Genes and mutations causing retinitis pigmentosa

Authors


  • The authors declare no conflict of interest.

Corresponding author: Stephen P. Daiger, PhD, Human Genetics Center, School of Public Health,

The University of Texas Health Science Center,

1200 Herman Pressler Drive,

Houston, TX 77030, USA.

Tel.: +1 713 500 9829;

fax: +1 713 500 0900;

e-mail: stephen.p.daiger@uth.tmc.edu

Abstract

Retinitis pigmentosa (RP) is a heterogeneous set of inherited retinopathies with many disease-causing genes, many known mutations, and highly varied clinical consequences. Progress in finding treatments is dependent on determining the genes and mutations causing these diseases, which includes both gene discovery and mutation screening in affected individuals and families. Despite the complexity, substantial progress has been made in finding RP genes and mutations. Depending on the type of RP, and the technology used, it is possible to detect mutations in 30–80% of cases. One of the most powerful approaches to genetic testing is high-throughput ‘deep sequencing’, that is, next-generation sequencing (NGS). NGS has identified several novel RP genes but a substantial fraction of previously unsolved cases have mutations in genes that are known causes of retinal disease but not necessarily RP. Apparent discrepancy between the molecular defect and clinical findings may warrant reevaluation of patients and families. In this review, we summarize the current approaches to gene discovery and mutation detection for RP, and indicate pitfalls and unsolved problems. Similar considerations apply to other forms of inherited retinal disease.

Inherited retinal diseases affect more than 200,000 Americans and millions of individuals worldwide [1-3]. Dozens of different types of disease are included in this set of diseases, and more than 190 genes have been identified as the cause of one or another form of inherited retinal disease [4, 5]. Retinitis pigmentosa (RP) accounts for approximately one-half of cases. RP itself is highly heterogeneous: mutations in more than 50 genes are known to cause non-syndromic RP and nearly 3100 mutations have been reported in these genes [5, 6]. Syndromic forms of RP are equally heterogeneous: mutations in 12 genes cause Usher syndrome and 17 genes are associated with Bardet-Biedl syndrome; together these two diseases account for another 1200 pathogenic mutations. In addition to genetic and mutational heterogeneity, different diseases may be caused by mutations in the same gene, symptoms of different diseases may overlap, and there is extensive variation in clinical expression even among individuals sharing the same mutation in the same gene.

Despite the complexity, significant progress has been made in recent years in identifying novel RP genes and in screening patients for pathogenic mutations. This is partly the result of development of high-throughput mapping and sequencing techniques, but is also testimony to the large number of investigators and research groups working in this area. In the past two decades, the number of research groups in the world focused on RP genetics has gone from a handful to dozens. The potential options for treatments have also increased markedly. The purpose of this review is to provide an overview of the current status of RP genes. References are largely chosen for illustration; a more comprehensive list is found in RetNet, http://www.sph.uth.tmc/edu/retnet [5]. Inherited retinopathies as a broad class of diseases are reviewed in other publications [4, 7]. This is a fast-moving field and it is encouraging to note that any review will be out of date sooner rather than later.

Heterogeneity

Retinitis pigmentosa is a progressive, degenerative disease of the retina leading to profound loss of vision or blindness [3]. The clinical hallmarks of RP are night blindness, often starting in adolescence, followed by progressive loss of peripheral vision and subsequent loss of central vision. By midlife, RP patients may retain a few degrees of central vision but in many cases the disease culminates in complete blindness. Findings on retinal examination include ‘bone spicule’ pigmentary deposits, retinal vessel attenuation, and characteristic changes in electroretinogram (ERG) patterns. At a cellular level, a simplified view of RP is progressive dysfunction and loss of rod photoreceptors, first affecting night vision in the rod-rich mid-peripheral retina, then progressing into the cone-rich central retina, with eventual loss of cones either as a direct result of the disease process or secondary to the death of rods.

