Presentation Information
[OE2-2]Genome, transcriptome, and epigenetic analysis of a tetrasomy 21 patient using long-read sequencing technology
○Kugui Yoshida1, Ko Ikemoto1, Takako Takano2,3, Akihiro Fujimoto1 (1.Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan, 2.Department of Child Health, Tokyo Kasei University, 3.Tokyo Metropolitan Tobu Medical Center for Children with Developmental Disabilities, Tokyo, Japan)
A previous study (Takano et al. EJMG(2020)) reported a Japanese female patient with tetrasomy 21, whose parents are both healthy. She did not have Down syndrome phenotype, and exhibited severe psychomotor retardation. Chromosome analyses in the previous study revealed that the patient had an extra dicentric chr21, with a 47,XX,+dic(21;21) karyotype. Although the previous study identified structural variations (SVs) in the extra chr21 using a short-read sequencer, the structure of the extra chr21 and the pathological mechanisms are unclear. We thus performed whole-genome sequencing and RNA sequencing for the patient and her parents using short-read and long-read (Oxford Nanopore) sequencing technologies. An analysis of the depth of coverage revealed that the patient has four or more copies in chr21 (21q21). Long-read identified SVs at the boundaries of the copy number variations. We then reconstructed sequences spanning the SVs using our long-read assembler (LoMA software) and revealed complex patterns of the extra chr21. An analysis of the DNA methylation using long-read suggested significant hypermethylation in centromeres of the extra chr21. We further compared gene expression levels between the patient and her mother using RNA-seq. RNA-seq by NGS and Nanopore showed that genes in the patient’s 21q21 had 2-6 fold higher expressions than those in her mother. Long-read RNA-seq did not detect abnormal splicing change. These results revealed the accurate structure and the abnormality of methylation and gene expression caused by the extra chr21.