Abstract
Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do not alter chromosome copy numbers, nor by short-read sequencing because of the unmappability of short reads against repetitive genomic regions. The precise localization of breakpoints is vital for exploring genetic causes in patients with balanced translocations or inversions. Long-read sequencing techniques may detect these structural variants in a more direct, efficient, and accurate manner. Here, we performed whole-genome, long-read sequencing using the Oxford Nanopore GridION sequencer to detect breakpoints in six balanced chromosome translocation carriers and one inversion carrier. The results showed that all the breakpoints were consistent with the karyotype results with only ~10× coverage. Polymerase chain reaction (PCR) and Sanger sequencing confirmed 8 out of 14 breakpoints; however, other breakpoint loci were slightly missed since they were either in highly repetitive regions or pericentromeric regions. Some of the breakpoints interrupted normal gene structure, and in other cases, micro-deletions/insertions were found just next to the breakpoints. We also detected haplotypes around the breakpoint regions. Our results suggest that long-read, whole-genome sequencing is an ideal strategy for precisely localizing translocation breakpoints and providing haplotype information, which is essential for medical genetics and preimplantation genetic testing.
Highlights
Structural variants (SVs), including translocations, inversions, deletions, and duplications, account for genetic disorders through damaging or changing functions of vital genes (Feuk et al, 2006; Conrad et al, 2010; Stankiewicz and Lupski, 2010; Collins et al, 2017)
Our results indicate that low-coverage, whole-genome sequencing is an ideal method for precisely localizing translocation breakpoints, which may be widely applied in SV detection, therapeutic monitoring, assisted reproduction technology (ART), and preimplantation genetic diagnosis (PGD)
Karyotype analysis is a lowresolution method that cannot identify exact breakpoints, which are often required for a better understanding of how translocations impact genes and phenotypes
Summary
Structural variants (SVs), including translocations, inversions, deletions, and duplications, account for genetic disorders through damaging or changing functions of vital genes (Feuk et al, 2006; Conrad et al, 2010; Stankiewicz and Lupski, 2010; Collins et al, 2017). In most of these cases, we can only speculate that the translocations and inversions damage normal gene expression or function as the precise breakpoints remain unknown. Designed FISH and Southern blot for specific cases can localize the breakpoints at a single gene level; results obtained with these strategies can not be used for generalization. These techniques cannot accurately retrieve the sequences of breakpoints, and it is difficult to determine the specific impact of the chromosome translocation on the gene structure (Schluth-Bolard et al, 2013). When breakpoints are located in complex repetitive regions with low mapping rate, it is difficult to accurately detect their location when using NGS
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