Within this broad picture, though, there is considerable variation in age of onset, rate of progression, rod vs cone involvement, involvement of other retinal cells such as RPE, secondary symptoms such as cystic macular edema, and many other features. RP which is present at birth or soon after is often referred to as Leber congenital amaurosis (LCA). RP may occur alone, as non-syndromic RP, without other clinical findings, or as syndromic or systemic RP with other neurosensory disorders, developmental abnormalities, or complex clinical phenotypes. Usher syndrome is RP with congenital or early onset deafness. Bardet-Biedl syndrome (BBS) is RP with kidney disease, obesity, polydactyly and developmental delay. RP may also be secondary to systemic disorders such as mitochondrial diseases or various forms of degenerative cerebellar disease. For simplicity, this review is limited to non-syndromic RP, Usher syndrome and BBS (for one reason, because the diseases overlap). Other syndromic and systemic forms of RP are listed in RetNet [5].

Retinitis pigmentosa is exceptionally heterogeneous. This includes (i) genetic heterogeneity—many different genes may cause the same disease phenotype; (ii) allelic heterogeneity—there may be many different disease-causing mutations in each gene; (iii) phenotypic heterogeneity—different mutations in the same gene may cause different diseases; and (iv) clinical heterogeneity—the same mutation in different individuals may produce different clinical consequences, even among members of the same family. The extent of heterogeneity of RP can be confusing to patients and clinicians alike, and is a confounding factor in diagnosis.

The most obvious complications are genetic and allelic. Currently, mutations in 56 genes are known to cause non-syndromic RP (Table 1). Twelve genes account for Usher syndrome and 17 account for BBS (Tables 2 and 3). If genes for LCA and for other syndromic or systemic forms of RP are included, at least 100 ‘RP-related’ genes are known. Allelic or mutational heterogeneity is equally striking. Counting all the genes known to cause non-syndromic RP, at nearly 3100 disease-causing mutations are reported in mutation databases (Table 1). Discounting overlaps with non-syndromic RP, genes causing Usher syndrome and BBS account for at least another 1200 mutations (Tables 2 and 3).

Table 1. Genes causing non-syndromic retinitis pigmentosaa
 SymbolLocationProteinType of retinitis pigmentosaOther diseasesMutations
  1. a

    Tables are based on the RetNet database, http://www.sph.uth.tmc.edu/retnet/, accessed May 2013 [5], and the Human Gene Mutation Database, http://www.hgmd.cf.ac.uk/, accessed May 2013 [6]. References are in RetNet. Some genes appear in more than one table so the sum total of distinct genes in the tables, 82, is less than the sum of the three tables together.

