Long-read sequencing reveals the complex structure of extra dic(21;21) chromosome and its biological changes

Abstract Complex congenital chromosome abnormalities are rare but often cause severe symptoms. The structures and biological impacts of such chromosome abnormalities have seldomly been analyzed at the molecular level. Previously, we reported a Japanese female patient with severe developmental defects. The patient had an extra dicentric chromosome 21 (chr21) consisting of two partial chr21 copies fused together within their long arms along with two centromeres and many copy number changes. In this study, we performed whole-genome, transcriptional, and DNA methylation analyses, coupled with novel bioinformatic approaches, to reveal the complex structure of the extra chromosome and its transcriptional and epigenetic changes. Long-read sequencing accurately identified the structures of junctions related to copy number changes in the extra chr21 and suggested the mechanism of the structural changes. Our allele-specific transcriptome analysis showed the overexpression of genes in extra chr21. Additionally, allele-specific DNA methylation analysis of the long-read sequencing data suggested that the centromeric region of extra chr21 was hypermethylated, which may cause inactivation of one centromere in the extra chromosome. Our comprehensive analysis provides insights into the molecular mechanism underlying the generation of the extra chromosome and its pathogenic roles.