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A large study that included patients and controls showed that rare variant association tests apply to multiple inherited retinal diseases.
Inherited retinal diseases (IRDs) lead to progressive retinal degeneration and visual loss. However, their missing heritability is estimated at 30% to 50%, likely because of limitations in detecting mutations with conventional methods.
To address this gap, Carlo Rivolta, PhD, MS, and colleagues examined the possible applicability of rare variant association tests (RVATs) to identify pathogenic mutations using statistical methods that are not commonly applied.
The researchers performed the combined multivariate and collapsing test, a type of RVAT, on patients with Stargardt disease and biallelic mutations in ABCA4, patients with all forms of IRDs, and controls to demonstrate its applicability in identifying novel disease genes. The findings were published in Investigative Ophthalmology & Visual Science.
Enrichment of Rare Damaging Variants Observed
Whole exome sequencing was done on 26 patients with Stargardt disease, 194 patients with genetically confirmed IRDs, and 242 controls of European descent.
After adjusting for quality control, relatedness, and ancestry filtering, 12 patients with Stargardt disease, 143 patients with IRD, and 199 unrelated controls passed the combined multivariate and collapsing test. Following variant calling and annotation, the researchers selected variants according to their population allele frequency, type of alteration, and predicted damaging scores. They calculated OR in all genes using a two-sided Fisher’s exact test with Bonferroni correction.
“This feasibility test shows enrichment of rare damaging variants in ABCA4, USH2A, RP1, and PRPH2 in all the patients analyzed,” Dr. Rivolta and colleagues wrote. “The effect of variant filtering on allele frequency and identical damaging properties was also clearly observed.”
The ABCA4 gene had the highest enrichment of variants in patients with Stargardt disease at 0.1% allele frequency. Among patients with IRDs, ABCA4, USH2A, RP1, and PRPH2 showed enrichment at different allele frequency thresholds (uncorrected P<0.05). However, the researchers noted that none of the genes in patients with IRDs were significantly enriched after Bonferroni correction due to insufficient sample quantities.
“This study demonstrates the potential applicability of RVATs in identifying IRD genes when a sufficiently large number of patients are analyzed,” the researchers wrote.
