Figure 5 - uploaded by Gemma Marfany
Content may be subject to copyright.
Fundus eye photographs (OS-left eye; OD-right eye) from one affected and several mutation carriers detected after genetic testing. (a) Incomplete penetrant IV.1. (b) Incomplete penetrant IV.5. (c) Incomplete penetrant IV.14. (d) Patient V.10, the view of the OD fundus is lateral to show the peripheral bone-spicule pigment deposits and vascular attenuation. (e) Previously undiagnosed female V.11, now showing early symptoms of RP, such as peripheric retinal pigmented epithelium atrophy.
Source publication
Fast and efficient high-throughput techniques are essential for the molecular diagnosis of highly heterogeneous hereditary diseases, such as retinitis pigmentosa (RP). We had previously approached RP genetic testing by devising a chip based on co-segregation analysis for the autosomal recessive forms. In this study, we aimed to design a diagnostic...
Contexts in source publication
Context 1
... IV.1, IV.5, IV.14 and V.11 volunteered and their phenotype were compared with that of patient V.10 (Table 2). As observed in Figure 5, patient V.10 showed conven- tional RP features, such as, severe night blindness, decreased visual acuity and loss of mid-peripheral visual field. In contrast, individuals IV.1, IV.5 and IV.14 presented normal ERGs and eye fundi, and hence were categorized as incomplete penetrants (Table 2 and Figures 5a-d). ...
Context 2
... observed in Figure 5, patient V.10 showed conven- tional RP features, such as, severe night blindness, decreased visual acuity and loss of mid-peripheral visual field. In contrast, individuals IV.1, IV.5 and IV.14 presented normal ERGs and eye fundi, and hence were categorized as incomplete penetrants (Table 2 and Figures 5a-d). The loss of visual acuity in individual IV.5 was due to cataracts (Table 2), but the retina was unaffected (Figure 5b). ...
Context 3
... contrast, individuals IV.1, IV.5 and IV.14 presented normal ERGs and eye fundi, and hence were categorized as incomplete penetrants (Table 2 and Figures 5a-d). The loss of visual acuity in individual IV.5 was due to cataracts (Table 2), but the retina was unaffected (Figure 5b). Remarkably, the clinical evaluation of the individual V.11, who had not been previously diagnosed with RP, revealed some of the early RP traits: mild Retinal Pigmented Epithelium (RPE) atrophy in the peripheral and nasal retina, and vascular attenuation (Figure 5e). ...
Context 4
... loss of visual acuity in individual IV.5 was due to cataracts (Table 2), but the retina was unaffected (Figure 5b). Remarkably, the clinical evaluation of the individual V.11, who had not been previously diagnosed with RP, revealed some of the early RP traits: mild Retinal Pigmented Epithelium (RPE) atrophy in the peripheral and nasal retina, and vascular attenuation (Figure 5e). In addition, this patient Comprehensive chip for RP-LCA molecular diagnosis E Pomares et al showed moderate night blindness and mild visual field constriction in both eyes, the ERG showed decreased amplitude and increased latency in both rod and cone waves, and flicker response with decreased amplitude (Table 2). ...
Similar publications
Fabry disease is an X-chromosome linked hereditary disease that is caused by loss of function mutations in the α-galactosidase A (α-Gal A) gene, resulting in defective glycolipid degradation and subsequent accumulation of globotriaosylceramide (Gb3) in different tissues, including vascular endothelial cells and neurons in the peripheral and central...
Citations
... The efforts have been made in the direct mutational screening of the suspected genes. However, it is recommended that laboratories use comprehensive linkage analysis in unassigned cases (45 %), where LCA microarray chips have failed to distinguish the causative gene from other candidate genes due to the new mutations or unidentified genes (Arélin et al. 2013;Pomares et al. 2010). ...
Leber’s congenital amaurosis (LCA) is considered as one of the main causes of congenital blindness. In view of the genetically heterogeneous nature of the disease, indirect diagnosis using linkage analysis has proven to be useful in molecular diagnosis procedure. Mutations in AIPL1 gene are one of the leading causes of LCA. In the present study, the application of three single nucleotide polymorphic (SNP) markers related to the gene, including rs7212734, rs11658369 and rs8066853 was evaluated for the first time in the Iranian population. The markers were genotyped using tetra-primer ARMS PCR in 154 unrelated healthy individuals. Haplotype frequency and other characteristics of the markers were examined by using the GENEPOP, PowerMarker and Cubic Exact Solution software. The data indicated the presence of six different haplotypes in the Iranian population. Among them, three haplotypes showed high informativeness with frequencies ≥0.05. Three unrelated Iranian LCA families were analyzed. The p.W278* mutation in exon 6 of AIPL1 was found in all the families using APEX microarray chips. SNP analysis for the families showed the conservation of T−A−A haplotype linked to p.W278* mutation. All families bearing the mutation were from the Isfahan province and a founder effect was suggested in this population. Prenatal diagnosis using the markers led to the successful prediction of the fetus genotypes in all the at risk pregnancies and showed that rs7212734, rs11658369 and rs8066853 can be considered as the three informative markers for linkage analysis in carrier detection and molecular diagnosis of LCA in the Iranian population.
