New guidance co-led by University of Otago researchers could help more people with suspected inherited diseases receive a clear genetic diagnosis.
Published in one of the world’s most prestigious medical journals, Genome Medicine, the Health Research Council-funded study provides new recommendations for using RNA testing to determine whether genetic changes are likely to cause disease – potentially helping clinicians resolve uncertain genetic test results and make more informed decisions about patients and their whānau.
Dr George Wiggins, from the University of Otago, Faculty of Medicine-Christchurch, co-led the international study with researchers in Australia and Spain. His colleagues in the Department of Pathology and Molecular Medicine, Professor Logan Walker and Associate Professor John Pearson, also contributed to the research.
Dr George Wiggins
Genetic testing can identify thousands of differences, or variants, in a person’s DNA. For patients and clinicians, however, identifying a genetic change is only part of the challenge: they also need to know whether that change is harmless or is responsible for disease.
“This is one of the major challenges in clinical genomics,” Dr Wiggins explains.
“Our study provides clinicians with greater certainty about results from specific RNA-based tests, allowing them to better understand the effect a DNA variant has on the fundamental biological process of RNA splicing.”
RNA is a molecule that carries instructions from DNA to help cells produce proteins. Before those instructions can be used, sections of RNA need to be joined together in a process called splicing.
Some genetic variants interfere with this process and can prevent a gene from working properly. Looking at RNA can therefore provide important evidence about whether a genetic variant is likely to cause disease.
The researchers reviewed more than 41,000 genetic variants across 5,458 genes from published studies using laboratory models known as minigene assays.
These models recreate the important parts of a gene involved in RNA splicing and can be particularly useful when RNA cannot be collected directly from a patient, such as when the relevant tissue is inaccessible.
The team found that well-designed traditional minigene assays produced results that closely matched testing using RNA taken directly from patients. Where both types of testing were available, there was 89 per cent complete or high agreement between the results.
In contrast, many high-throughput tests, which can assess very large numbers of genetic variants at once, did not yet provide enough reliable information for direct clinical use. Of seven high-throughput datasets assessed, only one showed characteristics considered suitable for clinical application.
“These findings show that well-designed RNA-based assays can provide strong evidence for the effect of a genetic variant, while caution should be applied when assays have important design limitations,” Dr Wiggins says.
The researchers also found that results from minigene testing could help improve predictions made by SpliceAI, an artificial intelligence tool used to predict whether genetic variants may disrupt RNA splicing.
The study identifies thresholds that could help laboratories distinguish between variants likely to have little effect and those more likely to cause significant disruption.
The researchers also compared their laboratory findings with clinical classifications in ClinVar, an international database of genetic variants. They found that variants producing 80 per cent or more abnormal RNA provided strong evidence that a variant was disease-causing, while variants producing 20 per cent or less abnormal RNA provided strong evidence against a disease-causing effect.
The findings support the use of carefully calibrated RNA evidence within the internationally recognised framework used by clinical laboratories to classify genetic variants.
“Ultimately, incorporating these results within an appropriate framework will improve accuracy and variant classification, pave the way for earlier intervention, and increase the number of patients who receive a genetic diagnosis,” Dr Wiggins explains.
The recommendations also include guidance for laboratories on designing and validating RNA tests, assessing their performance, presenting results and determining how much weight their findings should carry in clinical decision-making.
-Kōrero by Lorelei Mason
