Genotyping microarray for CSNB-associated genes

Invest Ophthalmol Vis Sci. 2009 Dec;50(12):5919-26. doi: 10.1167/iovs.09-3548. Epub 2009 Jul 2.


Purpose: Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disease. Although electroretinographic (ERG) measurements can discriminate clinical subgroups, the identification of the underlying genetic defects has been complicated for CSNB because of genetic heterogeneity, the uncertainty about the mode of inheritance, and time-consuming and costly mutation scanning and direct sequencing approaches.

Methods: To overcome these challenges and to generate a time- and cost-efficient mutation screening tool, the authors developed a CSNB genotyping microarray with arrayed primer extension (APEX) technology. To cover as many mutations as possible, a comprehensive literature search was performed, and DNA samples from a cohort of patients with CSNB were first sequenced directly in known CSNB genes. Subsequently, oligonucleotides were designed representing 126 sequence variations in RHO, CABP4, CACNA1F, CACNA2D4, GNAT1, GRM6, NYX, PDE6B, and SAG and spotted on the chip.

Results: Direct sequencing of genes known to be associated with CSNB in the study cohort revealed 21 mutations (12 novel and 9 previously reported). The resultant microarray containing oligonucleotides, which allow to detect 126 known and novel mutations, was 100% effective in determining the expected sequence changes in all known samples assessed. In addition, investigation of 34 patients with CSNB who were previously not genotyped revealed sequence variants in 18%, of which 15% are thought to be disease-causing mutations.

Conclusions: This relatively inexpensive first-pass genetic testing device for patients with a diagnosis of CSNB will improve molecular diagnostics and genetic counseling of patients and their families and gives the opportunity to analyze whether, for example, more progressive disorders such as cone or cone-rod dystrophies underlie the same gene defects.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Calcium Channels, L-Type / genetics
  • Calcium-Binding Proteins / genetics
  • Child
  • Cyclic Nucleotide Phosphodiesterases, Type 6 / genetics
  • DNA Mutational Analysis
  • Eye Proteins / genetics*
  • Female
  • Gene Expression Profiling*
  • Genotype
  • Heterotrimeric GTP-Binding Proteins / genetics
  • Humans
  • Male
  • Mutation*
  • Night Blindness / congenital*
  • Night Blindness / genetics*
  • Oligonucleotide Array Sequence Analysis*
  • Pedigree
  • Polymerase Chain Reaction
  • Proteoglycans / genetics
  • Receptors, Metabotropic Glutamate / genetics
  • Retinal Diseases / congenital
  • Retinal Diseases / genetics*
  • Rhodopsin / genetics
  • Transducin


  • CABP4 protein, human
  • CACNA1F protein, human
  • CACNA2D4 protein, human
  • Calcium Channels, L-Type
  • Calcium-Binding Proteins
  • Eye Proteins
  • GNAT1 protein, human
  • NYX protein, human
  • Proteoglycans
  • Receptors, Metabotropic Glutamate
  • metabotropic glutamate receptor 6
  • Rhodopsin
  • Cyclic Nucleotide Phosphodiesterases, Type 6
  • PDE6B protein, human
  • Heterotrimeric GTP-Binding Proteins
  • Transducin