Table 2.

Median (range) of per-genome sequencing measures for the 24 patients

TumorNormal
Genome-wide average coverage depth105 (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 ratio2.11 (1.96–2.23)2.11 (2.04–2.23)
Transition/transversion ratio2.13 (2.13–2.14)2.13 (2.13–2.14)
Tumor vs. Normala
Small indels and substitutions (≤50 bases)14,537 (9,684–21,445)
Genicb6,474 (4,004–9,709)
Exonic77 (33–229)
Single base substitutions5,309 (3,323–11,603)
A ↔ G transitions1,566 (927–4,511)
C ↔ T transitions1,588 (907–4,374)
A ↔ C transversions535 (364–853)
A ↔ T transversions589 (474–854)
C ↔ G transversions448 (272–640)
G ↔ T transversions542 (379–864)
CNAsc148 (1–3,557)
Losses41 (0–2,052)
Gains6 (1–1,820)
Rearrangements87 (29–309)
Deletions27 (9–106)
Duplications14 (7–82)
Inversions12 (0–92)
Translocations5 (0–22)
Complexd20 (11–58)
Chromoplexice7 (0–41)
Gene fusionsf4 (0–11)
  • aRefers to high-confidence somatic mutations (see Materials and Methods).

  • bGenic mutations are defined as those occurring in exons, introns, promoters, 5′UTR, 3′UTR, and splice site regions of RefSeq genes.

  • cCNAs are defined as tumor copy number of less than 1.5 (losses) or more than 2.5 (gains).

  • dComplex rearrangements are those not easily classified as any one of the other categories.

  • eChromoplexic rearrangements are those that are interdependent and adjacent to other rearrangements in the tumor genome (7).

  • fGene fusions can result from deletions, inversions, translocations, or complex rearrangements.