RNA sequencing applied as a tool to solve patients’ diagnostic mysteries

Recent advances in large-scale clinical DNA sequencing have led to genetic diagnoses for many rare disease patients, but the diagnosis rate based on these approaches is still far from perfect. On average, clinicians are unable to provide a genetic diagnosis for over half of patients in the clinic. The lack of a clear genetic diagnosis can lead to profound uncertainty about patients’ long-term prognoses, treatment options, and family planning decisions.
In a new Science Translational Medicine study, a team led by researchers from the Broad Institute of MIT and Harvard and the National Institute of Neurological Disorders and Stroke adds RNA sequencing to the diagnostic toolkit to identify disease-causing mutations buried inside the genome.
The researchers sequenced the RNA from muscle samples of 50 patients with undiagnosed genetic muscle disorders — who had undergone extensive genetic testing — and, in conjunction with DNA sequence information and a reference database, successfully located pathogenic mutations that had previously gone undetected in one-third of the patients. The study firmly positions RNA sequencing as a tool that adds additional power to the existing set of technologies deployed to solve genetic disease mysteries.
“For some patients, we know that there is variation in the human genome, with an effect on the transcript, that we just haven’t been capturing with our traditional genetic sequencing methods,” says senior author Daniel MacArthur, co-director of the Medical and Population Genetics Program at the Broad Institute and group leader at Massachusetts General Hospital. “With RNA sequencing, we were able to take a set of patients who had gone through diagnostic odysseys — often lasting many years, where many methods had been used to try to detect the cause of their disease without success — and find the biological answers that previous technologies had missed.”
Having a molecular diagnosis in-hand is a medical milestone for some patients and their families, and opens the door to potential therapies while offering some peace of mind. “For example, one patient’s family had opted to delay having other children until they knew the genetic basis of her condition,” MacArthur adds. “Our clinical collaborators were able to report that they had found the genetic cause, and now the parents have the option of prenatal testing for that mutation.”
The study demonstrates that RNA sequencing, or RNA-seq, applied to relevant tissue samples and coupled with genetic analysis, can detect pathogenic mutations hidden in the noncoding sections of a gene, highlight relevant mutations missed in the noise of whole-genome analysis, and rule out other genetic variants suspected to cause disease. Previously, the technology was rarely applied in a clinical setting, and then only for single patients when specific mutations were already suspected — but the research team saw the potential for RNA-seq to augment other clinical tools earlier in diagnostics.

Broad Institute of MIT and Harvard
www.broadinstitute.org/news/rna-sequencing-applied-tool-solve-patients%E2%80%99-diagnostic-mysteries