Skip to main content

Table 5 Comparison of QPCR and CARAT on HER2/neu locus across three cell lines.

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

HER2/NEU Region on Chr 17
Sample SNP 1720794 12.48 kb proximal HER2/neu 38231.31–38259.79 kb SNP 1738376 91.64 kb distal
  CARAT p-val 2ΔCt + 1 CARAT p-val
SK-BR-3 19.0 <10-20 12.4 19.0 <10-20
ZR-75-30 25.1 <10-20 27.7 25.1 <10-20
MCF-7 1.0 0.0003 0.8 2.1 0.567
  1. Note:
  2. 12ΔCt + 1: theoretical estimate of total copy number using QPCR
  3. 2CARAT: copy number estimated by CARAT
  4. 3p-val: The statistical significance of the copy number alteration. It is derived from the algorithm by comparing the target sample to a reference set consisting of normal individuals