Test Code: 8322

Eye Disorders: Comprehensive Sequencing Panel
Test Code: 8322
Turnaround time: 6 weeks

CONDITION DESCRIPTION

The Eye Disorder Comprehensive Sequencing Panel is an analysis of almost all clinically relevant genes identified as causing syndromic and non- syndromic inherited retinal and choroidal dystrophies, as well as ocular developmental disorders. There is a wide range of genetic and phenotypic heterogeneity in retinal and choroidal disorders making accurate clinical diagnosis difficult especially during early phases of the disease onset.

Retinal disorders can be congenital and present at birth (as in Leber congenital amaurosis), present in early childhood (as in early onset retinitis pigmentosa), or present in mid life (as in pattern dystrophy). The clinical features of retinal disorders include vision loss, vision distortion, loss of peripheral vision, and night blindness. Fundus exam findings can range from almost normal appearance of the retina (as in Leber congenital amaurosis) to pale optic nerve, narrowed arterioles, bone spicules, photoreceptor loss, retinal pigment epithelial changes, and chorioretinal atrophy. The fundus appearance in the end stage of many retinal disorders, such as pattern dystrophy and cone-rod dystrophy, may be similar to that of macular dystrophy or chorioretinal atrophy. Electroretinogram (ERG) findings can range from non-recordable ERG to loss of rod or cone responses and be non-specific. Rarely, characteristic findings in ERG as in congenital stationary night blindness may help in arriving at a more accurate diagnosis. Detailed history and clinical examination, optical coherence tomography (OCT), pattern of visual field loss and ERG may help narrow the selection of disease causing genes or groups of genes.

Some genes on this panel are available as single gene tests or as part of a more clinically specific eye disorders sub-panel (e.g. retinitis pigmentosa). As the distinction between disorders is difficult, the Eye Disorder Comprehensive Sequencing Panel may be ordered as a comprehensive test. Please note that some genes may cause more than one phenotype. In addition to the nuclear genes analyzed, seven targeted mitochondrial DNA mutations are also assessed.

General categorical overview of the eye disorders included on the panel:

  • Achromatopsia
  • Albinism
  • Bardet Biedl Syndrome
  • Bradyopsia
  • Choroideremia
  • Cone and Cone-rod Dystrophy: Please note, the RAB28 gene is not included on the NGS panel at this time due to the presence of at least 2 pseudogenes. For clinicians that would like RAB28 analysis if all other genes test negative, we request consultation with CEN4GEN.
  • Congenital Stationary Night Blindness: Please note, the GRK1 gene is not included on the NGS panel at this time as this gene is only partially annotated in hg19. GRK1 will be re-evaluated with the release of hg20.
  • Flecked Retina Disorders
  • Isolated Aniridia
  • Joubert Syndrome
  • Leber Congenital Amaurosis: Please note, the NMNAT1 gene is not included in the NGS panel at this time due to presence of at least 4 pseudogenes. For clinicians that would like NMNAT1 analysis if all other genes test negative, we request that you contact the CEN4GEN.
  • Leber hereditary optic neuropathy (LHON)
  • Microphthalmia, Anterior Segment Dysgenesis, and Related Anomalies
  • Neuronal Ceroid-Lipofuscinoses
  • Optic Atrophy Photoreceptor
  • Dystrophy Primary Open Angle
  • Glaucoma
  • Refsum disease
  • Retinitis pigmentosa and ataxia (NARP)
  • Retinitis pigmentosa, AD, AR and X-linked
  • Retinoschisis
  • Senior Loken Syndrome
  • Stargardt’s Disease and Macular Dystrophy
  • Stickler Syndrome
  • Usher Syndrome
  • Vitreoretinopathy

References:

  • Daiger et al. (1998) Invest Ophthalmol Vis Sci 39:S295.
  • OMIM.
  • GeneReviews.
  • Emory and Rimoin’s Principles and Practice of Medical Genetics, 5th Edition.

GENES

ABCA4, ABHD12, ADAM9, AHI1, AIPL1, ALMS1, ARL13B, ARL6, ATP13A2, B3GALTL, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, BCOR, BEST1, BMP4, C10orf11, C1QTNF5, C2orf71, C5orf42, C8orf37, CA4, CABP4, CACNA1F, CACNA2D4, CC2D2A, CDH23, CDH3, CDHR1, CEP290, CEP41, CERKL, CHM, CIB2, CLN3, CLN5, CLN6, CLN8, CLRN1, CNGA1, CNGA3, CNGB1, CNGB3, CNNM4, COL11A1, COL11A2, COL2A1, COL4A1, COL9A1, COL9A2, CRB1, CRX, CTSD, CYP1B1, CYP27A1, CYP4V2, DFNB31, DHDDS, EFEMP1, ELOVL4, EYS, FAM161A, FLVCR1, FOXC1, FOXE3, FRAS1, FREM1, FREM2, FSCN2, FZD4, GNAT1, GNAT2, GPR143, GPR179, GPR98, GRIP1, GRM6, GRN, GUCA1A, GUCA1B, GUCY2D, HARS, HCCS, IDH3B, IMPDH1, IMPG2, INVS, IQCB1, KCNJ13, KCNV2, KCTD7, KIF7, KLHL7, LCA5, LRAT, LRIT3, LRP5, LZTFL1, MAK, MERTK, MFN2, MFRP, MFSD8, MKKS, MKS1, MTTP, MYO7A, MYOC, NDP, NPHP1, NPHP3, NPHP4, NR2E3, NRL, NYX, OAT, OCA2, OFD1, OPA1, OPA3, OTX2, PAX6, PCDH15, PDE6A, PDE6B, PDE6C, PDE6G, PDE6H, PEX7, PHYH, PITPNM3, PITX2, PITX3, PLA2G5, PPT1, PRCD, PROM1, PRPF3, PRPF31, PRPF6, PRPF8, PRPH2, RAX2, RBP3, RBP4, RD3, RDH12, RDH5, RGR, RGS9, RGS9BP, RHO, RIMS1, RLBP1, ROM1, RP1, RP2, RP9, RPE65, RPGR, RPGRIP1, RPGRIP1L, RS1, SAG, SDCCAG8, SEMA4A, SLC24A1, SLC24A5, SLC45A2, SMOC1, SNRNP200, SOX2, SPATA7, STRA6, TCTN1, TCTN2, TCTN3, TIMM8A, TIMP3, TMEM126A, TMEM216, TMEM237, TMEM67, TOPORS, TPP1, TRIM32, TRPM1, TSPAN12, TTC21B, TTC8, TULP1, TYR, TYRP1, UNC119, USH1C, USH1G, USH2A, VAX1, VCAN, VSX2, WDPCP, WFS1, WT1, ZNF423, ZNF513

