Genetic Analysis of FAM46A in Spanish Families with Autosomal Recessive Retinitis Pigmentosa: Characterisation of Novel VNTRs

Retinitis pigmentosa (RP) is a group of retinal dystrophies characterised primarily by rod photoreceptor cell degeneration. Exhibiting great clinical and genetic heterogeneity, RP be inherited as an autosomal dominant (ad) and recessive (ar), X-linked (xl) and digenic disorder. RP25 , a locus for arRP, was mapped to chromosome 6p12.1-q14.1 where several retinal dystrophy loci are located. A gene expressed in the retina, FAM46A , mapped within the RP25 locus, and computational data revealed its involvement in retinal signalling pathways. Therefore, we chose to perform molecular evaluation of this gene as a good candidate in arRP families linked to the RP25 interval. A comprehensive bioinformatic and retinal tissue expression characterisation of FAM46A was performed, together with mutation screening of seven RP25 families.
Herein we present 4 novel sequence variants, of which one is a novel deletion within a low complexity region close to the initiation codon of FAM46A . Furthermore, we have characterised for the first time a coding tandem variation in the Caucasian population.
This study reports on bioinformatic and moleculardata for the FAM46A gene that may give a wider insight into the putative function of this gene and its pathologic relevance to RP25 and other retinal diseases mapping within the 6q chromosomal interval.     

Genetic mapping of loci for X-linked retinitis pigmentosa

Linkage analysis was performed in three Swedish families segregating for X-linked retinitis pigmentosa (XLRP), using five polymorphic DNA markers assigned to Xp. Individual recombination events were analyzed and two- and five-point linkage analysis was undertaken. In one family, a XLRP locus was mapped to the same position as OTC corresponding to RP3. In two families, a disease locus linked to OTC was excluded. In one family, recombination events indicate a locus for XLRP outside the interval (DXS84-OTC-DXS255-DXS14), most likely on the centromeric side of DXS14.     

Dominant PRPF31 Mutations Are Hypostatic to a Recessive CNOT3 Polymorphism in Retinitis Pigmentosa: A Novel Phenomenon of “Linked Trans‐Acting Epistasis”

Mutations in PRPF31 are responsible for autosomal dominant retinitis pigmentosa (adRP, RP11 form) and affected families show nonpenetrance. Differential expression of the wildtype PRPF31 allele is responsible for this phenomenon: coinheritance of a mutation and a higher expressing wildtype allele provide protection against development of disease. It has been suggested that a major modulating factor lies in close proximity to the wildtype PRPF31 gene on Chromosome 19, implying that a cis‐acting factor directly alters PRPF31 expression. Variable expression of CNOT3 is one determinant of PRPF31 expression. This study explored the relationship between CNOT3 (a trans‐acting factor) and its paradoxical cis‐acting nature in relation to RP11. Linkage analysis on Chromosome 19 was performed in mutation‐carrying families, and the inheritance of the wildtype PRPF31 allele in symptomatic–asymptomatic sibships was assessed—confirming that differential inheritance of wildtype chromosome 19q13 determines the clinical phenotype (P < 2.6 × 10^?7). A theoretical model was constructed that explains the apparent conflict between the linkage data and the recent demonstration that a trans‐acting factor (CNOT3) is a major nonpenetrance factor: we propose that this apparently cis‐acting effect arises due to the intimate linkage of CNOT3 and PRPF31 on Chromosome 19q13—a novel mechanism that we have termed “linked trans‐acting epistasis.”     

Retinitis pigmentosa in India: a genetic and segregation analysis

Seventy-eight families with retinitis pigmentosa, presenting at the genetic clinic of Sankara Nethralaya, Madras, over a period of 6 months, (from April to September 1993), were assessed to determine the different genetic types: 9% were autosomal dominant; 36%, autosomal recessive; 3%, X-linked recessive; 44%, isolated cases and 8%, undetermined genetic type. A high incidence of consanguinity was observed in autosomal recessive (57%) and isolated cases (37%). Segregation analysis showed good agreement in autosomal dominant (χ²=0.864) and recessive families (p=0.222). The high proportion of autosomal recessive and isolated cases in this study, when compared with other similar studies, is due to the high incidence of consanguineous marriages in the Indian subcontinent.     

Autosomal inheritance of "senile" retinitis pigmentosa. A report of a family with consanguinity

We describe two sisters affected with retinitis pigmentosa of late onset. Night blindness and progressive visual field loss occurred after 50 years of age in both cases. The parents of affected individuals were first cousins and there was no known history of other similar cases in previous generations. Autosomal recessive inheritance is suggested for such senile retinitis pigmentosa.     

