Zürich Seminars in Bioinformatics

Max Verbiest

Functional implications of Short tandem repeat (STR) variation in NGS data

Short tandem repeats (STRs) are genomic elements that consist of consecutive repetitions of a 1-6 nucleotide motif. They are abundant in the human genome and are known to be mutational hotspots. Several cancer types are known to have a microsatellite instability high (MSI-H) subtype wherein the DNA mismatch repair system is defective, leading to hypermutation of STRs.

This hypermutative state is linked to the expression of immunogenic neoantigens and better response to immune checkpoint inhibitors. There are, however, many functional and regulatory roles that STRs play in the human genome that are neglected by the binary MSI high/low classification currently in place. In this talk, I will present results from our investigation of human protein STRs in SwissProt, which highlight the known connection between protein STRs and intrinsically disordered regions. Functional overrepresentation analyses of STR-containing proteins suggests they are interesting targets to consider in the context of cancer. It is currently unclear how STR variation in MSI-H tumours affects these proteins. I will therefore end by outlining our current efforts to determine the functional implications of STR variation in NGS data from colorectal cancer patients.

@mbaudis 2021-10-28
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