Identification of variants in CNGA3 as cause for achromatopsia by exome sequencing of a single patient.

Abstract

OBJECTIVE:

To report disease-causing mutations in the cyclic nucleotide-gated channel α 3 gene (CNGA3) identified by exome sequencing and bioinformatics filtering in a single patient.

METHODS:

The entire protein-coding sequence of a patient with a retinal disease was enriched by in-solution targeted capture and massively parallel sequenced at 50-fold coverage. The assembled sequence was compared with databases of normal genomic sequences to identify nonsynonymous variants, which were further filtered (1) with a prioritization of genes associated with retinal diseases, (2) according to the likelihood of variant damage to protein function, (3) following the predictions of a recessive model, and (4) against common polymorphisms observed in normal genomes. Clinical evaluation and segregation analysis of the mutant alleles in the patient's family were performed; mutations were excluded in healthy controls.

RESULTS:

Analysis yielded a molecular diagnosis of achromatopsia. Two compound heterozygous mutations were identified in CNGA3 of this patient, c.829C>T p.R277C and c.1580T>G p.L527R; they were not observed in the normal population and cosegregated with the phenotype of achromatopsia in the patient's family.

CONCLUSION:

These mutations are the cause of achromatopsia in this family.

CLINICAL RELEVANCE:

The key advantages of massively parallel sequencing over linkage mapping and cloning are highlighted by (1) the small sample size required for successful analysis and (2) the rapid and high-throughput manner in which the mutations are identified. This new tool will likely have major effects on the management and research of rare genetic eye diseases in the new era of personalized genomic medicine.

• Authors: Kevin Lam, Haiyan Guo, Graham A Wilson, Susanne Kohl, Fulton Wong
• Journal: Archives of ophthalmology (Chicago, Ill. : 1960) (Arch Ophthalmol) Vol. 129 Issue 9 Pg. 1212-7 (Sep 2011) ISSN: 1538-3601 [Electronic] United States
• PMID: 21911670 (Publication Type: Case Reports, Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• CNGA3 protein, human
• Cyclic Nucleotide-Gated Cation Channels

Topics

• Base Sequence
• Color Vision Defects (diagnosis, genetics)
• Computational Biology
• Cyclic Nucleotide-Gated Cation Channels (genetics)
• DNA Mutational Analysis
• Female
• Gene Library
• Genetic Variation (genetics)
• Genome (genetics)
• Humans
• Male
• Molecular Sequence Data
• Pedigree
• Phenotype
• Point Mutation
• Polymerase Chain Reaction
• Sequence Analysis, DNA