arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs.
Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina-expressed noncoding RNAs (ncRNAs).



arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone-rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP.



In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delinsAGAATATG, p.(Glu212Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(Ala615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs.



The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD.Genet Med 19 4, 457-466.
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Caroline
0000-0002-1948-9091
C
Van Cauwenbergh
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Kristof
0000-0001-5299-8851
K
Van Schil
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.|Data Mining and Modeling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.|Department of Internal Medicine, Ghent University, Ghent, Belgium.
Robrecht
0000-0003-3641-729X
R
Cannoodt
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Miriam
0000-0003-0402-9006
M
Bauwens
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Thalia
T
Van Laethem
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Sarah
0000-0003-1192-8317
S
De Jaegere
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Wouter
W
Steyaert
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Tom
T
Sante
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Björn
0000-0001-8182-659X
B
Menten
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.|Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.|Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Bart P
BP
Leroy
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Frauke
F
Coppieters
Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
Elfride
E
De Baere
D000123:Acetyltransferases / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D056915:DNA Copy Number Variations; D016326:Extracellular Matrix Proteins / Q000235:genetics; D005260:Female; D020662:Guanine Nucleotide Exchange Factors / Q000235:genetics; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D022661:RNA, Untranslated / Q000235:genetics; D058499:Retinal Dystrophies / Q000235:genetics*; D017384:Sequence Deletion
D016326:Extracellular Matrix Proteins; D020662:Guanine Nucleotide Exchange Factors; C482643:RCBTB1 protein, human; D022661:RNA, Untranslated; C112735:USH2A protein, human; D000123:Acetyltransferases; C514442:HGSNAT protein, human