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

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 r...

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Bibliographic Details
Published in:Journal of human genetics 2022-06, Vol.67 (6), p.363-368
Main Authors: Mariya, Tasuku, Kato, Takema, Sugimoto, Takeshi, Miyai, Syunsuke, Inagaki, Hidehito, Ohye, Tamae, Sugihara, Eiji, Muramatsu, Yukako, Mizuno, Seiji, Kurahashi, Hiroki
Format: Article
Language:English
Subjects:
Chromosome rearrangements
Chromosomes
Cytogenetics
DNA microarrays
DNA sequencing
Genetic Markers
Genomes
Humans
In Situ Hybridization, Fluorescence
Inverted repeat
Microarray Analysis
Mosaicism
Sampling
Supernumerary
Whole genome sequencing
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Summary: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.
ISSN:1434-5161
1435-232X
DOI:10.1038/s10038-021-01004-x