Table 2.
Median (range) of per-genome sequencing measures for the 24 patients
| Tumor | Normal | ||
| Genome-wide average coverage depth | 105 (56–112) | 105 (56–113) | |
| Percent of genome with ≥ 10× | 99.2 (98.7–99.3) | 99.3 (98.6–99.4) | |
| Percent of genome with ≥ 20× | 98.1 (94.8–98.6) | 98.2 (93.9–98.6) | |
| Percent of genome with ≥ 40× | 91.9 (66.9–94.5) | 91.9 (67.6–94.7) | |
| Percent of genome fully called (all alleles) | 97.6 (97.1–97.8) | 97.6 (97.1–97.8) | |
| Single nucleotide polymorphisms (×1000) | 4,115 (3,975–4,183) | 4,110 (3,975–4,180) | |
| Heterozygous/homozygous ratio | 2.11 (1.96–2.23) | 2.11 (2.04–2.23) | |
| Transition/transversion ratio | 2.13 (2.13–2.14) | 2.13 (2.13–2.14) | |
| Tumor versus Normala | |||
| Small indels and substitutions (≤50 bases) | 14,537 (9,684–21,445) | ||
| Genicb | 6,474 (4,004–9,709) | ||
| Exonic | 77 (33–229) | ||
| Single base substitutions | 5,309 (3,323–11,603) | ||
| A ↔ G transitions | 1,566 (927–4,511) | ||
| C ↔ T transitions | 1,588 (907–4,374) | ||
| A ↔ C transversions | 535 (364–853) | ||
| A ↔ T transversions | 589 (474–854) | ||
| C ↔ G transversions | 448 (272–640) | ||
| G ↔ T transversions | 542 (379–864) | ||
| Copy number aberrationsc | 148 (1–3,557) | ||
| Losses | 41 (0–2,052) | ||
| Gains | 6 (1–1,820) | ||
| Rearrangements | 87 (29–309) | ||
| Deletions | 27 (9–106) | ||
| Duplications | 14 (7–82) | ||
| Inversions | 12 (0–92) | ||
| Translocations | 5 (0–22) | ||
| Complexd | 20 (11–58) | ||
| Chromoplexice | 7 (0–41) | ||
| Gene fusionsf | 4 (0–11) | ||
a
Refers to high-confidence somatic mutations (see Methods)
b
Genic mutations are defined as those occurring in exons, introns, promoters, 5’UTR, 3’UTR, and splice site regions of RefSeq genes.
c
Copy number aberrations are defined as tumor copy number of less than 1.5 (losses) or more than 2.5 (gains).
d
Complex rearrangements are those not easily classified as any one of the other categories
e
Chromoplexic rearrangements are those which are interdependent and adjacent to other rearrangements in the tumor genome (7).
f
Gene fusions can result from deletions, inversions, translocations, or complex rearrangements