SSVs identified by pipelines 1 and 2
| Non-recurrence | Recurrence | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Patient 1 | Patient 2 | Patient 5 | Patient 6 | Patient 19 | Patient 8 | Patient 10 | Patient 15 | Patient 16 | Patient 18 | |
| Pipeline 1 | 13 | 25 | 0 | 13 | 7 | 8 | 7 | 12 | 4 | 9 |
| Pipeline 2 | ND | ND | 5 | ND | ND | 13 | 14 | ND | 14 | 19 |
| Unique SSVs* | 13 | 25 | 5 | 13 | 7 | 14 | 15 | 12 | 16 | 20 |
| Number of SSVs analysed in plasma† | 5 | 5 | 4 | 4 | 6 | 5 | 4 | 2 | 3 | 6 |
| Number of SSVs detected in plasma | 0 | 2‡ | 0 | 3‡ | 3‡ | 3 | 3 | 2 | 3 | 3 |
*The total number of unique SSVs identified (the union of pipelines 1 and 2).
†For each patient, 4–8 of the unique SSVs (those supported by most reads or affecting loci harbouring genes known to drive CRC development, and preferably mapping to different chromosomes) were selected. Their breakpoints were mapped to nucleotide level by Sanger sequencing, and subsequently, ddPCR assays were designed to the SSVs with the breakpoints mapping to non-repetitive sequences. Only the SSVs for which high-performance ddPCR assays could be produced were analysed in plasma.
‡SSV was only detected in the plasma sample drawn prior to surgery.
CRC, colorectal cancer; ddPCR, droplet digital PCR; ND, not done; SSVs, somatic structural variations.