In the article titled,” Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing,” researchers aim to improve the diagnosis of rare genetic diseases by using transcriptome sequencing. By focusing on the patterns of gene activity, the researchers were able to diagnose previously unsolved cases. This type of sequencing can improve diagnostic rates by 7.5% to 36% depending on the tissue sampled and the patient’s condition. Rather than looking for specific genetic changes upfront, the methods used here searched for unusual patterns in gene activity that could point to underlying genetic issues. As a result, they were able to diagnose 12% of their cases overall, and 17% when excluding cases that were already answered by standard genetic testing. This approach looks specifically at how genes are being used to understand what may be going wrong at the genetic level. This method is distinct from typical genetic testing, which begins with looking at individual genetic abnormalities and attempts to match them with observed traits or phenotypes. Instead by focusing on gene activity patters, transcriptome sequencing can uncover issues that may be missed by standard testing. Such as noncoding genetic agents or small variations in DNA.

            In this study, the researchers used RNA sequencing as the first step in their process. They analyzed the gene activity patterns in patients’ blood and skin cells to guide their genetic analysis. While other studies have used this approach, this is the first study to apply this method to a wide range of conditions in patients. By analyzing the gene activity in both whole blood and fibroblast cells, which are commonly used in clinical research, they found that fibroblast cells in particular were more informative for a variety of conditions, especially those involving the nervous system. This is because they showed more consistent gene expression than whole blood, making them better for detecting relevant differences in gene expression. The researchers were also able to highlight the limitations of standard genetic testing such as exome sequencing and chromosomal microarray analysis. These tests have the potential to miss important genetic changes, particularly in the noncoding regions of DNA or when the changes are very small. The transcriptome-directed approach, which combines RNA sequencing with genetic analysis, proved to be more effective in finding these missed variations.

            Several cases proved to be very important. Including one in which RNA sequencing identified a genetic variant missed by other testing, leading to the diagnoses of Renpenning syndrome. In another case, RNA sequencing showed a deletion in CLTC gene, causing intellectual disability. In other cases, KANSL1 and NSD2 gene abnormalities were detected through RNA sequencing, leading to the diagnosis of Koolen-de Vries syndrome and NSD2-associated intellectual disability syndrome, respectively.

            In conclusion, this study shows thar analyzing gene activity patterns is effective in diagnosis rare Mendelian diseases that standard genetic testing may overlook. By focusing on how genes are being used, specifically in fibroblast cells, researchers can uncover genetic issues that traditional tests overlook. This approach could significantly improve the diagnostic rates for patients with challenging conditions. What was unique about this study is the diverse group of patients with various symptoms and age ranges. The researchers believe that integrating RNA sequencing into standard genetic testing will help diagnoses more patients, especially those who cannot be diagnoses through exome sequencing or chromosomal microarray analysis.

References

Murdock, D. et al. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing. The Journal of Clinical Investigation; https://doi.org/10.1172/JCI141500 (2021).