Retinitis pigmentosa: genetic mapping in X-linked and autosomal forms of the disease

Retinitis pigmentosa (RP) is an hereditary degenerative disease of the retina and a major cause of visual impairment, prevalence estimates ranging from 1 in 3000 to 1 in 7000. The condition may segregate as an autosomal dominant, autosomal recessive or an X-linked recessive trait and it may also occur on a sporadic basis in up to 50% of cases. In the autosomal dominant form, close linkage to the DNA marker C17 (D3S47) was recently established in a large family of Irish origin displaying early-onset disease (McWilliam et al. 1989), multipoint analysis indicating the gene for rhodopsin as a likely candidate (Farrar et al. 1990). In that gene, a C----A transversion in codon 23, resulting in a proline----histidine substitution has now been identified in 17 of 148 unrelated ADRP patients in the United States (Dryja et al. 1990). This mutation is absent however in the original Irish pedigree (it is also absent in 21 other dominant Irish pedigrees, representing approximately 70% of the estimated ADRP population) indicating that another mutation, either in rhodopsin itself, or in a gene very closely linked to rhodopsin is responsible for the disease in that family. Analysis of other dominant pedigrees using the C17 and/or rhodopsin probes has indicated either tight linkage (Bhattacharya, Personal Communication), looser linkage, possibly indicative of a second locus on 3q (Olsson et al. 1990) or no linkage (Farrar et al. 1990, Blanton et al. 1990, Inglehearn et al. 1990). Extensive genetic heterogeneity thus exists in the autosomal dominant form of this disease, and in the light of these new observations, earlier tentative evidence for linkage of ADRP to the Rhesus locus on chromosome 1 will be re-evaluated. A locus for type II Usher syndrome (classical RP combined with congenital pedial deafness, and normal vestibular function) has now been established on the long arm of chromosome 1 (Kimberling et al. 1990). Type I Usher families, in which hearing loss is more profound and vestibular function absent, do not segregate with the same chromosome 1q markers, indicating the existence of another, as yet unlocated gene. In the X-linked form of the disease, two genes, XLRP2 and XLRP3, have been located on the proximal short arm of the X chromosome using a combination of physical and linkage mapping techniques, and there is some evidence to suggest a possible third locus more distally located.(ABSTRACT TRUNCATED AT 400 WORDS)     

RP1L1 Variants are Associated with a Spectrum of Inherited Retinal Diseases Including Retinitis Pigmentosa and Occult Macular Dystrophy

In one consanguineous family with retinitis pigmentosa (RP), a condition characterized by progressive visual loss due to retinal degeneration, homozygosity mapping, and candidate gene sequencing suggested a novel locus. Exome sequencing identified a homozygous frameshifting mutation, c.601delG, p.Lys203Argfs*28, in RP1L1 encoding RP 1‐like1, a photoreceptor‐specific protein. A screen of a further 285 unrelated individuals with autosomal recessive RP identified an additional proband, homozygous for a missense variant, c.1637G>C, p.Ser546Thr, in RP1L1. A distinct retinal disorder, occult macular dystrophy (OCMD) solely affects the central retinal cone photoreceptors and has previously been reported to be associated with variants in the same gene. The association between mutations in RP1L1 and the disorder OCMD was explored by screening a cohort of 28 unrelated individuals with the condition; 10 were found to harbor rare (minor allele frequency ≤0.5% in the 1,000 genomes dataset) heterozygous RP1L1 missense variants. Analysis of family members revealed many unaffected relatives harboring the same variant. Linkage analysis excluded the possibility of a recessive mode of inheritance, and sequencing of RP1, a photoreceptor protein that interacts with RP1L1, excluded a digenic mechanism involving this gene. These findings imply an important and diverse role for RP1L1 in human retinal physiology and disease.     

