Major copy proportion analysis of tumor samples using SNP arrays

BMC Bioinformatics

Table 1 Comparison of MCP based on SNP arrays and major allele proportions (MAP, Max(A, B)./(A+B)) based on allele-specific Q-PCR or array-based allelic signals.

Sample	SNP	Chromo-some	Position(Mb)	PCR allele A Copy	PCR allele B Copy	PCR MAP	Array MAP	Array MCP	Array Copy
S0465T	1894228	3	183.975	25.18	1.68	0.94	0.86	0.8	4.8
S0515T	1894075	3	183.786	2.42	38.37	0.94	0.65	0.8	17.47
HCC827	2568690	7	54.606	135.92	1.97	0.99	0.82	0.8	8.07
H2087	2804962	8	128.906	1.23	6.03	0.83	0.74	0.7	6.05
H2122	2804228	8	128.037	58.46	3.39	0.95	0.98	0.95	6.55
HCC827	2804646	8	128.332	0.06	7.58	0.99	0.9	0.95	9.39
S0515T	589797	12	32.822	0.06	7.12	0.99	0.96	0.55	4.32
H2087	590880	12	33.8	17.32	0.03	1	0.88	0.95	10.42
H2087	611421	12	57.198	4.86	0.17	0.97	0.95	0.8	11.3
HCC1359	1679843	22	19.774	1.03	8.36	0.89	0.82	0.9	8.74

Both SNP arrays and Q-PCR yield allelic-specific copy numbers relative to sample ploidy. "Array Copy" is the array-based total copy number by median smoothing of raw copy numbers with a window size of 5 SNPs. The chromosome positions are based on the UCSC hg16 genome assembly.

ISSN: 1471-2105