High-coverage paleo-genome research identifies a pathogenic mutation on EXT1 in a Qing-period Chinese individual with...

Multiple osteochondromas (MO) is a rare bone disease with variable manifestations that make it difficult to distinguish from phenotypically similar diseases, both morphologically and radiologically. As a monogenic disorder associated with mutations in EXT1 or EXT2, ancient DNA analysis can provide genetically confirmed diagnoses and insights into the pathogenesis of suspected cases. To further investigate a previously reported suspected MO case from Qing-period Shandong, China, we generated ancient whole-exome sequencing data from the individual's petrous bone, yielding a mean sequencing coverage of 27.172×. We identified a pathogenic heterozygous mutation in the ligand-binding site Rossmann-2 subdomain of EXT1 (c.791T > C; p.Leu264Pro) with a sequencing depth of 17×, a mutation also found in an unrelated modern Latin American patient. Additionally, by predicting and analyzing the 3D structure of the EXT1 protein, we detected structural and functional damage. Our findings expand the known spectrum of EXT1 mutations and enhance the comprehensive genotype-phenotype map of rare MO, providing insights into its genetic pathology from a historical perspective. Furthermore, this research expands the understanding of disease landscapes in Northern China, both paleopathologically and paleogenetically.