Retinitis Pigmentosa Mutations of SNRNP200 Enhance Cryptic Splice‐Site Recognition

Mutations in SNRP200 gene cause autosomal‐dominant retinal disorder retinitis pigmentosa (RP). The protein product of SNRNP200 is BRR2, a DExD/H box RNA helicase crucial for pre‐mRNA splicing. In this study, we prepared p.S1087L and p.R1090L mutations of human BRR2 using bacterial artificial chromosome recombineering and stably expressed them in human cell culture. Mutations in BRR2 did not compromise snRNP assembly and both mutants were incorporated into the spliceosome just as the wild‐type (wt) protein. Surprisingly, cells expressing RP mutants exhibited increased splicing efficiency of the LDHA gene. Next, we found that depletion of endogenous BRR2 enhanced usage of a β‐globin cryptic splice site while splicing at the correct splice site was inhibited. Proper splicing of optimal and cryptic splice sites was restored in cells expressing BRR2‐wt but not in cells expressing RP mutants. Taken together, our data suggest that BRR2 is an important factor in 5′‐splice‐site recognition and that the RP‐linked mutations c.3260C>T (p.S1087L) and c.3269G>T (p.R1090L) affect this BRR2 function.     

显性视网膜色素变性家系已知连锁位点的筛查

目的 用连锁分析法对1个中国人显性视网膜色素变性家系进行已知位点的筛查,寻找其致病基因.方法 随机选取已知致病基因上下约5cM(JB)范围内的27对微卫星标记,确立单倍型,用两点法计箅最大优势对数(Lod score)值.结果 所选微卫星标记与该家系表型间最大Lod值小于1.结论 基本排除由已知常染色体显性遗传视网膜色素变性的候选基因导致该家系的病变.     

Autosomal recessive retinitis pigmentosa locus maps on chromosome 1q in a large consanguineous family from Pakistan

A large Pakistani family with several consanguineous marriages is described, in which autosomal recessive retinitis pigmentosa is segregating. Linkage studies revealed close linkage between the disease locus and six loci on chromosome 1q (D1S158, F13B, D1S422, D1S412, D1S413, and D1S53) with maximum lod scores ranging from 0.988-4.657 at Θ=0.065-0.235. However, the analysis of individual nuclear families showed very close linkage without recombination in three branches and several recombinants and negative lod scores throughout in the fourth branch. These results strongly suggest that mutations of two different genes are responsible for the disease in the 'linked' and 'unlinked' branches. Parallel to the linkage heterogeneity, clear phenotypic differences have been observed among the 'linked' and 'unlinked' parts. Our findings demonstrate that in case of recessive disorders the possibility of non-allelic genetic heterogeneity should always be considered, even within the same kindred and in genetic isolates if a largely extended pedigree is analysed.     

Retinitis pigmentosa, AD type I: exclusion of linkage to D3S47 (C17) in a large South African family of British origin

Linkage analysis has been performed on a large South African family of British origin in which 39 persons in 6 generations had early onset Type I autosomal dominant retinitis pigmentosa (ADRP). Tight linkage was excluded between the disease and the D3S47 locus on chromosome 3. This finding is further evidence for genetic heterogeneity in ADRP.     

Retinitis pigmentosa: problems associated with genetic classification

Haim M. Retinitis pigmentosa: problems associated with genetic classification.
Clin Genet 1993: 44: 62–70. © Munksgaard, 1993
Genetic classification of retinitis pigmentosa (RP) can be problematic, due to a large number of isolated cases, reduced penetrance, and considerable variation in expressivity. Another confounder is a high proportion of affected female carriers in X-linked RP. Based on the genetic definitions of five different authors, a reclassification experiment was conducted with 350 Danish families. Agreement existed about a small "nucleus" of familial cases. Most definitions favored autosomal dominant inheritance at the expense of X-linked. The experiment revealed that methodological differences to a large extent might explain the considerable variation among reported genetic frequencies of retinitis pigmentosa.     

A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC)

Inherited retinal diseases (IRDs) cause visual loss due to dysfunction or progressive degeneration of photoreceptors. These diseases show marked phenotypic and genetic heterogeneity. The Israeli IRD consortium (IIRDC) was established in 2013 with the goal of performing clinical and genetic mapping of the majority of Israeli IRD patients. To date, we recruited 2,420 families including 3,413 individuals with IRDs. On the basis of our estimation, these patients represent approximately 40% of Israeli IRD patients. To the best of our knowledge, this is, by far, the largest reported IRD cohort, and one of the first studies addressing the genetic analysis of IRD patients on a nationwide scale. The most common inheritance pattern in our cohort is autosomal recessive (60% of families). The most common retinal phenotype is retinitis pigmentosa (43%), followed by Stargardt disease and cone/cone–rod dystrophy. We identified the cause of disease in 56% of the families. Overall, 605 distinct mutations were identified, of which 12% represent prevalent founder mutations. The most frequently mutated genes were ABCA4, USH2A, FAM161A, CNGA3, and EYS. The results of this study have important implications for molecular diagnosis, genetic screening, and counseling, as well as for the development of new therapeutic strategies for retinal diseases.     

