Cancer SV dataset

Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN. The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.

Reference: Long-read sequencing for non-small-cell lung cancer genomes

Accession:JGAS00000000065 (JGAD00000000252 / JGAD00000000253)* Controlled Access.

Tumor Normal
sampleID Yields(Gb) Number of reads Coverage(x) Yields(Gb) Number of reads Coverage(x) Number of SVs Processed data
S1 99 14881240 33 57 11709609 19 7 S1_SV_gene_candidates.bedpe
S2 94 25379061 31 41 7016159 14 120 S2_SV_gene_candidates.bedpe
S3 77 15952312 25 48 12971173 15 41 S3_SV_gene_candidates.bedpe
S5 82 21640571 27 35 6503970 11 11 S5_SV_gene_candidates.bedpe
S6 76 11336329 25 48 7531078 16 72 S6_SV_gene_candidates.bedpe
S7 85 13880384 28 46 7555316 15 91 S7_SV_gene_candidates.bedpe
S8 100 18661003 33 54 8351411 18 67 S8_SV_gene_candidates.bedpe
S9 96 13179209 32 34 4483001 11 48 S9_SV_gene_candidates.bedpe
S10 85 12424087 28 42 7029224 14 64 S10_SV_gene_candidates.bedpe
S11 69 21140772 22 59 7832201 19 42 S11_SV_gene_candidates.bedpe
S12 73 15634853 24 84 12908975 27 2 S12_SV_gene_candidates.bedpe
S13 104 30719862 34 38 5506152 12 31 S13_SV_gene_candidates.bedpe
S14 74 14328017 24 56 6464828 18 53 S14_SV_gene_candidates.bedpe
S15 75 12278084 24 55 9585959 18 7 S15_SV_gene_candidates.bedpe
S16 74 20118226 24 55 7924757 18 103 S16_SV_gene_candidates.bedpe
S17 52 7086616 17 59 6766386 20 3 S17_SV_gene_candidates.bedpe
S18 62 7091142 20 44 5335320 15 14 S18_SV_gene_candidates.bedpe
S19 60 6352847 20 37 5025576 12 10 S19_SV_gene_candidates.bedpe
S20 58 5836744 19 47 5620346 15 87 S20_SV_gene_candidates.bedpe
S21 63 8985953 21 57 6166961 19 19 S21_SV_gene_candidates.bedpe

Viewer (Cell line data)

RERF-LC-KJ: STK11

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RERF-LC-KJ: NF1

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PC-14: SMARCA4

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PC-14: PTEN

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