Long read sequencing reveals a novel class of structural aberrations in cancers: identification and characterization of cancerous local amplifications

Abstract

Here we report identification of a new class of local structural aberrations in lung cancers. The whole-genome sequencing of cell lines using a long read sequencer, PromethION, demonstrated that typical cancerous mutations, such as point mutations, large deletions and gene fusions can be detected also on this platform. Unexpectedly, we revealed unique structural aberrations consisting of complex combinations of local duplications, inversions and micro deletions. We further analyzed and found that these mutations also occur in vivo, even in key cancer-related genes. These mutations may elucidate the molecular etiology of patients for whom causative cancerous events and therapeutic strategies remain elusive.

Recent advances in the detection of base modifications using the Nanopore sequencer

“…The maximum throughput of MinION is 10-30 Gb per single MinION flowcell based on the manufacturer's data. In a previous human genome study by our group, MinION stably generated over 3 Gb of DNA sequences in a single run [20]. The maximum length of its reads is greater than 2 Mb [21].…”

“…Therefore, PromethION can generate 7.6 Tb of sequence data. The average read length of human genome sequences without size selection is more than 10 kb for both the MinION and PromethION [20]. Although the throughput is becoming comparable with that of short-read sequencing, the accuracy of Nanopore sequencing (83-95%, depending on the library type) is lower than that of short-read sequencing using the Illumina platforms (99.9%) [22,23].…”

Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities

“…Some applications are more efficiently performed with NS compared to short-read sequencing: the detection of fusion transcripts, the opportunity of identifying allele-specific transcriptional events by phasing variants on the transcripts, and single-cell transcriptome analysis (Seki et al, 2019). Until now, most of the transcriptome studies in human research performed with NS namely were aimed at unambiguously characterizing and quantifying full-length isoforms and splice variants (Clark et al, 2018;Sakamoto et al, 2019;Rahimi et al, 2019;Hardwick et al, 2019), and identifying fusion transcripts and determining variants phasing (Byrne et al, 2017;Suzuki et al, 2017;Jeck et al, 2019), especially in cancer and neurological disorders.…”

Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome

“…ONT uses molecularly engineered nanopores to sequence long-reads of DNA in real-time using portable and low-cost sequencers [ 14 ]. Research shows that nanopore technology builds high-quality reference genomes [ 15 ], de novo assembly [ 16 ], and fills the gaps missed by SRS, thus, enabling easy characterization of SVs and discovery of novel variants [ 17 ].…”