Autosomal recessive retinitis pigmentosa in Spain: evaluation of four genes and two loci involved in the disease

Autosomal recessive retinitis pigmentosa (ARRP) is a genetically heterogeneous form of retinal degeneration. The genes for the β-subunit of rod phosphodiesterase (PDEB), rhodopsin (RHO), peripherin/RDS (RDS) and the rod outer segment membrane protein 1 (ROM1), as well as loci at 6p and 1q, have previously been reported as the cause of ARRP. In order to determine whether they are responsible for the disease in Spanish pedigrees, linkage and homozygosity studies using markers at these loci were carried out on 47 Spanish ARRP families. SSCP analysis was performed to search for mutations in the genes cosegregating with the disease in particular pedigrees. Three homozygous mutations in the PDEB gene were found, thus accounting for 6% of the cases. No other disease-causing mutation was observed in the other genes analysed, nor was significant evidence found for the involvement of the loci at 6p or 1q. On the basis of these data, it is unlikely that these genes and loci account for a considerable proportion of ARRP cases.     

一个X-连锁视网膜色素变性中国家系的RPGR基因的新突变

目的 对中国人X-连锁视网膜色素变性一家系进行分子遗传学检测，报告RPGR基因突变。方法 首先对该家系X染色体进行致病基因的连锁分析，然后用单链构象多态性技术和直接DNA测序方法进行基因突变分析。结果 连锁分析在多态性微卫星遗传标记DXSS012和DXS8025产生正的Lod值分别为2．41（Zmax=2．40，θ=0）和1．26。进一步单倍型分析确定该家系致病基因位于Xp21．1，与RP3连锁。用RPGR基因突变分析，在外显子ORF15＋483－484发现GA缺失，引起阅读框架的改变，该基因缺失突变在家系中共分离。结论 报告了中国人X-连锁视网膜色素变性RPGR基因外显子ORF15＋483-484的GA缺失突变，丰富了中国人RPGR基闪突变谱，为今后研究X-连锁视网膜色素变性的基因奠定基础。     

Artificial Intelligence–Assisted Early Detection of Retinitis Pigmentosa — the Most Common Inherited Retinal Degeneration

The purpose of this study was to detect the presence of retinitis pigmentosa (RP) based on color fundus photographs using a deep learning model. A total of 1670 color fundus photographs from the Taiwan inherited retinal degeneration project and National Taiwan University Hospital were acquired and preprocessed. The fundus photographs were labeled RP or normal and divided into training and validation datasets (n = 1284) and a test dataset (n = 386). Three transfer learning models based on pre-trained Inception V3, Inception Resnet V2, and Xception deep learning architectures, respectively, were developed to classify the presence of RP on fundus images. The model sensitivity, specificity, and area under the receiver operating characteristic (AUROC) curve were compared. The results from the best transfer learning model were compared with the reading results of two general ophthalmologists, one retinal specialist, and one specialist in retina and inherited retinal degenerations. A total of 935 RP and 324 normal images were used to train the models. The test dataset consisted of 193 RP and 193 normal images. Among the three transfer learning models evaluated, the Xception model had the best performance, achieving an AUROC of 96.74%. Gradient-weighted class activation mapping indicated that the contrast between the periphery and the macula on fundus photographs was an important feature in detecting RP. False-positive results were mostly obtained in cases of high myopia with highly tessellated retina, and false-negative results were mostly obtained in cases of unclear media, such as cataract, that led to a decrease in the contrast between the peripheral retina and the macula. Our model demonstrated the highest accuracy of 96.00%, which was comparable with the average results of 81.50%, of the other four ophthalmologists. Moreover, the accuracy was obtained at the same level of sensitivity (95.71%), as compared to an inherited retinal disease specialist. RP is an important disease, but its early and precise diagnosis is challenging. We developed and evaluated a transfer-learning-based model to detect RP from color fundus photographs. The results of this study validate the utility of deep learning in automating the identification of RP from fundus photographs.     

