Target enrichment long-read sequencing with adaptive sampling can determine the structure of the small supernumerary marker chromosomes

Tasuku Mariya, Takema Kato, Takeshi Sugimoto, Syunsuke Miyai, Hidehito Inagaki, Tamae Ohye, Eiji Sugihara, Yukako Muramatsu, Seiji Mizuno, Hiroki Kurahashi

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Structural analysis of small supernumerary marker chromosomes (sSMCs) has revealed that many have complex structures. Structural analysis of sSMCs by whole genome sequencing using short-read sequencers is challenging however because most present with a low level of mosaicism and consist of a small region of the involved chromosome. In this present study, we applied adaptive sampling using nanopore long-read sequencing technology to enrich the target region and thereby attempted to determine the structure of two sSMCs with complex structural rearrangements previously revealed by cytogenetic microarray. In adaptive sampling, simple specification of the target region in the FASTA file enables to identify whether or not the sequencing DNA is included in the target, thus promoting efficient long-read sequencing. To evaluate the target enrichment efficiency, we performed conventional pair-end short-read sequencing in parallel. Sequencing with adaptive sampling achieved a target enrichment at about a 11.0- to 11.5-fold higher coverage rate than conventional pair-end sequencing. This enabled us to quickly identify all breakpoint junctions and determine the exact sSMC structure as a ring chromosome. In addition to the microhomology and microinsertion at the junctions, we identified inverted repeat structure in both sSMCs, suggesting the common generation mechanism involving replication impairment. Adaptive sampling is thus an easy and beneficial method of determining the structures of complex chromosomal rearrangements.

Original languageEnglish
Pages (from-to)363-368
Number of pages6
JournalJournal of Human Genetics
Volume67
Issue number6
DOIs
Publication statusPublished - 06-2022

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

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