Comprehensive Inherited Retinal Dystrophies (includes RPGR ORF15) Panel

Inherited retinal disorders (IRD) are the leading cause of blindness in the western world (1 in 3,000 people). Identifying the genetic cause for the IRD is challenging due to genetic heterogeneity. According to the World Health Organization (WHO) and the American Academy of ophthalmology (AAO), ~80% of blindness can be prevented or cured or the disease progression slowed if detected at early stages (WHO Fact Sheet). Given these statistics, the importance of early and accurate diagnosis cannot be understated. Currently, molecular diagnosis of IRD is gaining importance due to emerging therapies such as gene therapy (Sahel et al. 2014. PubMed ID: 25324231; Chen et al. 2013. PubMed ID: 23661368).

Identifying the genetic cause for the IRD is challenging due to genetic heterogeneity. So far, ~300 loci have been mapped and over 250 genes have been identified to be involved with retinal disorders (RetNet).

Pathogenic variants in USH2A, ABCA4, PDE6A, PDE6B, RPE65, CNGA1, BEST1, PCARE (C2ORF71), C8ORF37, CLRN1, CNGB1, DHDDS, FAM161A, IDH3B, IMPG2, LRAT, MAK, MERTK, NRL, PDE6G, PRCD, PROM1, RBP3, RGR, RHO, RLBP1, RP1, SAG, SPATA7, TTC8, CERKL, TULP1, ZNF513, and ARL6 cause autosomal recessive (AR) retinal disorders (Chen et al. 2013. PubMed ID: 23661368; Fahim et al. 2013. PubMed ID: 20301590). Pathogenic variants in PRPF8, IMPDH1 and OTX2 cause autosomal dominant (AD) retinal disorders (Bowne et al. 2006. PubMed ID: 16384941; Henderson et al. 2009. PubMed ID: 19956411; Swaroop et al. 1999. PubMed ID: 9931337; Zhao et al. 2006. PubMed ID: 16612614). GUCY2D, KCNJ13, CRB1, RHO, NR2E3 and CRX are implicated in both AD and AR retinal disorders (Kohl et al. 2012. PubMed ID: 22901948; Piri et al. 2005. PubMed ID: 15629837; Wang et al. 2013. PubMed ID: 23847139; Weleber et al. 2013. PubMed ID: 20301475; Udar et al. 2003. PubMed ID: 12552567; Hanein et al. 2002. PubMed ID: 12325031; McKay et al. 2005. PubMed ID: 15623792; Abouzeid et al. 2006. PubMed ID: 16543197; Swaroop et al. 1999. PubMed ID: 9931337; Hejtmancik et al. 2008. PubMed ID: 18179896). Pathogenic variants in RPGR, CACNA1F, RP2, OFD1, RS1 and CHM are involved in X-linked retinal disorders (van den Hurk et al. 2003. PubMed ID: 12827496; Weleber. 2002. PubMed ID: 12187427; Wang et al. 2015. PubMed ID: 26047050; Wang et al. 2013. PubMed ID: 23847139; Online Mendelian Inheritance in Man; Human Gene Mutation Database).

See individual gene test descriptions for information on molecular biology of gene products and spectra of pathogenic variants.

A study that analyzed 105 genes in a diagnostic NGS test for Inherited retinal disorders identified a molecular diagnosis for 271 of the 537 referred patients in 62 genes (51%) (Ellingford et al. 2016. PubMed ID: 27208204). Another study that analyzed 105 genes in 170 patients with retinal dystrophies identified molecular diagnoses in 55–80% of patients (Glöckle et al. 2014. PubMed ID: 23591405). Out of these cases, 23 were positive in USH2A. The other major genes were EYS (8 cases), ABCA4 (5 cases), RHO (5 cases), NR2E3 (3 cases), CRB1 (3 cases), PRPH2 (3 cases) and MYO7A (3 cases). In other genes, causative variants were found only once or twice.

Genomic rearrangements in PRPF31 (causative for AD RP) are known to account for 2.5% of AD RP (Sullivan et al. 2006. PubMed ID: 17003455). Deletions and rearrangements are also found in ABCA4, which is causative for AR RP (Yatsenko et al. 2003. PubMed ID: 12754711). In addition, copy number variants have been reported in ABHD12, ARL6, BEST1, CACNA1F, CEP290, CHM, CRB1, CRX, EYS, GUCY2D, IMPG2, MERTK, NR2E3, PDE6B, PRPF31, PRPH2, RDH12, RHO, RLBP1, RP2, RPE65, RPGR, RPGRIP1, SAG, SPATA7, TULP1 and USH2A (Human Gene Mutation Database). A study by Perrault et al. (2000) identified two gross deletions and one duplication in GUCY2D out of 118 patients affected with Leber Congenital Amaurosis (Perrault et al. 2000. PubMed ID: 10951519).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

Additional Sanger sequencing is performed for a few exonic regions (such as in BEST1 and RPGR) regions that are not covered by the exome platform, but that contain documented causative variants.

Of note, all the genes will be sequenced and all variants of uncertain significance and above variants will be included in the report (upon request benign and likely benign variants will also be provided).

Average coverage information (Exome plus Sanger backfill) Total fraction of Covered bases (≥20X): 98.6%

Please note that ABCA4, ABCD1, ABHD12, AGBL5, BBIP1, BEST1, C1QTNF5, CAPN5, CDH23, CEP164, CEP250, CHM, CNNM4, GRM6, HMX1, IFT81, IMPDH1, INPP5E, INVS, IQCB1, KIAA1549, LRP5, MYO7A, NXNL1, OAT, OFD1, PCARE, PDZD7, PEX11B, PEX12, PEX7, PNPLA6, PRKCG, PRPF3, PRPF31, RP1L1, RPGR, RTN4IP1 , SLC24A1, TMEM231, TPP1, TTPA, TUBGCP4, USH1C, USH2A and VPS13B do not have 100% coverage for a few exonic regions as well as deep intronic variants (e.g., ABCA4). However, if we find a pathogenic or a likely pathogenic in one of these genes, we will perform Sanger backfill of the remainder of this gene.

Because analysis of the RPGR Exon 15 (ORF15) purine rich region is especially difficult; we utilize special Sanger sequencing chemistry for this region.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).