Genetic aspects of retinitis pigmentosa in China

We analyzed 151 pedigrees (209 cases) of retinitis pigmentosa in Shanghai, China. Of the 209 cases, the proportion of autosomal recessive (AR), autosomal dominant (AD), X-linked recessive (XR), and simplex cases is 33.1, 11, 7.7, and 48.3% respectively. The average age of onset was 24.7 years in the AD type, 22.9 years in the AR and five years in the XR type. The average refractive errors were ?1.88 D in the AD type, ?2.37 D in the AR type, and ?5.72 D in the XR type. In addition, 24, 100 persons were screened and six cases of retinitis pigmentosa were found. The gene frequencies of the AR (including simplex cases), AD, and XR types as calculated from the disease prevalence were 0.0142267, 0.0000137, and 0.0000384, respectively. The gene frequency of the AR type as calculated from the frequency of consanguinity (15.9%) was 0.00389, which is much less than that calculated from the prevalence. The probable explanation is that the AR type of retinitis pigmentosa really consists of several different disease entities, with each entity representing a separate gene mutation. The number of different mutations within the AR group is estimated to lie between 11 and 41.     

Linkage Analysis of Chromosome 1 with Essential Hypertension and Blood Pressure Quantitative Traits in Chinese Families

Several recent studies have linked human chromosome 1p to essential hypertension (EH) or blood pressure (BP) levels. In an independent population of 148 hypertensive families from China we tested these findings. Thirty highly informative microsatellite markers spanning about 284 cM were genotyped. Qualitative linkage analysis was conducted using non‐parametric linkage analysis implemented within the GENEHUNTER 2.0 software, whereas quantitative analysis was performed with the variance‐component method integrated in the S.O.L.A.R. 1.7.4. software with an additional Haseman‐Elston method using the SAGE/SIBPAL2 program. We observed suggestive linkage between D1S2890 (1p31, 80.9 cM) and hypertension using the multipoint non‐parametric linkage analysis (NPL = 2.19, P = 0.01). In the quantitative analysis we didn't observe a significant excess of identity‐by‐descent allele sharing between the systolic blood pressure levels and the markers. However, the D1S207 microsatellite marker (1p21) which is located about 107 cM from the telomere of 1p showed weak linkage evidence with the diastolic blood pressure levels (LOD = 1.42). These findings suggest linkage of 1p31 with essential hypertension in the ethnic Chinese, and provide a potential clue for future studies involving candidate genes for hypertension.     

一个视网膜色素变性家系的视紫红质基因突变分析

目的　确定常染色体显性遗传视网膜色素变性家系的致病基因及其突变位点,并研究其临床表型。方法　对一个常染色体显性遗传视网膜色素变性(autosomal dominat retinitis pigmentosa,ADRP)家系成员进行了视力、视野及眼底镜检查,并对该家系中先证者进行了视网膜电流图分析。应用聚合酶链反应和直接测序技术,对该家系的所有现存人员的视紫红质基因的外显子进行测序分析。结果　该家系的2 5名成员中12例患者有视紫红质基因(rhodopsin,RH O)的5 12 C>T(P171L)突变,均呈杂合子,该错义突变使密码子171由CCA变成CTA。而未受累者的视紫红质基因表现为野生型。该家系患者的临床表现为5～6岁时出现夜盲,在2 0～30岁逐渐出现视力和视野损害,并先后在4 0～5 0岁前后失明,其中2例患者并发青光眼,先证者的闪烁视网膜电图呈熄灭型。结论　视紫红质基因RH O的一种已知突变5 12 C>T(P171L)是该家系的病因。与国外相同的基因突变类型相比较,该家系发病早、病情进展快、视功能损害较重。     

Genetic testing and gene therapy in retinal diseases: Knowledge and perceptions of optometrists in Australia and New Zealand

With advances in gene-based therapies for heritable retinal diseases, primary eye care clinicians should be informed on ocular genetics topics. This cross-sectional survey evaluated knowledge, attitudes, and concerns regarding genetic testing and gene therapy for retinal diseases among optometrists in Australia and New Zealand. Survey data included practitioner background, attitudes and practices towards genetic testing for monogenic inherited retinal disease (IRDs) and age-related macular degeneration, and knowledge of ocular genetics and gene therapy. Responses were received from 516 optometrists between 1 April and 31 December 2022. Key perceived barriers to accessing genetic testing were lack of clarity on referral pathways (81%), cost (65%), and lack of treatment options if a genetic cause is identified (50%). Almost all respondents (98%) believed that ophthalmologists should initiate genetic testing for IRDs and fewer understood the role of genetic counsellors and clinical geneticists. This study found that optometrists in Australia and New Zealand have a high level of interest in ocular genetics topics. However, knowledge gaps include referral pathways and awareness of genetic testing and gene therapy outcomes. Addressing perceived barriers to access and promoting sharing of knowledge between interdisciplinary networks can set the foundation for genetic education agendas in primary eye care.