Diagnostic utility of transcriptome sequencing for rare Mendelian diseases

Abstract

Purpose: We investigated the value of transcriptome sequencing (RNAseq) in ascertaining the consequence of DNA variants on RNA transcripts to improve the diagnostic rate from exome or genome sequencing for undiagnosed Mendelian diseases spanning a wide spectrum of clinical indications.Methods: From 234 subjects referred to the Undiagnosed Diseases Network, University of California-Los Angeles clinical site between July 2014 and August 2018, 113 were enrolled for high likelihood of having rare undiagnosed, suspected genetic conditions despite thorough prior clinical evaluation. Exome or genome sequencing and RNAseq were performed, and RNAseq data was integrated with genome sequencing data for DNA variant interpretation genome-wide. Results:The molecular diagnostic rate by exome or genome sequencing was 31%. Integration of RNAseq with genome sequencing resulted in an additional seven cases with clear diagnosis of a known genetic disease. Thus, the overall molecular diagnostic rate was 38%, and 18% of all genetic diagnoses returned required RNAseq to determine variant causality. Conclusion:In this rare disease cohort with a wide spectrum of undiagnosed, suspected genetic conditions, RNAseq analysis increased the molecular diagnostic rate above that possible with genome sequencing analysis alone even without availability of the most appropriate tissue type to assess.

Human in vitro models for understanding mechanisms of autism spectrum disorder

“…In cases where whole exome sequencing does not yield a diagnosis, transcriptomic analysis of relevant tissue has shown some promise [98][99][100][101]. In cases when the relevant tissue is inaccessible (which is the majority of cases in neurodevelopmental and psychiatric disorders), blood transcriptomics sequencing has been suggested as an alternative and was shown to be informative in 7.5-16.7% of cases [101,102]. However, many cases still remain undiagnosed, and it is reasonable to believe that transcriptomics sequencing from cells mimicking the relevant tissue by using stem cell-derived cultures would further increase this rate of diagnosis.…”

Is Gene-Size an Issue for the Diagnosis of Skeletal Muscle Disorders?

“…A correct evaluation of elusive splice variants, using bioinformatic tools and RNASeq, can result into a similar increase in the diag-nostic yield in most of the other rare genetic diseases. Similarly, the integration of RNAseq with genome sequencing has resulted in an improved diagnostic rate for a wide spectrum of undiagnosed Mendelian diseases [133]. Moreover, the availability of the most appropriate tissue for RNA extraction/analysis further increases the diagnostic rate [18,128].…”

“…A different approach, described by Lee and colleagues, is of the extreme interest [133]. Instead of analyzing the entire transcriptome to search for an outlier (as described in ref.…”

“…Instead of analyzing the entire transcriptome to search for an outlier (as described in ref. [127,134]), they used RNAseq to evaluate the effect on the transcripts of rare, potentially causative, genetic variants using the splicing predictors as a prioritizing method [133].…”

“…The introduction of HTS has allowed us to overcome the technical difficulties related to the size of the gene. DNA and RNAsequencing and, above all, their combined use enable an exhaustive analysis of most of the human genes and their size is not an issue anymore [133].…”