A population-based approach for gene prioritization in understanding complex traits.

Gene prioritization is the process of determining which variants and genes identified in genetic analyses are likely to cause a disease or a variation in a phenotype. For many genes, neither in vitro nor in vivo testing is available, thus assessing their pathogenic role could be challenging, leading to false-positive or false-negative results. In this paper, we propose an innovative score of gene prioritization based on the population of interest. We introduce the concept of singleton-cohort variants (SC variant), a variant that has allele count equal to one in the cohort under study. The difference between the normalized count of SC variants in the coding region and the normalized count of SC variants in the non-coding region should give a hint regarding the level of constraints for that gene in a specific population. This scoring system is negative when there are constraints that allow the presence of SC variants only in the non-coding region; on the contrary, it is positive when there are no constraints. A complimentary score is the sum of SC variants normalized count in both coding and non-coding regions, which could be used as a proxy of positive or strong purifying selection in a specific population. Our methodology showed a high level of constraining for genes such as USP34 in all subpopulations tested (1000 G dataset). In contrast, some genes showed a high negative score only in specific populations, e.g., MYT1L in Europeans, UBR5 in East Asians, and FBXO11 in Africans.

First-trimester absent nasal bone: is it a predictive factor for pathogenic CNVs in the low-risk population?

OBJECTIVE: To evaluate the association of first-trimester absent nasal bone (NB) and genetic abnormalities at G-banding karyotype and chromosomal microarray analysis (CMA) according to the nuchal translucency (NT) thickness. METHODS: This is a retrospective cohort study of fetuses that underwent the first-trimester scan for the combined test at 11+0 to 13+6 weeks' gestation. Invasive test with G-banding karyotype and/or CMA was performed based on the result of the combined test or if fetal defects were detected or for patient's choice, after genetic counseling. All cases with absent NB in the first and second trimester underwent a detailed anomaly scan with echocardiography in the second trimester, had a longitudinal ultrasound, and postnatal follow-up up to at least 1 year. RESULTS: Between 2013 and 2018, 7228 women underwent the first-trimester scan at 11+0 to 13+6 weeks. Overall prevalence of absent NB was 1.3% (96/7228). Of those, in 86 pregnancies (1.2%), the absence of NB was confirmed also in the second trimester: 0.58% (40/6909) in the group with NT <95th centile; 6%(14/233) in the group with NT between 95 and 99th centile; and 37.2% (32/86) in the group with NT >99th centile, respectively. CMA pathogenic variants were found only in the group with NT >99th centile with a diagnostic yield of 9.4%. Fetuses with absent NB and NT between 95 and 99th centile had in 57% (8/14) a major chromosomal anomaly, while in the NT <95 centile group, there were 5% (2/40) of chromosomal abnormalities (one inherited from the father). CONCLUSION: In the first trimester, the risk for genetic syndromes detectable by CMA is related mainly to the NT thickness rather than to the absence of NB per se. In fetuses with absent NB and NT >99th centile, CMA should be performed after karyotype analysis, while for NT between 95 and 99th centile, a karyotype should be proposed as first-line procedure. Data provided by our study may be helpful in counseling women/couples when an absent NB is identified in the first trimester.

MORPHOFUNCTIONAL EVALUATION IN DOME-SHAPED MACULA: A MICROPERIMETRY AND OPTICAL COHERENCE TOMOGRAPHY STUDY.

