September 2016
Volume 57, Issue 12
Open Access
ARVO Annual Meeting Abstract  |   September 2016
Coding and non-coding copy number variations explaining unsolved retinal dystrophies: role of genomic architectural features and underlying mechanisms
Author Affiliations & Notes
  • Kristof Van Schil
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Sarah Naessens
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Stijn Van de Sompele
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Miriam Bauwens
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Hannah Verdin
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Caroline Van Cauwenbergh
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Anja Kathrin Mayer
    Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
  • Susanne Kohl
    Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
  • Bart Peter Leroy
    Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
    Division of Ophthalmology, The Children’s Hospital of Philadelphia, Philadelphia, Maryland, United States
  • Elfride De Baere
    Center for Medical Genetics, Ghent University, Ghent, Belgium
  • Footnotes
    Commercial Relationships   Kristof Van Schil, None; Sarah Naessens, None; Stijn Van de Sompele, None; Miriam Bauwens, None; Hannah Verdin, None; Caroline Van Cauwenbergh, None; Anja Kathrin Mayer, None; Susanne Kohl, None; Bart Leroy, None; Elfride De Baere, None
  • Footnotes
    Support  Government agency for Innovation by Science and Technology (IWT) doctoral grant to K.V.S. Funds for Research in Ophthalmology (FRO) grant to K.V.S. Ghent University Special Research Fund (BOF15/GOA/011), Belspo IAP project P7/43 (Belgian Medical Genomics Initiative: BeMGI). E.D.B. and B.P.L. are Senior Clinical Investigators of the The Research Foundation - Flanders (FWO).
Investigative Ophthalmology & Visual Science September 2016, Vol.57, No Pagination Specified. doi:
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      Kristof Van Schil, Sarah Naessens, Stijn Van de Sompele, Miriam Bauwens, Hannah Verdin, Caroline Van Cauwenbergh, Anja Kathrin Mayer, Susanne Kohl, Bart Peter Leroy, Elfride De Baere; Coding and non-coding copy number variations explaining unsolved retinal dystrophies: role of genomic architectural features and underlying mechanisms. Invest. Ophthalmol. Vis. Sci. 201657(12):.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : It was our aim to gain insight into susceptibility factors for the formation of copy number variations (CNVs) affecting retinal dystrophy (RD) genes, and to identify and assess the underlying mechanism of coding and non-coding CNVs in RDs.

Methods : Genomic architectural features contributing to CNV formation were investigated in regions containing known RD genes listed in RetNet (https://sph.uth.edu/retnet/). Detection of CNVs in a diagnostic cohort of RD patients without a molecular genetic diagnosis after sequence-based mutation screening was performed by SNP arrays, multiplex ligation-dependent probe amplification (MLPA) or qPCR. For breakpoint mapping we used conventional PCR, qPCR, targeted arrays, long-range PCR and sequencing of junctions. Targeted Locus Amplification (TLA) on extracted DNA was used to characterize CNVs at the nucleotide level.

Results : Genomic architectural features like gene size, intron length, repetitive elements, sequence motifs, non-B DNA conformations were assessed for all RetNet genes. A hypothetical ranking of RD genomic regions prone to CNV formation was proposed. This was first tested by extensive mining of reported CNVs in known RD genes. Secondly, 17 distinct newly identified CNVs including 14 deletions and three duplications in nine different RD genes (BEST1, EYS, KCNV2, MERTK, OPA1, PCDH15, PRPH2, SPATA7 and USH2A) were further studied here. Eleven of these are novel, including two deletions in PRPH2 in which no CNVs have been reported previously. Three of these (two in EYS, one in PCDH15) affect non-coding, putative regulatory regions of their target gene. Fine-mapping of the breakpoints was performed for all CNVs. TLA, a recent strategy based on the crosslinking of physically proximal sequences, was used to map six CNVs at the nucleotide level, for the first time on extracted human DNA instead of living cells. Finally, bio-informatic analyses contributed to the underlying genetic mechanisms of all delineated CNVs studied here.

Conclusions : This study proposed a ranking of CNV-prone RD disease genes, which was validated by investigating genomic data of reported and newly identified RD-associated CNVs, of which 11 are novel. In addition, we demonstrated the efficacy of TLA on extracted genomic DNA to characterize CNVs in a hypothesis neutral manner.

This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.

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