Tell me if this sounds familiar: A patient presents with a puzzling set of symptoms, their clinician suspects a rare genetic disorder and orders an exome test, and that test comes back negative. Now, the patient and clinical team are in limbo.
Only around one in three rare disease patients get an answer from DNA testing alone.
DNA-based testing analyzes the exons, or the parts of a gene’s DNA retained after a gene is transcribed, and small portions of the introns, or the segments of genes transcribed into pre-messenger RNA. Further, many DNA tests are inconclusive, meaning the test identifies a variant of uncertain significance (VUS), a genetic change that may or may not be the cause of disease, but can’t determine a root cause of the phenotype. In some of these cases, the tests yield inconclusive results because they cannot measure how DNA variants affect actual gene expression and splicing—two key pieces of information needed to make a molecular diagnosis.
| Genetic variants can be classified as benign, likely benign, pathogenic, likely pathogenic, or as variants of uncertain significance (VUS). Clinical genetic testing reports use the 2015 ACMG/AMP guidelines as the foundational framework for variant classification, supplemented by subsequent ClinGen recommendations that refine the application of individual ACMG/AMP criteria. |
Enter RNA
RNA is the temporary messenger molecule that instructs DNA to build proteins and regulates gene activity. It offers critical information, showing whether a DNA variant disrupts gene expression, or causes faulty splicing or misprocessed transcripts. As an example, where a DNA test might identify a VUS near a splice site, an RNA analysis can reveal that the variant is damaging by showing that the transcript is missing an exon or including an intron. This information can prove vital, turning an inconclusive test result into something from which a clinician can make a diagnosis.
Clinical lab tests that combine RNA and DNA analysis are necessary for providing more clinicians and patients diagnostic clarity. A recent study published in Genetics in Medicine Open demonstrated that DNA/RNA integration in exome testing improves diagnostic yield by generating the necessary functional evidence to accurately interpret a variants’ impact, boosting diagnostic yield by several points.
Read More: What Are the Differences Between DNA and RNA Probes?
Closing the diagnostic gap
Advancing rare disease diagnosis also means ensuring these innovations benefit all patients equally. Historically, genomic research and reference datasets have disproportionately represented individuals of European ancestry, creating diagnostic challenges when testing patients from underrepresented populations because genetic variants found in these patients are not as well understood. As a result, these patients are more likely to receive inconclusive results or VUS classifications, delaying a clear diagnosis and the next steps it can bring. As clinical labs continue to expand access to more comprehensive genomic testing, addressing these longstanding gaps is essential to delivering equitable care.
RNA analysis concurrent with DNA testing is an important part of that equation. More broadly, advances in genomic technologies, such as pangenome technology, are improving variant detection by using multiple reference genomes that better capture human genetic diversity. By showing how identified variants affect gene expression and splicing, RNA analysis helps laboratories interpret their clinical significance with greater confidence. Together, these advances help ensure patients of all backgrounds receive more accurate genetic diagnoses.
Ending diagnostic odysseys for all
As clinical labs, we have a duty to the clinicians we serve and the patients they treat to find answers. By ending patient diagnostic odysseys, we provide so much more than answers families desperately need. Our work is the first step toward successful treatments and enrolling eligible patients in clinical trials. But it’s also needed for families whose children’s diseases don’t have treatments so that they can build community with other families facing the same challenges, consider whether to further expand their families, and plan for their children’s future care needs.
We have a responsibility to leverage RNA in testing on our journey to help these patients and their clinicians find answers.
