Mapping the genomic landscape of inherited retinal disease genes prioritizes genes prone to coding and noncoding copy-number variations

Genet Med. 2018 Feb;20(2):202-213. doi: 10.1038/gim.2017.97. Epub 2017 Jul 27.

Abstract

PurposePart of the hidden genetic variation in heterogeneous genetic conditions such as inherited retinal diseases (IRDs) can be explained by copy-number variations (CNVs). Here, we explored the genomic landscape of IRD genes listed in RetNet to identify and prioritize those genes susceptible to CNV formation.MethodsRetNet genes underwent an assessment of genomic features and of CNV occurrence in the Database of Genomic Variants and literature. CNVs identified in an IRD cohort were characterized using targeted locus amplification (TLA) on extracted genomic DNA.ResultsExhaustive literature mining revealed 1,345 reported CNVs in 81 different IRD genes. Correlation analysis between rankings of genomic features and CNV occurrence demonstrated the strongest correlation between gene size and CNV occurrence of IRD genes. Moreover, we identified and delineated 30 new CNVs in IRD cases, 13 of which are novel and three of which affect noncoding, putative cis-regulatory regions. Finally, the breakpoints of six complex CNVs were determined using TLA in a hypothesis-neutral manner.ConclusionWe propose a ranking of CNV-prone IRD genes and demonstrate the efficacy of TLA for the characterization of CNVs on extracted DNA. Finally, this IRD-oriented CNV study can serve as a paradigm for other genetically heterogeneous Mendelian diseases with hidden genetic variation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Cadherins / genetics
  • Chromosome Mapping*
  • DNA Copy Number Variations*
  • Databases, Genetic
  • Eye Proteins / genetics
  • Genetic Predisposition to Disease
  • Genome, Human*
  • Genome-Wide Association Study
  • Genomics* / methods
  • Humans
  • Open Reading Frames*
  • RNA, Untranslated*
  • Regulatory Sequences, Nucleic Acid
  • Retinal Diseases / diagnosis
  • Retinal Diseases / genetics*
  • Sequence Analysis, DNA
  • Sequence Deletion

Substances

  • Cadherins
  • EYS protein, human
  • Eye Proteins
  • PCDH15 protein, human
  • RNA, Untranslated