Clinical applications of and molecular insights from RNA sequencing in a rare disease cohort

RNA sequencing (RNA-seq) is emerging as a valuable tool for identifying disease-causing RNA transcript aberrations that cannot be identified by DNA-based testing alone. Previous studies demonstrated some success in utilizing RNA-seq as a first-line test for rare inborn genetic conditions. However, DNA-based testing (increasingly, whole genome sequencing) remains the standard initial testing approach in clinical practice. The indications for RNA-seq after a patient has undergone DNA-based sequencing remain poorly defined, which hinders broad implementation and funding/reimbursement.

In this study, we identified four specific and familiar clinical scenarios, and investigated in each the diagnostic utility of RNA-seq on clinically accessible tissues: (i) clarifying the impact of putative intronic or exonic splice variants (outside of the canonical splice sites), (ii) evaluating canonical splice site variants in patients with atypical phenotypes, (iii) defining the impact of an intragenic copy number variation on gene expression, and (iv) assessing variants within regulatory elements and genic untranslated regions.

These hypothesis-driven RNA-seq analyses confirmed a molecular diagnosis and pathomechanism for 45% of participants with a candidate variant, provided supportive evidence for a DNA finding for another 21%, and allowed us to exclude a candidate DNA variant for an additional 24%. We generated evidence that supports two novel Mendelian gene-disease associations (caused by variants in PPP1R2 and MED14) and several new disease mechanisms, including the following: (1) a splice isoform switch due to a non-coding variant in NFU1, (2) complete allele skew from a transcriptional start site variant in IDUA, and (3) evidence of a germline gene fusion of MAMLD1-BEND2. In contrast, RNA-seq in individuals with suspected rare inborn genetic conditions and negative whole genome sequencing yielded only a single new potential diagnostic finding.

In summary, RNA-seq had high diagnostic utility as an ancillary test across specific real-world clinical scenarios. The findings also underscore the ability of RNA-seq to reveal novel disease mechanisms relevant to diagnostics and treatment.