Table 3.
Analysis metrics of SI- and LI-WGS libraries for patients 1, 2 and 3
| Metric | Patient 1 |
Patient 2 |
Patient 3 |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SI |
LI |
SI |
LI |
SI |
LI |
|||||||
| Normal | Tumor | Normal | Tumor | Normal | Tumor | Normal | Tumor | Normal | Tumor | Normal | Tumor | |
| Number of tumor cellularity | n/a | 50 | n/a | 50 | n/a | 50 | n/a | 50 | n/a | n/a | n/a | n/a |
| Median insert size | 328.00 | 330.00 | 865.00 | 861.00 | 285.00 | 293.00 | 852.00 | 860.00 | 274.00 | 275.00 | 901.00 | 901.00 |
| Mean insert size | 326.70 | 327.81 | 848.90 | 850.22 | 289.01893 | 292.970983 | 849.78 | 848.03 | 291.669719 | 289.751541 | 901.04 | 898.37 |
| Insert size standard deviation | 29.91 | 32.80 | 113.24 | 100.82 | 45.67 | 50.13 | 110.67 | 135.52 | 57.61 | 56.75 | 108.42 | 117.62 |
| Average mapped sequence coverage | 8.13 | 8.13 | 8.05 | 8.05 | 8.29 | 8.29 | 8.05 | 8.05 | 8.29 | 8.29 | 8.05 | 8.05 |
| Average mapped physical coverage | 26.04 | 13.26.13 | 67.66 | 67.76 | 23.03 | 23.35 | 67.72 | 67.58 | 23.24 | 23.09 | 71.81 | 71.59 |
| Power to detect event | 0.52 | 0.85 | 0.48 | 0.86 | n/a | n/a | ||||||
| GC dropout | 5.76 | 7.46 | 4.45 | 5.25 | 2.74 | 2.69 | 3.86 | 4.40 | 2.73 | 2.76 | 5.32 | 4.95 |
| AT dropout | 2.02 | 2.78 | 2.15 | 2.58 | 0.98 | 0.86 | 2.07 | 2.17 | 0.87 | 0.92 | 2.71 | 2.44 |
| Median GC normalized coverage | 0.69 | 0.70 | 0.81 | 0.79 | 0.88 | 0.90 | 0.84 | 0.82 | 0.86 | 0.86 | 0.79 | 0.79 |
| Total number reads | 250 023 370 | 250 031 044 | 250 027 715 | 250 019 339 | 249 978 232 | 249 998 124 | 250 002 762 | 250 009 726 | 250 002 357 | 249 991 693 | 250 009 553 | 250 001 078 |
| Number of somatic translocations | 4 | 16 | 3 | 5 | 3 | 15 | ||||||
| Number of somatic translocations detected that affect a COSMIC gene | 0 | 0 | 0 | 0 | 0 | 1 | ||||||
| Total number of common translocations | 3 | 0 | 0 | |||||||||
| Number of CNVs identified | 48 | 4 | 2 | 0 | 0 | 2 | ||||||
| Number of genes affected by CNVs | 752 | 12 | 0 | 0 | 0 | 12 | ||||||
| Number of COSMIC genes affected by CNVs | 16 | 0 | 0 | 0 | 0 | 2 | ||||||
| Total number of common genes affected by CNVs | 11 | 0 | 0 | |||||||||
SI- and LI-WGS bam files were each randomly normalized to ∼250 million mapped reads using SAMtools to allow for a direct comparison across SI and LI data sets.
aPower was calculated assuming that a minimum of eight anomalous read pairs are required for detection. Because the tumor cellularity of patient 3 is not known, power calculations were not performed. n/a (not available).