Table 6.
Allele specific Taqman results
| Sample | SK-BR-3 | ZR-75-30 | ||||||||
| SNPID | Chr | Pos | P-Value | CN_A | CN_B | DM Call | P-Value | CN_A | CN_B | DM Call |
| 1724728 | 4 | 9565339 | 0.0001 | 0.89 (0.85) | 0.22 (0.0) | AA | 0.0006 | 1.77 (1.5) | 0.19 (0.02) | NC |
| 1726250 | 8 | 89504951 | <10-20 | 0.83 (0.97) | 14.83 (10.8) | BB | 0.141 | 0.43 (0.0) | 0.84 (1.21) | BB |
| 1700191 | 8 | 112018158 | 5.03 × 10-11 | 0.34 (0.08) | 4.57 (5.54) | BB | 3.77 × 10-19 | 0.81 (0.01) | 8.99 (8.93) | BB |
| 1746553 | 8 | 120342175 | 1.72 × 10-20 | 18.45 (14.32) | 1.17 (1.43) | AA | 8.09 × 10-20 | 10.44 (5.7) | 1.19 (0.68) | AA |
| 1710029 | 8 | 121176983 | 1.53 × 10-20 | 19.05 (35.5) | 3.30 (1.02) | AA | 3.61 × 10-20 | 13.60 (9.1) | 2.46 (0.77) | NC |
| 1736669 | 12 | 41456018 | 0.843 | 1.10 (1.08) | 0.90 (0.99) | NC | 0.075 | 1.68 (1.61) | 1.39 (0.03) | AA |
| 1693987 | 17 | 39301708 | 1.38 × 10-16 | 6.20 (10.64) | 0.28 (0.28) | AA | 0.002 | 0.08 (0.0) | 1.06 (0.66) | NC |
| 1718017 | 17 | 48767363 | 0.0001 | 0.93 (0.9) | 0.15 (0.0) | NC | 5.96 × 10-19 | 6.53 (5.58) | 2.04 (1.12) | NC |
| 1670177 | 19 | 20287003 | 1.01 × 10-9 | 0.0 (0.0) | 0.03 (0.0) | NC | 0.310 | 0.11 (0.36) | 1.47 (0.74) | NC |
Note: WGSA results for 9 SNPs are shown in columns labeled CN_A (copy number of A allele) and CN_B (copy number of B allele). Allelic copy number estimates by TaqMan reactions are shown in parentheses. DM Call refers to the genotype call made using the Dynamic Model algorithm (DM) using a confidence rank score of 0.05. The VIC reporter dye was measuring the A allele for all SNPs except SNP 1710029 (B allele). The FAM reporter dye was measuring the B allele for all SNPs except SNP 1710029 (A allele).