In a paper appearing in Nature Methods, a team from GeneDX, the Foundation of Biological Data Science, Baylor College of Medicine, and elsewhere presents a software package known as the PanGenome Research Tool Kit (PGR-TK) that is designed to uncover small-to-large forms of genetic variation in human genome assemblies. Along with analyses of the class II major histocompatibility complex, for example, the researchers used PGR-TK tools to dig into infertility- and eye disease-related regions on the Y chromosome and X chromosome, respectively, before applying the approach to Human Pangenome Reference Consortium sequence data spanning nearly 400 repeat-rich, medically relevant genes originally found in the Genome in a Bottle (GIAB) dataset. "Our initial analysis of the GIAB clinical and medically important genes … with a pangenome graph approach will help the research community to adapt the pangenome resource for clinical and medical genetic applications," the authors report. "Tools for visualizing and analyzing complicated rearrangement loci such as PGR-TK will be essential for better variant calling and understanding how structural variations with repeats affect the results for the community."
Analytical Approach Applied to Repeat-Rich, Clinically Relevant Pangenome Sequences
Jun 28, 2023