DMD exon 2 duplication due to a complex genomic rearrangement is associated with a somatic mosaicism

Akatsuki Kubota; Hiroyuki Ishiura; Kristine Joyce Linay Porto; Masaki Tanaka; Jun Mitsui; Atsushi Unuma; Hisataka Maki; Issei Komuro; Shoji Tsuji; Jun Shimizu; Tatsushi Toda

doi:10.1016/j.nmd.2021.12.004

DMD exon 2 duplication due to a complex genomic rearrangement is associated with a somatic mosaicism

Neuromuscul Disord. 2022 Mar;32(3):263-269. doi: 10.1016/j.nmd.2021.12.004. Epub 2021 Dec 17.

Authors

Affiliations

¹ Department of Neurology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan. Electronic address: akatsuki-tky@umin.net.
² Department of Neurology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
³ Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
⁴ Institute of Medical Genomics, International University of Health and Welfare, 4-3, Kozunomori, Narita-shi, Chiba 286-8686, Japan.
⁵ Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1, Ogawa-higashimachi, Kodaira-shi, Tokyo 187-8551, Japan.
⁶ Department of Cardiology, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
⁷ Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan; Institute of Medical Genomics, International University of Health and Welfare, 4-3, Kozunomori, Narita-shi, Chiba 286-8686, Japan.
⁸ Department of Physical Therapy, Tokyo University of Technology, 5-25-8, Nishi-kamata, Ohta-ku, Tokyo 144-0051, Japan.

PMID: 35093299
DOI: 10.1016/j.nmd.2021.12.004

Abstract

We report the case of a patient with dystrophinopathy caused by DMD exon 2 duplication, showing marked asymmetric muscle atrophy. Immunostaining of the biopsied muscle tissue showed a mosaic staining, suggesting a somatic mosaicism. Polymerase chain reaction (PCR) analysis showed only one breakpoint, and long-read whole-genome sequencing revealed the entire structure of the rearranged sequence. The complex rearrangement was composed of two tandem duplications: one showed a microhomology near the breakpoint, suggesting a microhomology-mediated mechanism, whereas the other was associated with flanking short tandem repeats. The long-read sequencing also suggested the presence of a wild-type nonduplicated sequence, supporting somatic mosaicism. Whereas complementary DNA and western blot analyses were not useful, droplet digital PCR (ddPCR) analysis showed an average copy number of 1.61, enabling accurate estimation of the proportion of cells containing the duplication. Long-read sequencing and ddPCR analysis were useful for revealing the rearrangements and the precise copy number.

Keywords: Complex rearrangements; Droplet digital PCR; Dystrophinopathy; Long-read sequencing; Somatic mosaicism.

Publication types

Case Reports
Research Support, Non-U.S. Gov't

MeSH terms

Exons
Genomics*
Humans
Mosaicism*
Polymerase Chain Reaction
Whole Genome Sequencing