Long-read RNA sequencing improves isoform and splicing outlier detection in whole blood from rare disease trios

Full-length long-read RNA-seq from whole blood, compared with paired short-read RNA-seq

The authors generated an average of 13.4 million full-length long-read RNA reads from the whole blood of a cohort of 20 individuals with rare diseases and their unaffected biological parents, and compared transcriptome coverage with paired short-read RNA-seq, overall and in known disease-associated genes. Long-read sequencing gave more uniform coverage across transcripts, and 20.2% of its transcripts exceeded 10 kb, versus less than 5% with short-read. Of a mean of 24,439 isoforms, 18.5% were unannotated in GENCODE, 74.3% of which were in disease-associated genes; the mean of 13 unique fusion transcripts per sample were all intrachromosomal, and none had an associated structural variant on paired long-read DNA sequencing. In one individual with ReNU syndrome (de novo RNU4-2 variant), long-read sequencing revealed the expected transcriptome-wide spliceopathy pattern of 5' splice site variation that short-read sequencing did not detect.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

Preprint on medRxiv, not peer reviewed. The work is mainly valuable as a resource and proof of feasibility: the only diagnostic benefit illustrated concerns an already diagnosed patient, and no gain in yield is measured across the cohort. The RNU4-2 demonstration is nonetheless worth following: it suggests that long-read RNA could provide functional evidence for variants in this non-coding gene that short-read sequencing does not reveal.

Analysis by Dr Thibaut Benquey