Table 2 SVs called from HCC1395 and HCC1395BL cell lines. The somatic SV and germline SV raw calls are the number of SVs counted after Survivor software tool merge of all replicate call sets for each platform. The total merged somatic SV raw calls contain the merged tumor-only calls from tumor-normal paired subtraction analysis. The total merged germline SV calls contain the merged germline SV calls from all replicates from HCC1398BL cell line
NGS Technologies | Initial SVs call set | High-confidence SVs call set | ||||||
|---|---|---|---|---|---|---|---|---|
HCC1395 (tumor cell line) | HCC1395BL (normal cell line) | HCC1395 (tumor cell line) | ||||||
Somatic SVs (raw calls) | Germline SVs (raw calls) | Deletions | Duplications | Insertions | Inversions | Translocations | BNDs | |
Illumina WGS | 9155 | 105,732 | 375 | 226 | 4 | 82 | 143 | 10 |
10x GenomicsWGS | 16,886 | 37,059 | 42 | 86 | N/A | 78 | 119 | 5 |
PacBio WGS | 9574 | 27,069 | 643 | 138 | 549 | 94 | 99 | 10 |
HiC WGS | 137 | 1 | 8 | 6 | N/A | 9 | 5 | 1 |
Oxford NanoporeWGS | 21,245 | 63,061 | 664 | 180 | 549 | 65 | 96 | 4 |
Total Merged SVs | 46,284 | 168,401 | 717 | 230 | 551 | 133 | 146 | 11 |