Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

BMC Genomics

Table 2 Summary of analysis results from the application of Seurat on an experimentally derived cancer dataset

Metrics(example tumor/normal dataset)
Average genomic coverage on normal tissue genome	55×
Average genomic coverage on tumor tissue genome	40×
Somatic base substitutions	29526
Somatic base substitutions (Quality > 20)	17044
Transition/Transversion ratio for somatic base substitutions	1.433
Transition/Transversion ratio for somatic base substitutions (Quality > 20)	1.922
dbSNP build 135 rate	0.146
dbSNP build 135 rate (Quality > 20)	0.088
Somatic insertions	1430
Somatic deletions	4067
Somatic structural variance sites	272
Somatic loss of heterozygosity sites	1523
Non-synonymous/Synonymous mutation ratio	0.00435

Detailed Legend: Summary of somatic mutation analysis details from the application of Seurat on a normal/tumor genome pair of a patient with a rare lymphoma. The dbSNP rate refers to the proportion of candidate somatic variants that are included in the public genomic variation database dbSNP [20]. This number is an indicator of known germline variants that were falsely identified as tumor-specific. The calculation of the transition/transversion and the non-synonymous/synonymous variant ratios was performed using snpEff [21].

ISSN: 1471-2164