PURPOSE: To investigate retinal sensitivity (Se) in dome-shaped macula (DSM) using microperimetry and to correlate functional findings to specific spectral domain optical coherence tomography features. METHODS: Patients affected by DSM in at least 1 eye were consecutively enrolled in a prospective, cross-sectional study. All studied eyes performed best-corrected visual acuity measurement, microperimetry to assess Se and optical coherence tomography to investigate DSM pattern and to measure bulge height and retinal and choroidal thicknesses. RESULTS: Fifty-three eyes of 29 patients were studied. Dome-shaped macula was vertically oriented (V-DSM) in 23 (43.4%), symmetric (S-DSM) in 17 (32.1%), and horizontally oriented (H-DSM) in 13 eyes (24.5%). Foveal subretinal fluid was present in 29/53 (54.7%) cases; it correlated to the bulge height (P < 0.0001) and determined a reduction of Se (P < 0.0001) not of best-corrected visual acuity (P = 0.7105). Mean Se was 13.9 ± 3.2 dB. Microperimetry parameters did not differ among the different DSM patterns. However, Se was significantly impaired if foveal subretinal fluid was present in V-DSM and in S-DSM, but not in H-DSM (V-DSM: P < 0.0001; S-DSM: P = 0.0252; H-DSM: P = 0.5723). In H-DSM, inferior choroidal thickness was thicker in cases with foveal subretinal fluid compared with those without it (P = 0.0363). CONCLUSION: In DSM, Se evaluation better reflects the central functional impairment than best-corrected visual acuity, particularly when some optical coherence tomography features, such as foveal subretinal fluid and higher bulge height, are present.

Two novel compound heterozygous SAG mutations in an Italian patient with Oguchi disease: A genetic and multimodal retinal imaging study.

BACKGROUND: Oguchi disease is a rare autosomal recessive retinal dystrophy, characterized by congenital stationary blindness and caused by pathogenic variants in SAG and GRK1 genes. The present study aimed to report an Italian patient affected by Oguchi disease, evaluated by means of a multimodal retinal imaging study and harboring two novel heterozygous pathogenic variants in the SAG gene. MATERIALS AND METHODS: A 60-year-old female complaining congenital stationary night blindness was investigated through fundus photograph, optical coherence tomography (OCT), electroretinography (ERG), and genetic testing. RESULTS: Fundus examination showed a golden-grayish fundus aspect. The rod response of the scotopic ERG was undetectable and mixed rod-cone response was electronegative. Fundus photographs obtained in light and in prolonged dark-adapted conditions allowed to detect the Mizuo-Nakamura phenomenon. Light condition OCT over the abnormal retinal regions showed high-intensity areas in the outer photoreceptor segment layer, that reduced with prolonged dark adaption. Genetic testing identified two rare heterozygous sequence variants in the SAG gene: NM_000541.5:c.807delA p.(Glu270Lysfs*9) and NM_000541.5:c.1047-1G>C confirming the diagnosis of Oguchi disease. CONCLUSIONS: We identified the first Italian compound heterozygous patient harboring two novel alterations in the SAG gene (a frameshift deletion and a splicing variant). The involvement of the SAG gene in Oguchi disease is a common finding in Japanese population, but rarely identified in Caucasians. Clinical suspicion should prompt the molecular analysis of genes associated with this condition.

Early OCT angiography changes of type 1 CNV in exudative AMD treated with anti-VEGF.

AIMS: To investigate, with optical coherence tomography angiography (OCTA), short-term changes of type 1 choroidal neovascularisation (CNV), secondary to exudative age-related macular degeneration, after anti-vascular endothelial growth factor (VEGF) treatment. METHODS: Patients affected by type 1 CNV treated with intravitreal anti-VEGF were consecutively enrolled. All patients underwent OCTA examination before and 48 hours after anti-VEGF treatment. Quantitative and qualitative vascular and morphological macular changes were evaluated. RESULTS: Sixteen eyes were included (11 treated with aflibercept and 5 with ranibizumab). Both CNV mean area and pigment epithelium detachment significantly reduced (p=0.0004 and p=0.0007, respectively) after treatment. Cystoid macular oedema (four eyes) decreased in all cases. Neuroretinal detachment (13 eyes) decreased in 85% of cases (11 eyes). Fine CNV vessels density decreased in 75% (12 eyes), whereas larger CNV vessels density remained stable in 66.7% (10 eyes), choroidal flow void signal (7 eyes at baseline) increased in 42.9% (3 eyes) of them and remained stable in 57.1% (4 eyes). Interoperator reproducibility for OCT examination was good for all measurements (intraclass correlation coefficient>0.65). CONCLUSION: Early remodelling of type 1 CNV network after treatment may be non-invasively and reproducibly analysed by means of OCTA. Choroidal perfusion impairment, choroidal flow void signal, surrounding CNV may change during treatment.

The clinical spectrum of CASQ1-related myopathy.

