RNA sequencing framework IsoRanker finds disease-causing variants missed by standard genome analysis
Researchers developed IsoRanker, a framework that uses long-read RNA sequencing to prioritize pathogenic non-coding variants in Mendelian conditions. The team generated paired cycloheximide-treated and untreated fibroblast transcriptomes from 31 individuals: 3 with known transcript-altering rare variants and 28 with unsolved conditions. They linked transcripts to phased long-read genomes. IsoRanker successfully recovered known transcript alterations in this cohort. Exploratory subsampling analyses suggested that prioritization was largely preserved down to cohorts of 11 individuals and approximately 5 million full-length transcripts per individual. Among 28 previously unsolved cases, IsoRanker deprioritized 8 out of 10 fibroblast-expressed candidate splice-site variants while nominating 4 new leads. In one individual, IsoRanker prioritized HARS1, revealing bi-allelic non-coding variants that together produced a partial HARS1 loss of function and informed targeted therapy in this individual. Performance was dependent upon de novo isoform caller choice, particularly for nonsense-mediated decay-sensitive and previously unannotated isoforms.
The framework detects genes and isoforms with outlier expression, allelic imbalance, or nonsense-mediated decay to generate isoform-level functional evidence. This improves classification of non-coding variants and supports diagnosis of individuals with rare genetic conditions whose cases remain unsolved by genome sequencing alone.
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