Using a novel filtering approach in the analysis of whole-genome sequencing data, researchers identified ultra-rare disease-associated variants in the SMAD4 gene. In their study published in the American Journal of Human Genetics, they generated a functional filter to detect variants in non-coding DNA regions with experimental evidence of functionality. Sequencing of the entire genome of an individual reveals millions of variations compared to reference sequences. To analyze this data with regard to disease-causing genetic changes, it is necessary to prioritize and filter variants. In clinical sequencing, primarily protein-coding sequences are prioritized. However, non-coding DNA regions harbor many sequences that are essential for regulating gene expression. Many of these regions are not yet fully understood in terms of their precise function.

The analytical tool used in the study published in the American Journal of Human Genetics uses biological experimental data that is stored in publicly available databases and provides information on which genomic regions more or less likely possess functional relevance. Using this approach, the researchers analyzed the genome data of nearly 100 patients with hereditary hemorrhagic telangiectasia (HHT), an autosomal dominantly inherited vascular disorder that involves the formation of abnormal connections between arteries and veins. It is known that loss-of-function variants of SMAD4 can cause HTT associated with juvenile polyposis. SMAD4 is a transcription factor and an essential component of TGF-beta signaling and has also a tumor suppressor function. The identified SMAD4 variants were deletions located at a distance of more than 5 kb away from coding DNA, within the 3’ untranslated region of SMAD4. They affected structures that are needed for RNA processing (cleavage, polyadenylation) and for posttranslational modifications necessary for protein production.