... Overall, mutations in splicing factor genes are the second most common cause of adRP [2]. We identified heterozygous mutations in adRP splicing genes (SNRNP200, PRPF8, PRPF31) in 17 probands (Table 1) [2,26,28,[47][48][49]. ...
Purpose
Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition.
Methods
Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization). Identified variants were classified following American College of Medical Genetics and Genomics (ACMG) recommendations.
Results
Molecular genetic screening revealed mutations in 48/86 cases (56%). In total, 17 novel pathogenic mutations were identified: four missense mutations in RHO, five frameshift mutations in RP1, six mutations in genes encoding spliceosome components (SNRNP200, PRPF8, and PRPF31), one frameshift mutation in PRPH2, and one frameshift mutation in TOPORS. The proportion of RHO mutations in our cohort (14%) is higher than reported in a French adRP population (10.3%), but lower than reported elsewhere (16.5–30%). The prevalence of RP1 mutations (10.5%) is comparable to other populations (3.5%-10%). The mutation frequency in genes encoding splicing factors is unexpectedly high (altogether 19.8%), with PRPF31 the second most prevalent mutated gene (10.5%). PRPH2 mutations were found in 4.7% of the Belgian cohort. Two families (2.3%) have the recurrent NR2E3 mutation p.(Gly56Arg). The prevalence of the recurrent PROM1 mutation p.(Arg373Cys) was higher than anticipated (3.5%).
Conclusions
Overall, we identified mutations in 48 of 86 Belgian adRP cases (56%), with the highest prevalence in RHO (14%), RP1 (10.5%) and PRPF31 (10.5%). Finally, we expanded the molecular spectrum of PRPH2, PRPF8, RHO, RP1, SNRNP200, and TOPORS-associated adRP by the identification of 17 novel mutations.
... Using these, proof-of-concept was achieved on single-nucleotide polymorphisms, genomic free polymerase-chain-reaction (PCR) detection at attomolar level, genomic pathogen identification of antibiotic resistance stains and others microbial susceptibility theranostics microfluidic systems [1][2][3][4]. Such systems can use body fluids such as blood and diluted sputum for diagnosis of septicemia and respiratory infectious investigations, or saliva and sweat for genomic, proteomic and metabolomics assays [5][6][7][8]. ...
... In the field of IRDs, commercially available microarrays for direct mutational screening (http://www.asperbio.com/asperophthalmics), customized resequencing microarrays (restricted to several large diagnostic centres/units) [10] and whole genome or targeted gene SNP genotyping arrays for linkage analysis (cosegregation and homozygosity studies) have paved the way either for mutation screening in reported known genes, or for the highlighting of new loci for candidate causal genes [11] . Diagnostic efficiency ranged from 15%-44% in direct mutation screening microarrays-depending on the pathogenic allelic frequencies in the population, to 30%-70% for resequencing microarrays-depending on the number of genes included and the sequence quality [12] . ...
The advent of next generation sequencing (NGS) techniques has greatly simplified the molecular diagnosis and gene identification in very rare and highly heterogeneous Mendelian disorders. Over the last two years, these approaches, especially whole exome sequencing (WES), alone or combined with homozygosity mapping and linkage analysis, have proved to be successful in the identification of more than 25 new causative retinal dystrophy genes. NGS-approaches have also identified a wealth of new mutations in previously reported genes and have provided more comprehensive information concerning the landscape of genotype-phenotype correlations and the genetic complexity/diversity of human control populations. Although whole genome sequencing is far more informative than WES, the functional meaning of the genetic variants identified by the latter can be more easily interpreted, and final diagnosis of inherited retinal dystrophies is extremely successful, reaching 80%, particularly for recessive cases. Even considering the present limitations of WES, the reductions in costs and time, the continual technical improvements, the implementation of refined bioinformatic tools and the unbiased comprehensive genetic information it provides, make WES a very promising diagnostic tool for routine clinical and genetic diagnosis in the future.
