Genetic variations in human opsin genetics: Understanding color vision phenotypes and defects

Purpose: The aim of this study was to analyze human opsin genes, OPN1LW and OPN1MW, for single nucleotide polymorphisms (SNP) and structural variants (SV) impacting color vision in subjects diagnosed with color vision deficiency.

Methods: Nineteen subjects underwent anomaloscope examination to diagnose color vision deficiency phenotypes (dichromatic: protanopia and deuteranopia). First, a previously published method of long range-PCR and sequencing was performed to identify variations in OPN1LW, OPN1MW, and OPN1SW. In the case of discrepancy, ultra-long nanopore sequencing was utilized to identify possible SVs.

Results: The long range-PCR and sequencing genetically validated the color vision diagnosis for 17 of the 19 individuals. For two individuals the genetic and functional diagnoses conflicted. Ultra-long nanopore sequencing of these two revealed possible rearrangements in the opsin gene cluster that could affect the color vision and explain the conflicting results based on the long-PCR method.

Conclusions: The large size of the human opsin gene cluster and the high degree of sequence homology between OPN1LW and OPN1MW genes have been a challenge for genetic studies of color vision deficiencies. The development of ultra-long nanopore sequencing technology allows for a more comprehensive genetic analysis of this region, especially for the detection of pathogenic SVs. In this study, we were able to identify possible SVs underlying color vision deficiency in cases that were missed by the long range-PCR. However, alignment of the ultra-long sequences to the reference genome at the variable opsin gene cluster region remains a challenge for the data analysis.