INDICATIONS
This test is indicated for:

  • Confirmation of a clinical diagnosis of a syndromic and/or non-syndromic retinal and optic nerve disorders.
  • Carrier testing in adults with a family history of a syndromic and/or non-syndromic retinal and optic nerve disorders.

METHODOLOGY
Next Generation Sequencing: In-solution hybridization of all coding exons is performed on the patient’s genomic DNA. Although some deep intronic regions may also be analyzed, this assay is not mean to interrogate most promoter regions, deep intronic regions, or other regulatory elements, and does not detect single or multi-exon deletions or duplications. Direct sequencing of the captured regions is performed using next generation sequencing. The patient’s gene sequences are then compared to a standard reference sequence. Potentially causative variants and areas of low coverage are Sanger-sequenced. Sequence variations are classified as pathogenic, likely pathogenic, benign, likely benign, or variants of unknown significance. Variants of unknown significance may require further studies of the patient and/or family members.

DETECTION
Clinical Sensitivity: Unknown. Pathogenic variants in the promoter region, some pathogenic variants in the introns and other regulatory element pathogenic variants cannot be detected by this analysis. Large deletions will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient’s clinical and/or biochemical phenotype.

Analytical Sensitivity: ~99%.

Seven targeted mtDNA pathogenic variants: Leber Hereditary Optic Neuropathy (LHON)
Four pathogenic variants (that account for 90% of cases of LHON) will be detected by this assay: 11778G>A, 3460G>A, 14459G>A, & 14484T>C.

Retinitis Pigmentosa and Ataxia (NARP)
Two pathogenic variants (that account for 50% of cases of NARP) will be detected by this assay: 8993T>G and 8993T>C.

Chronic Progressive External Ophthalmoplegia (CPEO)
One pathogenic variant will be detected by this assay: 3243A>G.

Note: These mtDNA variants will be detected down to approximately 15-20% heteroplasmy.

SPECIMEN REQUIREMENTS

Submit only 1 of the following specimen types

Type: Whole Blood
Specimen Requirements: In EDTA (purple top) tube: Infants (2 years): 3-5 ml
Older Children & Adults: 5-10 ml.

Specimen Collection and Shipping: Ship sample at room temperature with overnight delivery.

Type: Isolated DNA
Specimen Requirements: In microtainer: 60 μg
Isolation using the QiagenTM Puregene kit for DNA extraction is recommended.

Specimen Collection and Shipping: Refrigerate until time of shipment in 100 ng/ul of TE buffer. Ship sample at room temperature with overnight delivery.

SPECIAL INSTRUCTIONS
Please include fundus photographs, electroretinogram (ERG) findings, visual field findings, and visual acuity, if available.

RELATED TESTS

  • Achromatopsia, Cone, and Cone-rod Dystrophy: Sequencing and Deletion/Duplication Panels. Bardet-Biedl Syndrome: Sequencing and Deletion/Duplication Panels.
  • Congenital Stationary Night Blindness: Sequencing and Deletion/Duplication Panels.
  • Flecked-retina Disorders: Sequencing and Deletion/Duplication Panels. Albinism: Sequencing and Deletion/Duplication Panels.
    Joubert Syndrome: Sequencing Panel.
  • Leber Congenital Amaurosis: Sequencing and Deletion/Duplication Panels.
  • Macular Dystrophy, Degeneration, Stargardt Disease: Sequencing and Deletion/Duplication Panels. Anophthalmia/Microphthalmia/Anterior Segment Dysgenesis/Anomaly: Sequencing Panel.
  • Neuronal Ceroid-Lipofuscinoses: Sequencing Panel.
  • Retinitis Pigmentosa: Sequencing and Deletion/Duplication Panels. Optic Atrophy: Sequencing and Deletion/Duplication Panels. Retina/Photoreceptor Dystrophy: Sequencing and Deletion/Duplication Panels.
  • Senior-Loken Syndrome: Sequencing and Deletion/Duplication Panels. Stickler Syndrome: Sequencing Panel.
  • Usher Syndrome: Sequencing Panel.
  • Vitreoretinopathy: Sequencing and Deletion/Duplication Panels. Eye Disorders: Deletion/Duplication Panel.