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

Abstract

Purpose

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.

Methods

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

Results

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).

Conclusion

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.

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Fig. 1: Identification of splicing events inadequately represented by clinically accessible tissues (CATs).
Fig. 2: Mapping transcriptome variations identified in clinically accessible tissues (CATs) vs. non-CATs.
Fig. 3: Expression and pathogenicity of inadequately represented genes.
Fig. 4: MAJIQ-CAT enables clinicians and scientists to explore inadequate representation of splicing by clinically accessible tissues (CATs) in specific genes and tissues of interest.

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Acknowledgements

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R01GM128096. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. J.K.A. acknowledges salary support by NIH/Eunice Kennedy Shriver National Institute of Child Health (NICHD) fellowship F30HD098803.

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Correspondence to Yoseph Barash PhD or Elizabeth J. Bhoj MD, PhD.

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Aicher, J.K., Jewell, P., Vaquero-Garcia, J. et al. Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med 22, 1181–1190 (2020). https://doi.org/10.1038/s41436-020-0780-y

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Keywords

  • clinical genetics
  • medical genetics
  • alternative splicing
  • diagnostic markers
  • RNA-seq

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