... PRPF31 encodes a ubiquitous splicing factor 19 , and mutations at this locus account for ~6% of adRP pedigrees 20 ; previous reports of incomplete penetrance with up to ~35% of carriers reported as asymptomatic are consistent with our observations of this adRP family [21][22][23][24] (Suppl. Table 3) . ...
... Here we have described a multigeneration pedigree with ad RP and an unusual pattern of inheritance, wherein there is variable age on onset, apparent female-specific bias and nonpenetrance. Our genetic studies have identified an inherited heterozygous deletion in PRPF31 as the primary driver of RP in this pedigree, with non-penetrance and variable expressivity both documented previously for this locus [21][22][23][24][30][31][32][33][34] . We cannot differentiate between variable expressivity and non-penetrance as a function of time. ...
Purpose:
Mutations at some retinitis pigmentosa (RP) loci are associated with variable penetrance and expressivity, exacerbating diagnostic challenges. The purpose of this study was to dissect the genetic underpinnings of nonsyndromic RP with variable age of onset in a large Mexican family.
Methods:
We ascertained members of a large, multigenerational pedigree using a complete ophthalmic examination. We performed whole exome sequencing on two affected first cousins, an obligate carrier, and a married-in spouse. Confirmatory sequencing of candidate variants was performed in the entire pedigree, as well as genotyping and mRNA studies to investigate expression changes in the causal locus.
Results:
We identified a 14-base pair (bp) deletion in PRPF31, a gene implicated previously in autosomal dominant (ad) RP. The mutation segregated with the phenotype of all 10 affected females, but also was present in six asymptomatics (two females and four males). Studies in patient cells showed that the penetrance/expressivity of the PRPF31 deletion allele was concordant with the expression levels of wild-type message. However, neither the known PRPF31 modulators nor cis-eQTLs within 1 Mb of the locus could account for the variable expression of message or the clinical phenotype.
Conclusions:
We have identified a novel 14-bp deletion in PRPF31 as the genetic driver of adRP in a large Mexican family that exhibits nonpenetrance and variable expressivity, known properties of this locus. However, our studies intimate the presence of additional loci that can modify PRPF31 expression.
... To improve diagnosis, we have focused on a comprehensive strategy based on the clinical phenotype and all available genetic data prior to either analyze a reduced manageable number of candidate genes or resort to massive sequencing. We have generated and optimized a SNP-based chip for haplotype cosegregation analysis [12,13] to genotype 7-10 SNP markers of one hundred genes associated to the most prevalent RDs: Cone Dystrophies (CD), Cone-Rod Dystrophies (CRD), Congenital Stationary Night Blindness (CSNB), Leber Congenital Amaurosis (LCA), Macular Degeneration (MD) and RP. Based on this methodology, a multi-tiered approach has been devised to costeffectively diagnose [14] a panel of 36 Spanish families with nonsyndromic retinal dystrophies plus 5 patients with Usher's syndrome. ...
... The RD chip for the molecular diagnosis of Mendelian nonsyndromic retinal dystrophies was an optimized version of a previous cosegregation chip for RP-LCA disorders [12,13]. Seven to ten SNPs were selected for each candidate (100 genes in total), and genotyped on a customized Golden Gate Genotyping Assay (Illumina). ...
Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3-up to now only associated to Leber Congenital Amaurosis- was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.
... Other high-throughput methods that have recently been in use include resequencing and genotyping arrays that can cover all known loci at once. Screening devices based on these are the retina-array which has 93 genes involved in retinal diseases [106] and an SNP chip representing SNPs covering 40 genes for retinal diseases [107]. ...
Leber congenital amaurosis (LCA) is a hereditary condition involving severe visual loss or blindness that develops within the first year of life. LCA occurs as syndromic and nonsyndromic forms, and is mostly of autosomal-recessive inheritance. To date, mutations in 19 genes are known to be associated with nonsyndromic LCA phenotypes. Mutations in all known genes account for disease in 70% or less of LCA patients, suggesting that unidentified genes are responsible in the remaining cases. High-throughput screening methods such as mutation chips and exome sequencing have accelerated the pace of genetic discovery in LCA. Genetic testing is useful in counseling families and in confirming diagnosis in ambiguous cases. Gene-based therapy with the RPE65 gene has completed the first phase of clinical trials and shows promising results. Various other gene-specific and other modes of therapy are in experimental stages and are expected to progress to human trials in the near future.
