Enhancing genomic diagnostic testing using RNA-Sequencing

Our DNA contains all the instructions telling our bodies how to work. Each individual instruction is a gene. We have two copies of most genes, having inherited one copy from our mum and the other from our dad. A dominant genetic disorder is one caused by having a mistake in only one copy of a gene. A recessive disorder is caused by having a mistake in both copies of a gene.

When we carry out genetic testing, we usually look for mistakes in DNA. However, this can have limitations:

We often see changes in genes that haven’t been seen before: variants of unknown significance (VUS).  When we see a VUS, we need additional information to try and figure out whether this is the cause of someone’s medical problems, or just part of the normal genetic variation seen in the population.

There are certain types of genetic changes that are difficult to detect with standard DNA sequencing.  This means that in some people with a dominant genetic disorder, no change is found in any of the genes known to be associated with this.  In individuals with a recessive disorder, we sometimes find a mistake in only one copy of the relevant gene and are therefore unable to confirm the cause of the condition.

Using other technologies can help us detect changes not seen on DNA sequencing, and can sometimes clarify whether a VUS is medically important or not.

How will this project make a difference?

DNA is how we store genetic information. However, to use a gene, the DNA is first copied into a molecule called RNA. This is the working copy of a gene. We currently don’t look at RNA when carrying out genetic testing for most conditions.  However, looking at RNA can give us information that DNA testing can’t.

For example:

  • Some changes in DNA that are not detected on routine testing can prevent a gene being copied into RNA – as if the gene has been switched off.
  • After being copied into RNA, parts of the DNA code that are not needed are removed through a process called splicing. Changes that affect this process may not be detected on routine genetic testing.  In addition, around 1 in 10 variants of unknown significance detected on DNA testing are thought to affect splicing.

The aim of this project is to evaluate whether RNA sequencing (RNA-Seq) can improve diagnosis of genetic conditions and should be used as a standard part of testing in the NHS.


What are we doing?

We are performing RNA-Seq in 174 individuals with a range of genetic conditions from the NEY area and across the UK.  The clinical questions we aim to answer are:

  • Does a variant of unknown significance cause someone’s condition through abnormal splicing?
  • Does an observed chromosome change cause someone’s condition by stopping one copy of a gene working?
  • Can we identify changes in genes causing disease that have not been detected on DNA sequencing?
  • In the case of someone who has a recessive condition and a mistake in one copy of a relevant gene, can we identify a mistake in the other copy of the gene that hasn’t been detected on DNA sequencing?

To carry out this testing, we are mostly using RNA extracted from blood and fibroblasts (cells grown following skin biopsy).  This is because which genes are used, and how they are used, differs between cell types.

What is the current status of the project?

All of the samples collected for this project have now been processed.  Our analysis and reporting team, comprising clinical scientists and experts in bioinformatics, are currently analysing the data and will begin reporting soon.

How can I learn more?

Contact us to learn more.

[email protected] 

Our project team are:

Project co-ordination

Brian Wilson, Consultant in Clinical Genetics, Newcastle upon Tyne Hospitals NHS Trust

Mark Hurrell, Project Manager, NEY GMSA

Neville Gaukroger, Programme Manager, NEY GMSA

Analysis and reporting

Claire Kyle, Clinical Scientist, Newcastle upon Tyne Hospitals NHS Trust

Ciaron McAnulty, Clinical Scientist, Newcastle upon Tyne Hospitals NHS Trust

Christian Atallah, Bioinformatics Support Unit, Newcastle University

John Casement, Bioinformatics Support Unit, Newcastle University

Ann Hedley, Bioinformatics Support Unit, Newcastle University

Sample processing

Carmen Martin-Ruiz & team, BioScreening Facility, Newcastle University

Jonathan Coxhead & team, Genomics Core Facility, Newcastle University

GMSA Sponsor

Michael Wright, Clinical Director, NEY GMSA