risks for offspring of STGD1-affected individuals and carriers of pathogenic ABCA4 variants. The risk for offspring of an STGD1-affected individual with the "severe vertical bar severe"genotype or a "severe vertical bar mild with complete penetrance"genotype to develop STGD1 at some moment in life was estimated at 2.8%-3.1% (1 in 36-32 individuals) and 1.6%-1.8% (1 in 62-57 individuals), respectively. The risk to develop STGD1 in childhood was estimated to be 2-to 4-fold lower: 0.68%-0.79% (1 in 148-126) and 0.34%-0.39% (1 in 296-252), respectively. In conclusion, we established personalized recurrence risk calculations for STGD1-affected individuals with different combinations of variants. We thus propose an expanded genotype-based personalized counseling to appreciate the variable recurrence risks for STGD1-affected individuals. This represents a conceptual breakthrough because risk calculations for STGD1 may be exemplary for many other inherited diseases

Enhanced Intrinsic Skin Aging in Nephropathic Cystinosis Assessed by High-Definition Optical Coherence Tomography

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Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability

: The ABCA4 gene is the most frequently mutated Mendelian retinopathy-associated gene. Biallelic variants lead to a variety of phenotypes, however, for thousands of cases the underlying variants remain unknown. Here, we aim to shed further light on the missing heritability of ABCA4-associated retinopathy by analyzing a large cohort of macular dystrophy probands. A total of 858 probands were collected from 26 centers, of whom 722 carried no or one pathogenic ABCA4 variant while 136 cases carried two ABCA4 alleles, one of which was a frequent mild variant, suggesting that deep-intronic variants (DIVs) or other cis-modifiers might have been missed. After single molecule molecular inversion probes (smMIPs)-based sequencing of the complete 128-kb ABCA4 locus, the effect of putative splice variants was assessed in vitro by midigene splice assays in HEK293T cells. The breakpoints of copy number variants (CNVs) were determined by junction PCR and Sanger sequencing. ABCA4 sequence analysis solved 207/520 (39.8%) naïve or unsolved cases and 70/202 (34.7%) monoallelic cases, while additional causal variants were identified in 54/136 (39.7%) of probands carrying two variants. Seven novel DIVs and six novel non-canonical splice site variants were detected in a total of 35 alleles and characterized, including the c.6283-321C>G variant leading to a complex splicing defect. Additionally, four novel CNVs were identified and characterized in five alleles. These results confirm that smMIPs-based sequencing of the complete ABCA4 gene provides a cost-effective method to genetically solve retinopathy cases and that several rare structural and splice altering defects remain undiscovered in STGD1 cases

PRPH2 mutation update: In silico assessment of 245 reported and 7 novel variants in patients with retinal disease

Mutations in PRPH2, encoding peripherin-2, are associated with the development of a wide variety of inherited retinal diseases (IRDs). To determine the causality of the many PRPH2 variants that have been discovered over the last decades, we surveyed all published PRPH2 variants up to July 2020, describing 720 index patients that in total carried 245 unique variants. In addition, we identified seven novel PRPH2 variants in eight additional index patients. The pathogenicity of all variants was determined using the ACMG guidelines. With this, 107 variants were classified as pathogenic, 92 as likely pathogenic, one as benign, and two as likely benign. The remaining 50 variants were classified as variants of uncertain significance. Interestingly, of the total 252 PRPH2 variants, more than half (n = 137) were missense variants. All variants were uploaded into the Leiden Open source Variation and ClinVar databases. Our study underscores the need for experimental assays for variants of unknown significance to improve pathogenicity classification, which would allow us to better understand genotype-phenotype correlations, and in the long-term, hopefully also support the development of therapeutic strategies for patients with PRPH2-associated IRD