1ABCA41p22.1ATP-binding cassette transporter—retinalAutosomal recessiveRecessive macular dystrophy; recessive fundus flavimaculatus; recessive cone-rod dystrophy680
2BEST111q12.3Bestrophin 1Autosomal dominant; autosomal recessiveDominant vitreoretinochoroidopathy; recessive bestrophinopathy; dominant Best type macular dystrophy232
3C2ORF712p23.2Chromosome 2 open reading frame 71Autosomal recessive 13
4C8ORF378q22.1Chromosome 8 open reading frame 37Autosomal recessiveRecessive cone-rod dystrophy4
5CA417q23.2Carbonic anhydrase IVAutosomal dominant 6
6CERKL2q31.3Ceramide kinase-like proteinAutosomal recessiveRecessive cone-rod dystrophy with inner retinopathy8
7CLRN13q25.1Clarin-1Autosomal recessiveRecessive Usher syndrome23
8CNGA14p12Rod cGMP-gated channel alpha subunitAutosomal recessive 8
9CNGB116q13Rod cGMP-gated channel beta subunitAutosomal recessive 6
23CRB11q31.3Crumbs homolog 1Autosomal recessiveRecessive Leber congenital amaurosis; dominant pigmented paravenous chorioretinal atrophy183
11CRX19q13.32Cone-rod otx-like photoreceptor homeobox transcription factorAutosomal dominantRecessive, dominant and de novo Leber congenital amaurosis; dominant cone-rod dystrophy51
12DHDDS1p36.11Dehydrodolichyl diphosphate synthetaseAutosomal recessive 1
13EYS6q12Eyes shut/spacemaker (Drosophila) homologAutosomal recessive 118
14FAM161A2p15Family with sequence similarity 161 member AAutosomal recessive 6
15FSCN217q25.3Retinal fascin homolog 2, actin bundling proteinAutosomal dominantDominant macular dystrophy1
16GUCA1B6p21.1Guanylate cyclase activating protein 1BAutosomal dominantDominant macular dystrophy3
17IDH3B20p13NAD(+)-specific isocitrate dehydrogenase 3 betaAutosomal recessive 2
18IMPDH17q32.1Inosine monophosphate dehydrogenase 1Autosomal dominantDominant Leber congenital amaurosis14
19IMPG23q12.3Interphotoreceptor matrix proteoglycan 2Autosomal recessive 10
20KLHL77p15.3Kelch-like 7 protein (Drosophila)Autosomal dominant 3
21LRAT4q32.1Lecithin retinol acyltransferaseAutosomal recessiveRecessive Leber congenital amaurosis10
22MAK6p24.2Male germ-cell associated kinaseAutosomal recessive 9
23MERTK2q13c-mer protooncogene receptor tyrosine kinaseAutosomal recessive 27
24NR2E315q23Nuclear receptor subfamily 2 group E3Autosomal dominant; autosomal recessiveRecessive Stargardt disease; Goldmann-Favre syndrome; recessive enhanced S-cone syndrome45
25NRL14q11.2Neural retina lucine zipperAutosomal dominant; autosomal recessiveRecessive retinitis pigmentosa14
26OFD1Xp22.2Oral-facial-digital syndrome 1 proteinX-linkedOrofaciodigital syndrome 1, Simpson-Golabi-Behmel syndrome 2127
27PDE6A5q33.1cGMP phosphodiesterase alpha subunitAutosomal recessive 16
28PDE6B4p16.3Rod cGMP phosphodiesterase beta subunitAutosomal recessiveDominant congenital stationary night blindness39
29PDE6G17q25.3Phosphodiesterase 6G cGMP-specific rod gammaAutosomal recessive 1
30PRCD17q25.1Progressive rod-cone degeneration proteinAutosomal recessive 2
31PROM14p15.32Prominin 1Autosomal recessiveDominant Stargardt-like and bulls eye macular dystrophy; dominant cone-rod dystrophy9
32PRPF31q21.2Human homolog of yeast pre-mRNA splicing factor 3Autosomal dominant 3
33PRPF620q13.33Human homolog of yeast pre-mRNA splicing factor 6Autosomal dominant 2
34PRPF817p13.3Human homolog of yeast pre-mRNA splicing factor C8Autosomal dominant 21
35PRPF3119q13.42Human homolog of yeast pre-mRNA splicing factor 31Autosomal dominant 65
36PRPH26p21.1Peripherin 2Autosomal dominant; digenic with ROM1Dominant macular dystrophy; dominant vitelliform MD; dominant cone-rod dystrophy; dominant central areolar choroidal dystrophy123
37RBP310q11.22Retinol binding protein 3, interstitialAutosomal recessive 2
38RDH1214q24.1Retinol dehydrogenase 12Autosomal dominant; autosomal recessiveRecessive Leber congenital amaurosis66
39RGR10q23.1RPE-retinal G protein-coupled receptorAutosomal recessiveDominant choroidal sclerosis7
40RHO3q22.1RhodopsinAutosomal dominant; autosomal recessiveDominant congenital stationary night blindness161
41RLBP115q26.1Retinaldehyde-binding protein 1Autosomal recessiveRecessive Bothnia dystrophy; recessive retinitis punctata albescens; recessive Newfoundland rod-cone dystrophy20
42ROM111q12.3Retinal outer segment membrane protein 1Autosomal dominant; digenic w/ PRPH2 11
43RP18q12.1RP1 proteinAutosomal dominant; autosomal recessiveAutosomal dominant and recessive67
44RP2Xp11.23Retinitis pigmentosa 2 (X-linked)X-linked 76
45RP97p14.3RP9 protein or PIM1-kinase associated protein 1Autosomal dominant 2
46RPE651p31.2Retinal pigment epithelium-specific 65 kDa proteinAutosomal dominant; autosomal recessiveRecessive Leber congenital amaurosis134
47RPGRXp11.4Retinitis pigmentosa GTPase regulatorX-linkedX-linked cone dystrophy 1; X-linked atrophic macular dystrophy151
48SAG2q37.1Arrestin (s-antigen)Autosomal recessiveRecessive Oguchi disease11
49SEMA4A1q22Semaphorin 4AAutosomal dominantDominant cone-rod dystrophy3
50SNRNP2002q11.2Small nuclear ribonucleoprotein 200 kDa (U5)Autosomal dominant 7
51SPATA714q31.3Spermatogenesis associated protein 7Autosomal recessiveRecessive Leber congenital amaurosis15
52TOPORS9p21.1Topoisomerase I binding arginine/serine rich proteinAutosomal dominant 8
53TTC814q32.11Tetratricopeptide repeat domain 8Autosomal recessiveRecessive Bardet-Biedl syndrome14
54TULP16p21.31Tubby-like protein 1Autosomal recessiveRecessive Leber congenital amaurosis31
55USH2A1q41UsherinAutosomal recessiveRecessive Usher syndrome392
56ZNF5132p23.3Zinc finger protein 513Autosomal recessive 1
     Total3064
Table 2. Genes causing Usher syndromea
 SymbolLocationProteinType of Usher syndromeOther diseasesMutations
  1. RP, retinitis pigmentosa.

