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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

Caroline Van Cauwenbergh (UGent) , Kristof Van Schil (UGent) , Robrecht Cannoodt (UGent) , Miriam Bauwens (UGent) , Thalia Van Laethem (UGent) , Sarah De Jaegere (UGent) , Wouter Steyaert (UGent) , Tom Sante (UGent) , Björn Menten (UGent) , Bart Leroy (UGent) , et al.
(2017) GENETICS IN MEDICINE. 19(4). p.457-466
Author
Organization
Abstract
Purpose: 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). Methods: 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. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delins AGAATATG, p.(G1u2 I 2Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(A1a615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: 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.
Keywords
RECESSIVE RETINITIS-PIGMENTOSA, USH2A GENE, MUTATIONS, REVEALS, EYE, DELETIONS, PROTEIN, IDENTIFICATION, EXPRESSION, VARIANTS, copy-number variation, customized array CGH, HGSNAT, inherited retinal, dystrophy, ncRNA

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MLA
Van Cauwenbergh, Caroline, et al. “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.” GENETICS IN MEDICINE, vol. 19, no. 4, 2017, pp. 457–66, doi:10.1038/gim.2016.119.
APA
Van Cauwenbergh, C., Van Schil, K., Cannoodt, R., Bauwens, M., Van Laethem, T., De Jaegere, S., … De Baere, E. (2017). 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. GENETICS IN MEDICINE, 19(4), 457–466. https://doi.org/10.1038/gim.2016.119
Chicago author-date
Van Cauwenbergh, Caroline, Kristof Van Schil, Robrecht Cannoodt, Miriam Bauwens, Thalia Van Laethem, Sarah De Jaegere, Wouter Steyaert, et al. 2017. “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.” GENETICS IN MEDICINE 19 (4): 457–66. https://doi.org/10.1038/gim.2016.119.
Chicago author-date (all authors)
Van Cauwenbergh, Caroline, Kristof Van Schil, Robrecht Cannoodt, Miriam Bauwens, Thalia Van Laethem, Sarah De Jaegere, Wouter Steyaert, Tom Sante, Björn Menten, Bart Leroy, Frauke Coppieters, and Elfride De Baere. 2017. “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.” GENETICS IN MEDICINE 19 (4): 457–466. doi:10.1038/gim.2016.119.
Vancouver
1.
Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S, et al. 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. GENETICS IN MEDICINE. 2017;19(4):457–66.
IEEE
[1]
C. Van Cauwenbergh et al., “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,” GENETICS IN MEDICINE, vol. 19, no. 4, pp. 457–466, 2017.
@article{8522618,
  abstract     = {{Purpose: 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). 
Methods: 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. 
Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delins AGAATATG, p.(G1u2 I 2Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(A1a615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. 
Conclusion: 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.}},
  author       = {{Van Cauwenbergh, Caroline and Van Schil, Kristof and Cannoodt, Robrecht and Bauwens, Miriam and Van Laethem, Thalia and De Jaegere, Sarah and Steyaert, Wouter and Sante, Tom and Menten, Björn and Leroy, Bart and Coppieters, Frauke and De Baere, Elfride}},
  issn         = {{1098-3600}},
  journal      = {{GENETICS IN MEDICINE}},
  keywords     = {{RECESSIVE RETINITIS-PIGMENTOSA,USH2A GENE,MUTATIONS,REVEALS,EYE,DELETIONS,PROTEIN,IDENTIFICATION,EXPRESSION,VARIANTS,copy-number variation,customized array CGH,HGSNAT,inherited retinal,dystrophy,ncRNA}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{457--466}},
  title        = {{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}},
  url          = {{http://doi.org/10.1038/gim.2016.119}},
  volume       = {{19}},
  year         = {{2017}},
}
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