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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
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BMC Bioinformatics

ISSN: 1471-2105

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