  2. a

    Tables are based on the RetNet database, http://www.sph.uth.tmc.edu/retnet/, accessed May 2013 [5], and the Human Gene Mutation Database, http://www.hgmd.cf.ac.uk/, accessed May 2013 [6]. References are in RetNet. Some genes appear in more than one table so the sum total of distinct genes in the tables, 82, is less than the sum of the three tables together.

1ABHD122p11.21Abhydrolase domain containing protein 12Autosomal recessive type 3-likeRecessive PHARC syndrome type5
2CDH2310q22.1Cadherin-like gene 23Autosomal recessive 1d; digenic with PCDH15Recessive deafness without retinitis pigmentosa167
3CIB215q25.1Calcium and integrin binding family member 2Autosomal recessive type 1J 7
4CLRN13q25.1Clarin-1Autosomal recessive type 3Recessive retinitis pigmentosasee RP
5DFNB319q32WhirlinAutosomal recessive type 2Recessive deafness without retinitis pigmentosa13
6GPR985q14.3Monogenic audiogenic seizure susceptibility 1 homologAutosomal recessive type 2Dominant/recessive febrile convulsions54
7HARS5q31.3Histidyl-tRNA synthetaseAutosomal recessiveRecessive HARS syndrome2
8MYO7A11q13.5myosin VIIARecessive type 1b; recessive USH3-likeRecessive deafness without retinitis pigmentosa263
9PCDH1510q21.1Protocadherin 15Autosomal recessive type 1f; digenic with CDH23Recessive deafness without retinitis pigmentosa52
10USH1C11p15.1harmoninAutosomal recessive AcadianRecessive deafness without retinitis pigmentosa; recessive RP with late-onset hearing loss26
11USH1G17q25.1Human homolog of mouse scaffold protein containing ankyrin repeats and SAM domainAutosomal recessive Usher syndrome 11
12USH2A1q41UsherinAutosomal recessive type 2aRecessive retinitis pigmentosasee RP
     Total600
Table 3. Genes causing Bardet-Biedl syndrome (BBS)a
 SymbolLocationProteinType of BBSOther diseasesMutations
  1. RP, retinitis pigmentosa.

  2. a

    Tables are based on the RetNet database, http://www.sph.uth.tmc.edu/retnet/, accessed May 2013 [5], and the Human Gene Mutation Database, http://www.hgmd.cf.ac.uk/, accessed May 2013 [6]. References are in RetNet. Some genes appear in more than one table so the sum total of distinct genes in the tables, 82, is less than the sum of the three tables together.

