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Table 6 Allele specific Taqman results

From: CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays

   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
  1. 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).