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Non-canonical Variants: The Dark Horse of Rare Genetic Diseases

Written by Isobel Young, Science Writer

By the end of 2018, Genomics England had completed their 100,000 Genome Project (100KGP), where they successfully sequenced the whole genome of 100,000 participants. A team of researchers from the University of Southampton have now performed a systematic analysis of the data provided by the project, focusing on identifying non-canonical splicing variants.

The study, published in Genome Medicine, was conducted in the hopes of identifying non-canonical splicing variants that are important in rare genetic diseases, with the aim of increasing the diagnostic yield of these diseases.

What is non-canonical splicing?

Splicing is a mechanism by which introns (non-coding genes) are cut from pre-mRNA sequences, resulting in an mRNA strand of just exons (coding genes). Splicing is performed by a group of small-nuclear riboproteins (snRNPs), which make up the spliceosome. Over 99% of splicing is known as ‘canonical splicing’, which is where the sequence of the intron being spliced begins with a GU base pair and ends with an AG base pair. Less than 1% of splicing is ‘non-canonical’ splicing variants – the introns being spliced do not start with GU and end with AG base pairs. These variants are difficult to clinically interpret and so have historically been overlooked in genetic research.

Conducting the study

To conduct this analysis, the research group utilized a metric called ‘mutability-adjusted proportion of singletons (MAPS)’ to help identify any variant that is likely to be deleterious due the variants susceptibility to purification selection. The team also employed a machine-based learning tool, SpliceAI, to predict splice sites and splice-disrupting variants.


From the analysis, the team concluded that from 258 known variants, 35 variants that are likely to be disease-causing were originally missed in the 100kGP. The study also mentions how the researchers were able to confirm a new molecular diagnosis for 6 of the participants from the study by using the data they obtained. “We demonstrate the clinical value of examining non-canonical splicing variants in individuals with unsolved rare diseases,” says the author of the study. It is evident that despite the challenges that come with attempting to identify non-canonical splicing variants, it’s important in increasing the diagnostic yield of those with rare genetic diseases. This will allow the scientific community to strengthen our knowledge of these diseases and hopefully lead to more targeted therapeutics.

Future directions

While this piece of research is a useful starting point, the researchers notes that, “the contribution of non-canonical variants is still under-recognized.” Further research is needed to validate the results of this study and to provide a wider breadth of knowledge about non-canonical splicing variants. In the meantime, this research has opened a door to a world of new research opportunities, helping researchers to get one step closer to understanding rare genetic diseases.

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