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. 2004 May 17;32(9):e69.
doi: 10.1093/nar/gnh072.

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA

Kwong-Kwok Wong  1 , Yvonne T M Tsang, Jianhe Shen, Rita S Cheng, Yi-Mieng Chang, Tsz-Kwong Man, Ching C Lau
Affiliations

Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA

Kwong-Kwok Wong et al. Nucleic Acids Res. .

Abstract

Besides their use in mRNA expression profiling, oligonucleotide microarrays have also been applied to single-nucleotide polymorphism (SNP) and loss of heterozygosity (LOH) or allelic imbalance studies. In this report, we evaluate the reliability of using whole genome amplified DNA for analysis with an oligonucleotide microarray containing 11 560 SNPs to detect allelic imbalance and chromosomal copy number abnormalities. Whole genome SNP analyses were performed with DNA extracted from osteosarcoma tissues and patient-matched blood. SNP calls were then generated by Affymetrix GeneChip DNA Analysis Software. In two osteosarcoma cases, using unamplified DNA, we identified 793 and 1070 SNP loci with allelic imbalance, respectively. In a parallel experiment with amplified DNA, 78% and 83% of these SNP loci with allelic imbalance was detected. The average false-positive rate is 13.8%. Furthermore, using the Affymetrix GeneChip Chromosome Copy Number Tool to analyze the SNP array data, we were able to detect identical chromosomal regions with gain or loss in both amplified and unamplified DNA at cytoband resolution.

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Figures

Figure 1
Figure 1
Correlation between the estimated copy number of 11 560 SNPs from amplified and unamplified osteosarcoma DNA. The copy number is estimated by the Affymetrix® GeneChip® Chromosome Copy Number Tool and is in log2 scale. The Pearson correlation coefficient is 0.77.
Figure 2
Figure 2
Copy number of individual SNPs in chromosome 6 detected with amplified and unamplified tumor DNA from case OST197. The copy number results are plotted using two colors: green for values above the threshold (2) and magenta for values below the threshold. Included in the graph is a representation of the genotype calls associated with the SNPs (small color bars to the right of the ideogram). Green represents heterozygous calls while magenta represents homozygous calls. An ideogram showing the corresponding cytoband locations of each SNPs on chromosome 6 is aligned in the bottom of the graph.
Figure 3
Figure 3
Probability plot of LOH calls in amplified and unamplified tumor DNA without reference to the normal DNA. An example for chromosome 6 of OST197 is shown.
Figure 4
Figure 4
Significance graph of detecting copy number changes in amplified and unamplified genomic DNA. An example for chromosome 6 of OST197 is shown.
See this image and copyright information in PMC

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