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. |
|||||||||
|
Li et al. BMC Bioinformatics 2008 9:204 doi:10.1186/1471-2105-9-204 |
|||||||||