1ARL63q11.2ADP-ribosylation factor-like 6Autosomal recessive 14
2BBS111q13BBS1 proteinAutosomal recessive 65
3BBS216q12.2BBS2 proteinAutosomal recessive 61
4BBS415q24.1BBS4 proteinAutosomal recessive 29
5BBS52q31.1Flagellar apparatus-basal body protein DKFZp7621194Autosomal recessive 18
6BBS74q27BBS7 proteinAutosomal recessive 26
7BBS97p14.3Parathyroid hormone-responsive B1 proteinAutosomal recessive 27
8BBS1012q21.2BBS10 (C12orf58) chaperoninAutosomal recessive 76
9BBS124q27BBS12 proteinAutosomal recessive 45
10CEP29012q21.32Centrosomal protein 290 kDaAutosomal recessiveRecessive Joubert syndrome; recessive Leber congenital amaurosis; recessive Meckel syndrome; recessive Senior-Loken syndrome157
11INPP5E9q34.3Inositol polyphosphate-5-phosphatase EAutosomal recessiveRecessive MORM syndrome; recessive Joubert syndrome7
12LZTFL13p21.31Leucine zipper transcription factor-like 1Autosomal recessive 1
13MKKS20p12.2McKusick-Kaufman syndrome proteinAutosomal recessive 44
14MKS117q22Meckel syndrome type 1 proteinAutosomal recessiveRecessive Meckel syndrome26
15SDCCAG81q43Serologically defined colon cancer antigen 8Autosomal recessiveRecessive ciliopathy-related nephronophthisis,13
16TRIM329q33.1Tripartite motif-containing protein 32Autosomal recessiveRecessive limb-girdle muscular dystrophy8
17TTC814q32.11Tetratricopeptide repeat domain 8Autosomal recessiveRecessive retinitis pigmentosasee RP
     Total617

Although some of the publically reported mutations may, later, turn out to be non-pathogenic, this is still a significant underestimate because many novel mutations are listed in private databases and are not yet in the public domain. Among other concerns, there is need for more systematic collection of mutation phenotype–genotype information for inherited retinal diseases, a need addressed, for example, by the Leiden Open Variation Database [8].

Equally confusing is the overlap between disease types, disease names, and clinical consequences. First, different mutations in the same gene may cause distinctly different conditions. For example, even though most rhodopsin mutations cause autosomal-dominant RP and most RPE65 mutations cause recessive LCA, some rhodopsin mutations may be recessive acting and some RPE65 mutations may be dominant acting [9-13]. Usher syndrome mutations are recessive and cause both deafness and RP, but mutations in two Usher genes, CLRN1 and USH2A, may cause recessive RP only [14, 15].

For non-syndromic RP, mutations in 23 genes are known to cause autosomal-dominant RP, 36 genes cause recessive RP, and 3 genes cause X-linked RP [5]. However, Table 1 shows that several of these diseases overlap with each other and Tables 1-3 show that many genes cause multiple diseases. In some cases the ‘secondary’ disease is rare (e.g. recessive rhodopsin or dominant RPE65 mutations), but in some cases it is common (e.g. recessive RP and USH2A). Generally, there is no simple mapping between gene and disease in most cases.

Finally, even identical mutations within the same gene may produce different clinical findings. Variation between individuals in age of onset or rate of progression is not unexpected, but, for example, mutations in PRPF31 are non-penetrant in some family members, [16, 17] and mutations in PRPH2 (RDS) produce a wide range of macular, peripheral or pan-retinal symptoms [18, 19]. One consequence is that members of the same family, seen by different clinicians, may have diagnoses that are consistent with findings in the individual but inconsistent with the family. Overall, there is considerable overlap between diseases caused by RP genes even though different names are given to specific types of disease. This is well illustrated by the overlapping disease nomenclature proposed by Berger et al. for inherited retinal diseases [4].

Fortunately, molecular techniques allow identification of the underlying gene and mutation or mutations in many cases, adding a molecular diagnosis to the clinical diagnosis. Nevertheless, in some cases this leads to apparent contradictions that require further analysis to resolve.