... The resequencing chip theoretically circumvents this limitation, but the prerequisite step of amplifying all known RD genes represents a major challenge (Booij et al. 2011). We and others have shown that the autozygome approach can be very effective in guiding the mutation analysis (Aldahmesh et al. 2009;Pomares et al. 2010). Interestingly, this approach was also used successfully in populations where consanguinity is uncommon (Hildebrandt et al. 2009;Collin et al. 2011;Hagiwara et al. 2011;Schuurs-Hoeijmakers et al. 2011). ...
Retinal dystrophy (RD) is a heterogeneous group of hereditary diseases caused by loss of photoreceptor function, and contributes significantly to the etiology of blindness globally but especially in the industrialized world. The extreme locus and allelic heterogeneity of these disorders pose a major diagnostic challenge and often impedes the ability to provide a molecular diagnosis that can inform counseling and gene-specific treatment strategies. In a large cohort of nearly 150 RD families, we used genomic approaches in the form of autozygome-guided mutation analysis and exome sequencing to identify the likely causative genetic lesion in the majority of cases. Additionally, our study revealed six novel candidate disease genes (C21orf2, EMC1, KIAA1549, GPR125, ACBD5 and DTHD1), two of which (ACBD5 and DTHD1) were observed in the context of syndromic forms of RD that are described for the first time.
... More than 65 associated genes have been identified, 43 of which correspond to non-syndromic RP as of May 2012 (http://www.sph.uth.tmc.edu/retnet/). Most genes for RP cause only a small proportion of cases, with the exception of the rhodopsin (RHO), the USH2A and the RPGR genes which together cause $30% of all cases of RP (Daiger, Bowne, & Sullivan, 2007;Hamel, 2006;Hartong, Berson, & Dryja, 2006;Musarella & Macdonald, 2011;Pomares et al., 2010;Sergouniotis et al., 2011;Waseem et al., 2007). However, these genes account for only about 60% of all RP patients, while heritability in about 40% of RP patients remains unknown (Daiger, Bowne, & Sullivan, 2007;Ferrari et al., 2011;Sahni et al., 2011). ...
With a worldwide prevalence of about 1 in 3500-5000 individuals, Retinitis Pigmentosa (RP) is the most common form of hereditary retinal degeneration. It is an extremely heterogeneous group of genetically determined retinal diseases leading to progressive loss of vision due to impairment of rod and cone photoreceptors. RP can be inherited as an autosomal-recessive, autosomal-dominant, or X-linked trait. Non-Mendelian inheritance patterns such as digenic, maternal (mitochondrial) or compound heterozygosity have also been reported. To date, more than 65 genes have been implicated in syndromic and non-syndromic forms of RP, which account for only about 60% of all RP cases. Due to this high heterogeneity and diversity of inheritance patterns, the molecular diagnosis of syndromic and non-syndromic RP is very challenging, and the heritability of 40% of total RP cases worldwide remains unknown. However new sequencing methodologies, boosted by the human genome project, have contributed to exponential plummeting in sequencing costs, thereby making it feasible to include molecular testing for RP patients in routine clinical practice within the coming years. Here, we summarize the most widely used state-of-the-art technologies currently applied for the molecular diagnosis of RP, and address their strengths and weaknesses for the molecular diagnosis of such a complex genetic disease.
... Homozygosity mapping establishes loci of autosomal recessive disorders. 16 More complex forms of single-gene disorders, such as retinitis pigmentosa 17 and hearing loss, with different inheritance modes have been reported based on SNP arrays. Allelic association studies of case-control design are suitable for identifying highly associated SNPs with the complex diseases. ...
Traditional approaches for gene mapping from candidate gene studies to positional cloning strategies have been applied for Mendelian disorders. Since 2005, next-generation sequencing (NGS) technologies are improving as rapid, high-throughput and cost-effective approaches to fulfill medical sciences and research demands. Using NGS, the underlying causative genes are directly distinguished via a systematic filtering, in which the identified gene variants are checked for novelty and functionality. During the past 2 years, the role of more than 100 genes has been distinguished in rare Mendelian disorders by means of whole-exome sequencing (WES). Combination of WES with traditional approaches, consistent with linkage analysis, has had the greatest impact on those disorders following autosomal mode of inheritance; in more than 60 identified genes, the causal variants have been transmitted at homozygous or compound heterozygous state. Recent literatures focusing on identified new causal genes in Mendelian disorders using WES are reviewed in the present survey.
