Modeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring

BMC Bioinformatics

Table 1 Pipeline test of Pre-SCNAClonal on HCC1954

Sample name	n5t95	n20t80	n40t60	n60t40	n80t20	n95t5
Pre-SCNAClonal–MixClone (%)	0.874	0.722	0.523	0.374	0.200	0.054
MixClone (%)	0.645	0.589	0.471	0.199	0.144	0.188
Pre-SCNAClonal–THetA (%)	0.572	0.461	0.281	0.163	-	-
THetA (%)	0.463	0.374	0.269	0.148	-	-

Here ‘n5t95’, ‘n20t80’, ‘n40t60’, ‘n60t40’ and ‘n95t5’ respectively denote the tumor sample ‘HCC1954.mix1.n5t95’, ‘HCC1954.mix1.n20t80’, ‘HCC1954.mix1.n40t60’, ‘HCC1954.mix1.n60t40’, ‘HCC1954.mix1.n80t20’ and ‘HCC1954.mix1.n95t5’. Each of these sample contains one tumor subclone. Numbers in the table are the tumor subclonal frequencies predicted by the pipeline

ISSN: 1471-2105