OBJECTIVE: To identify and characterize patients with calsequestrin 1 (CASQ1)-related myopathy. METHODS: Patients selected according to histopathologic features underwent CASQ1 genetic screening. CASQ1-mutated patients were clinically evaluated and underwent muscle MRI. Vacuole morphology and vacuolated fiber type were characterized. RESULTS: Twenty-two CASQ1-mutated patients (12 families) were identified, 21 sharing the previously described founder mutation (p.Asp244Gly) and 1 with the p.Gly103Asp mutation. Patients usually presented in the sixth decade with exercise intolerance and myalgias and later developed mild to moderate, slowly progressive proximal weakness with quadriceps atrophy and scapular winging. Muscle MRI (n = 11) showed a recurrent fibrofatty substitution pattern. Three patients presented subclinical cardiac abnormalities. Muscle histopathology in patients with p.Asp244Gly showed vacuoles in type II fibers appearing empty in hematoxylin-eosin, Gomori, and nicotinamide adenine dinucleotide (NADH) tetrazolium reductase stains but strongly positive for sarcoplasmic reticulum proteins. The muscle histopathology of p.Gly103Asp mutation was different, showing also NADH-positive accumulation consistent with tubular aggregates. CONCLUSIONS: We report the clinical and molecular details of the largest cohort of CASQ1-mutated patients. A possible heart involvement is presented, further expanding the phenotype of the disease. One mutation is common due to a founder effect, but other mutations are possible. Because of a paucity of symptoms, it is likely that CASQ1 mutations may remain undiagnosed if a muscle biopsy is not performed.

Microperimetry Features of Geographic Atrophy Identified With En Face Optical Coherence Tomography.

IMPORTANCE: Progressive geographic atrophy (GA) of the retinal pigment epithelium leads to loss of central vision. To identify GA in age-related macular degeneration and assess treatment, correlation of function observed on microperimetry with structure observed on optical coherence tomographic (OCT) images may be of value. OBJECTIVE: To characterize the microperimetric function of GA as identified from en face OCT imaging. DESIGN, SETTING, AND PARTICIPANTS: In a case-series study, 20 patients (22 eyes) entered the study at the University of Padova according to preplanned conditions. From March 1 to July 30, 2014, en face OCT images were obtained at the outer retinal layer and choroidal layer levels. The microperimetry sensitivity map was superimposed on the en face OCT images, which had been used to measure GA areas. Relative and dense scotoma rates were calculated in the GA areas. After data collection, the study eyes were divided into 3 groups according to the macular residual mean sensitivity. MAIN OUTCOMES AND MEASURES: Retinal sensitivity measured by microperimetry within areas of GA identified by en face OCT images. RESULTS: Twenty patients (5 men and 15 women) were included in the study, with a mean (SD) age of 79.5 (7.0) years (range, 69-98 years). Macular residual mean retinal sensitivity was less than 5 dB in 7 eyes (group 1), 5 to 10 dB in 9 eyes (group 2), and greater than 10 dB in 6 eyes (group 3). Mean (SD) GA area differed among the groups at the outer retinal (13.13 [5.03] mm2 [range, 5.75-21.04 mm2] in group 1; 7.80 [3.25] mm2 [range, 3.31-13.52 mm2] in group 2; and 3.94 [2.35] mm2 [range, 1.46-7.90 mm2] in group 3; P = .001) and choroidal (11.83 [5.55] mm2 [range, 4.55-22.14 mm2] in group 1; 7.00 [4.29] mm2 [range, 0.90-13.83 mm2] in group 2; and 3.27 [2.29] mm2 [range, 0.91-7.23 mm2] in group 3; P = .007) layer levels. Mean (SD) GA area imaged at the outer retinal layer level was significantly larger than that imaged at the choroidal level in group 3 (difference, 0.67 mm2; 95% CI, 0.31-1.03 mm2; P = .005), but not in groups 1 or 2. Mean (SD) rate of relative scotoma was significantly higher in the GA area imaged at the outer retinal layer level than at the choroidal level in group 3 (47.70% [31.30%] [range, 13.60%-100%] vs 34.00% [37.30%] [range, 0%-100%]; difference, 13.74%; 95% CI, 3.84%-23.63%; P = .02), but not in groups 1 or 2. CONCLUSIONS AND RELEVANCE: In the early stage of GA, when retinal sensitivity is relatively good, these data suggest that the GA area imaged on en face OCT at the outer retinal level correctly detects the wide functional degenerative involvement of the photoreceptors. These findings provide novel data that correlate function and structure, which may be of value when assessing treatments that might prevent or reduce the rate of growth of GA.

