Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq

RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing. RNA-seq is typically performed on clinically accessible tissues (CATs) from blood and skin. RNA tissue specificity makes it difficult to identify aberrations in relevant but nonaccessible tissues (non-CATs). We determined how RNA-seq from CATs represent splicing in and across genes and non-CATs.

Researchers at the University of Pennsylvania quantified RNA splicing in 801 RNA-seq samples from 56 different adult and fetal tissues from Genotype-Tissue Expression Project (GTEx) and ArrayExpress. They identified genes and splicing events in each non-CAT and determined when RNA-seq in each CAT would inadequately represent them. The researchers developed an online resource, MAJIQ-CAT, for exploring our analysis for specific genes and tissues.

In non-CATs, 40.2% of genes have splicing that is inadequately represented by at least one CAT; 6.3% of genes have splicing inadequately represented by all CATs. A majority (52.1%) of inadequately represented genes are lowly expressed in CATs (transcripts per million (TPM) < 1), but 5.8% are inadequately represented despite being well expressed (TPM > 10).

Many splicing events in non-CATs are inadequately evaluated using RNA-seq from CATs. MAJIQ-CAT allows users to explore which accessible tissues, if any, best represent splicing in genes and tissues of interest.

(a) Different precursor mRNA (pre-mRNA) splicing decisions can have significant, potentially pathogenic, functional consequences. (b) Splicing events in inaccessible tissues (non-CATs) can only be adequately represented by accessible tissues as a proxy if the gene is both expressed and similarly spliced. (c) We used MAJIQ on RNA-seq samples from 56 different tissues to define and identify inadequately represented splicing events between inaccessible and accessible tissues.