Technical approaches

The standard techniques for gene discovery and muta-tion detection—linkage mapping and DNA sequencing—have been used for many years. However, development of high-density and high-throughput techniques in the past 10 years has increased the power of these methods by orders of magnitude.

For linkage mapping, high-density SNP (single-nucleotide polymorphism) arrays, such as the Affymetrix 6.0 SNP/CNV array, [20] allow linkage testing against nearly 1 million genetic markers. For practical purposes, these are often collapsed to around 10,000 most-informative markers, with known relationships to contiguous markers. However, even with smaller marker sets, there is a serious issue of the large number of independent tests (multiple comparisons) leading to apparent linkage ‘hits’ by chance alone. Fortunately, there are many more, highly-variable genetic markers in the human genome that can be used to refine linkage mapping [9]. Several RP genes have first been localized by linkage mapping in recent years [21-25].

One consequence of availability of dense SNP marker sets is that it is possible to identify regions on homologous chromosomes that are identical-by-descent, that is, regions on a matching pair of chromosomes that derive from a single chromosome in a relatively recent ancestor. This identifies the chromosomal location of identical recessive mutations in families with consanguinity or recent within-family matings. This approach to mapping recessive genes is called homozygosity mapping or autozygosity mapping [26]. It has been very productive in identifying RP genes in inbred families and in ethnic populations where inbreeding is common [27-31]. Surprisingly, even in families without evidence of consanguinity, recessive RP mutations are more often identical-by-descent than expected, thus expanding the utility of homozygosity mapping [26].

Methods for detecting mutations at a DNA sequence level include Sanger sequencing, still called the gold standard of sequencing, array-based detection of specific mutations (e.g. APEX, ‘array-primer extension’ [32-34]), ultra-high-throughput sequencing and others. Of these, the major advance in recent years in finding RP genes is application of ultra-high-throughput sequencing, generally referred to as next-generation sequencing (NGS) [35]. Conventional Sanger sequencing is usually done using semiautomated, multilane capillary electrophoresis (itself a major improvement over earlier methods). In contrast, NGS does millions of sequencing runs in parallel on micron-sized beads or in comparable micro-wells, completing up to a billion base-pair reads per run. That is, NGS sequencing is at least 1000 times faster than conventional sequencing, and much less expensive per sequence.

There are several NGS methods and numerous distinct applications [36, 37]. What most methods have in common is short-read, shot-gun sequencing: DNA is first fragmented into short sequences, read lengths are in the range of 100 to 200 base pairs, and computational methods are used to ‘reassemble’ the short reads into larger constructs. This allows highly accurate, extremely rapid sequencing of large regions of the human genome, but certain features of human DNA, such as deletions and rearrangements, expanded repeats, and haplotypes, are not accessible to NGS without additional steps. Also, because of the sheer volume of data produced by NGS, dedicated bioinformatic resources are required to fully utilize the results.

Despite these limitations, NGS has been exceptionally productive in gene discovery and mutation detection for RP. Broadly, there are three NGS strategies: whole-exome NGS, whole-genome NGS and targeted-capture NGS. Whole-exome NGS involves capture of all protein-coding regions, that is, all exons, constituting about 1.5% of the human genome, followed by NGS. By definition this technique is limited to finding mutations in coding regions only, but nonetheless it has led to identification of several RP genes and novel mutations [9, 38, 39]. Whole-genome NGS covers nearly all the human genome (about 98%), and avoids potential artifacts introduced by exon capture, but is not yet in routine use for gene discovery. The principal limitations are sequencing costs, and management and analysis of the resulting massive data sets. However, it is likely that whole-genome sequencing will become routine in the near future, especially with development of ‘third generation’ technologies [40].

Targeted capture, the third NGS strategy, limits testing to exons of known disease-causing genes [41]—in the case of retinal diseases, for example, testing only the 190-plus genes in RetNet [5]. The disadvantage, of course, is that no new genes can be identified. The advantages are that the analysis ‘space’ is much smaller, more is known, a priori, about each gene, and costs are much lower. Thus this is currently an optimal approach to mutation screening for RP, with many applications [42-47].