En Face Optical Coherence Tomography to Detect and Measure Geographic Atrophy.

PURPOSE: To detect and quantify geographic atrophy (GA) secondary to age-related macular degeneration using en face optical coherence tomography (OCT) and to correlate it to GA measured with fundus autofluorescence (FAF). METHODS: Twenty-four consecutive patients (27 eyes) were studied with both standard (STD)- and enhanced depth imaging (EDI)-OCT. En face OCT images were obtained at the outer retinal layer (OR) and at the choroidal layer (CH) level for both STD- and EDI-OCT. Areas of GA were measured on the en face OCT images and were correlated with the GA areas measured on blue (B)- and near infrared (NIR)-wavelength FAF images. RESULTS: The intraoperator agreement in GA measurement was excellent with en face OCT at both OR and CH levels (intraclass correlation coefficient [ICC] = 0.99 in EDI and 0.98 in STD at OR level; 0.99 in EDI and 0.99 in STD at CH level). The interoperator agreement was excellent at OR level (ICC = 0.97 in EDI and 0.98 in STD), good at CH level (ICC = 0.95 in EDI, 0.90 in STD). The geographic atrophy area, at both B-FAF and NIR-FAF, was significantly equivalent to the GA area at OR level (B-FAF versus SDT-OR and EDI-OR: P = 0.0057 and 0.0090, respectively; NIR-FAF versus STD-OR and EDI-OR: P = 0.0131 and 0.0036, respectively), but not at CH level. CONCLUSIONS: En face OCT is a reliable method to detect and quantify GA, particularly when analyzed at the OR level, where the photoreceptors' loss creates an abrupt transition in OCT reflectivity.

Progressing geographic atrophy: choroidal thickness and retinal sensitivity identify two clinical phenotypes.

PURPOSE: To analyse changes in choroidal thickness and retinal sensitivity (Se) in patients with geographic atrophy (GA) with or without choroidal neovascularisation (CNV) in the fellow eye. PARTICIPANTS: Patients with bilateral GA (B-GA group) and patients with unilateral GA and CNV in the fellow eye (U-GA group) were followed every 6 months, and enhanced depth imaging optical coherence tomography (OCT), blue and near infrared-wavelength fundus autofluorescence (B- and NIR-FAF), and microperimetry were evaluated. METHODS: GA area, choroidal thickness, and Se were measured in the eye with GA at baseline and every 6 months up to the last follow-up visit. RESULTS: 19 patients (8 in the B-GA group (16 eyes) and 11 in the U-GA group (11 eyes)) were studied. The mean±SD follow-up was 1.66±0.71 years (range 0.74-2.60 years) in the U-GA group, and 1.51±0.86 years (range 0.58-2.95 years) in the B-GA group (p=0.6766). Mean GA area was not significantly different between groups at baseline (p=0.4118 in the B-FA and p=0.6806 in the NIR-FAF) or at follow-up (p=0.5734 in the B-FAF and p=0.8945 in the NIR-FAF). Mean GA area significantly increased in both groups during follow-up (p=0.0050 for B-FAF and p=0.0052 for NIR-FAF in the U-GA group; p=0.0049 for B-FAF and p=0.0072 for NIR-FAF in the B-GA group). Choroidal thickness was significantly greater in the B-GA group compared with the U-GA group both at baseline (mean choroidal thickness 170.5±78.5 µm vs 129.1±36.1 µm; p=0.0371) and at last follow-up (173.2±86.1 µm vs 123±32.1 µm; p=0.0340). During follow-up mean choroidal thickness significantly decreased only in the U-GA group (p=0.0276); conversely mean Se significantly decreased only in B-GA group (p=0.0405). CONCLUSIONS: During follow-up, changes in Se and choroidal thickness differed in patients with GA with or without CNV in the fellow eye. These results identify at least two GA phenotypes, in which the development and progression of GA may be primarily due to different pathophysiologic mechanisms.

