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Analysis Characterizes Discrepant Regions Between Genome Assemblies

There are dozens of large-scale genomic regions that differ between the telomere-to-telomere human genome assembly and the most recent human reference genome, according to an analysis in Genome Biology. A Shanghai Jiao Tong University-led team used three different alignment tools to identify 67 large-scale discrepant regions between the assemblies, in addition to the previously reported regions. They additionally developed a tool called SynPlotter to visualize and validate these regions, finding that most discrepant regions outside of the telomeric and centromeric regions were more structurally polymorphic than other genomic regions. The researchers also noted that these discrepant regions were associated with human disease, including, for example, the KLRC gene cluster and natural killer cell differentiation. "We believe the results of this work not only contribute to our biological understanding of these diverse regions but will benefit future studies by helping to eliminate reference biases," the researchers write. "We should stress that our study focused solely on the large-scale discrepant regions between two 'completed' genome assemblies and, as such, represents limited sample size."