Finally, some mutations are not easily detected by conventional sequencing or NGS, particularly large deletions and rearrangements. Some deletions can be detected by SNP arrays, and the Affymetrix 6.0 SNP/CNV arrays includes copy-number probes (CNVs) for deletion detection [20]. PCR-amplification based methods, such as MLPA or qPCR, can detect much smaller deletions. This is a significant issue as nearly 3% of cases of autosomal-dominant RP are caused by deletions in PRPF31 not detectable by sequencing [17, 48]. Similar deletions and rearrangements are found in ABCA4, a common cause of recessive RP, and in RPGR, the principal cause of X-linked RP [49]. However, X-linked deletions are easily detected in hemizygous males, and the principal problem in sequencing RPGR is the repetitive nature of ORF15.

Current status of gene discovery and mutation detection

Identification of novel genes causing inherited retinal diseases, including RP, has progressed at a steady, linear rate for nearly 20 years (Fig. 1). Although the tools for gene discovery are much more powerful, the steady rate in recent years suggests that, in general, each new gene is rarer than preceding genes and thus more difficult to detect. Whole-genome NGS may accelerate gene discovery, but it is possible that the remaining, unknown RP genes are very rare. However, there is no meaningful way to predict the remaining number of RP genes.

Figure 1.

Mapped and identified retinal disease genes over three decades.

The meaningful questions in this context are (i) in what fraction of RP patients can disease-causing mutations be detected today, and (ii) when will it be possible to find mutations in nearly all patients, say, at least 95%? The answer to the first question depends on the technology used and the type of RP. Combining results from conventional Sanger sequencing and targeted-capture NGS, using rough estimates, it is possible to detect the underlying pathogenic mutation or mutations in 20–30% of autosomal recessive RP cases, 60–70% of autosomal-dominant cases, 80–85% of X-linked cases, and more than 85% of Usher and BBS cases [44, 50] [and S.P. Daiger, unpublished data].

Simplex (isolated) RP cases are more complicated. Traditionally, simplex RP cases are predicted to be recessive, with unaffected carrier parents. This is true in many cases, but there are exceptions. At least 15% of males with RP and no other affected family members have mutations in the X-linked genes RPGR or RP2 [51]. De novo autosomal-dominant mutations account for at least 1–2% of simplex cases [45, 52]. Targeted NGS identifies mutations in 19–36% of simplex RP cases, but confirming pathogenicity in these cases is problematic [44-47]. A further complication is that the carrier frequency for all inherited retinal disease mutations in unaffected individuals may exceed 20% [53]. That is, each mutation is extremely rare, but there are so many genes and so many mutations, that in aggregate they are common.

Prediction is risky, but given rapid advances in DNA sequencing methods, and continued identification of new RP genes, it is reasonable to expect that within 5 years it will be possible to detect the disease-causing gene and mutation or mutations in 95% of patients. This is assuming that most of the remaining cases are monogenic, that is, caused by a single gene in each individual. Since digenic forms of RP and triallelic forms of BBS are already known, polygenic inheritance of retinal diseases cannot be discounted [54, 55].

Finally, genetic diagnosis of RP may change the family diagnosis or raise questions about the relationship between genotype and phenotype. For example, at least 8% of families with a provisional diagnosis of autosomal-dominant RP actually have mutations in X-linked RP genes [56]. Mutations in genes commonly associated with Usher syndrome or BBS may cause non-syndromic RP [14, 15, 57]. Other examples arise from targeted-capture NGS. This can be confusing for the patient and requires thoughtful explanation and counseling. In some cases, it may require redefining the family's disease. Reconciling the clinical phenotype, family history and genetic findings is a critical, new step in the diagnosis of inherited retinal diseases.

Acknowledgements

Supported by grants from the Foundation Fighting Blindness and NIH grant EY007142. Dr Daiger is Director of a CLIA Certified Laboratory in the eyeGENE® Ophthalmic Disease Genotyping Network which includes financial support for genetic testing.

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