Fundus autofluorescence and microperimetry in progressing geographic atrophy secondary to age-related macular degeneration.

PURPOSE: To prospectively analyse microperimetry, standard short-wavelength fundus autofluorescent (SW-FAF) and near infrared-wavelength FAF (NIR-FAF) changes in eyes with geographic atrophy (GA) secondary to age-related macular degeneration. METHODS: Twenty consecutive eyes (14 patients) affected by GA were enrolled. Repeated microperimetric examinations and FAF images were obtained over a mean follow-up period of 12.3±4.5 months. RESULTS: GA area was always wider on NIR-FAF versus SW-FAF images (5.05±2.40 mm(2) vs 4.45±2.41 mm(2), p=0.005 baseline; 5.78±2.87 mm(2) vs 5.21±2.77 mm(2), p<0.0001 follow-up). Mean retinal sensitivity significantly decreased during follow-up from 7.68±3.92 dB to 6.71±4.37 dB (p=0.0013). 47.3% of the relative dense scotomas (≤5 dB) progressed to dense scotoma (0 dB). Retinal areas showing relative dense scotoma and characterised by hypo-SW-FAF or hyper-NIR-FAF at baseline had a higher risk of evolving to dense scotoma compared with normo-FAF and hyper-FAF on SW-FAF (OR=2.62 and 2.77, respectively), or normo-FAF at NIR-FAF (OR=2.96). CONCLUSIONS: SW-FAF, compared with NIR-FAF, underestimates GA area at baseline and at follow-up. The enlargement rate of progression based on NIR-FAF is not greater than on SW-FAF. Different SW-FAF and NIR-FAF patterns show different relative risk of progression from relative to dense scotoma. Microperimetry, SW-FAF and NIR-FAF should be combined to obtain adequate morphological and functional prospective information.

Microperimetry, fundus autofluorescence, and retinal layer changes in progressing geographic atrophy.

OBJECTIVE: To analyze correlation among microperimetry, inner and outer retinal layers, and fundus autofluorescence (FAF) changes in eyes with progressing geographic atrophy (GA) secondary to age-related macular degeneration. METHODS: Microperimetry, spectral-domain optical coherence tomography (SD-OCT), standard short-wavelength FAF (SW-FAF), and near-infrared-wavelength FAF (NIR-FAF) were performed for all patients at both baseline and follow-up visits. FAF pattern, integrity of photoreceptor inner segment/outer segment (IS/OS) junction, total retinal thickness (RT), inner retinal layers (IRL), and outer retinal layers (ORL) thickness changes of every microperimetry extrafoveal tested point were analyzed. RESULTS: A total of 366 microperimetry tested points were analyzed (6 patients, 7 eyes). Mean retinal sensitivity significantly decreased (p = 0.0149), and the percentage of dense scotomas significantly increased (p = 0.0125). Mean RT and mean ORL thickness significantly decreased (both p < 0.0001). Mean IRL thickness significantly increased (p = 0.0001). The decrease of ORL thickness was inversely correlated to the IRL thinning (rho = -0.710). FAF pattern at baseline was correlated to RT and ORL thickness (both p < 0.0001) and was significantly correlated to the risk to evolve to dense scotoma during follow-up (p = 0.0001 at SW-FAF, p < 0.0001 at NIR-FAF). Tested points showing at baseline the loss of photoreceptor IS/OS junction had a greater risk for evolving to dense scotoma compared with those with intact photoreceptor IS/OS junction (odds ratio 3.56, 95% CI 2.41-5.27). CONCLUSIONS: Retinal sensitivity changes are correlated to IRL and ORL thickness changes, and to photoreceptor IS/OS junction integrity. FAF patterns remain a relevant factor in predicting GA evolution. Microperimetry, SW-FAF and NIR-FAF, and SD-OCT should be combined to obtain adequate morphologic and functional prospective information.