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. 2011 Dec 6;6(12):e28250. doi: 10.1371/journal.pone.0028250

Figure 1. SNP array imaging results for chr3 and chr9 of the benign serous tumour 1781T.

Figure 1

SNP array imaging results for chr3 (A, C, E) and chr9 (B, D, F) of the benign serous tumour 1781T, using Illumina's HumanHap300-Duo Genotyping BeadChip (A and B) and Illumina's Human610-Quad Genotyping BeadChip (C–F). Two different DNA preparations were used with the HumanHap610-Quad Genotyping BeadChip. The top plot of each figure shows the B allele frequency (BAF) for each SNP marker aligned to its chromosomal position. In heterozygous diploid cells, alleles are present in AA, AB or BB pairs. The B Allele frequencies for these possible allele pairs are 0, 0.5 or 1, respectively. Any deviation from this ratio indicates a chromosomal aberration. In one DNA preparation, the double row in the BAF plot indicates allelic imbalance of SNP markers across the entire chromosome (C and D). A 9.1 Mb ROH is observed on chr3 and is highlighted in blue. No markers are located in the centromeric region of either chromosome, as noted by a lack of markers in both the B allele frequency and Log R ratio (LRR) plots. The bottom plot of each figure contains the Log R ratio, which provides an indication of the copy number for each SNP marker aligned to its chromosomal position. Note the absence of a drop in the Log R ratio in the highlighted ROH.