Allelic Imbalance in Cell Lines
The ability of the HumanHap550 genotyping BeadChip to detect chromosomal aberrations in the cancer cell lines HL60 (promyelocytic leukemia) and MCF7 (breast adenocarcinoma) are demonstrated in Figure 3. In HL60, deletions of varying size on chromosome 9—a ~20-Mb deletion on the p arm and a ~1.8-Mb deletion on the q arm—are shown in Figure 3a. These hemizygous deletions, from two copies to one copy, are manifest as a downward deflection in the log R ratio and a loss of heterozygotes in the AF.
The LOH+ module of BeadStudio allows for the user to annotate regions of interest, shown by the various bookmarks superimposed on the profiles. Other examples of aberrations in HL60 include monoallelic duplication of chromosome 18 as indicated by an increase in the log R ratio and split of the heterozygotes into two states: one at 0.67 (2:1 ratio) AF and another at 0.33 (1:2 ratio) AF (Figure 3b). Figure 3c demonstrates several small amplifications in HL60 on chromosome 8. Two adjacent homozygous and hemizygous deletions are observed in MCF7 (Figure 3d).
The gene annotation provided in the LOH+ module allows users to quickly analyze affected gene regions, and in this case, both copies of MTAP are homozygously deleted, whereas CDKN2A and CDKN2B are hemizygously deleted.
SNP-CGH provides a rapid means for simultaneous genomic profiling of physical and genetic anomalies. The foremost advantage of Illumina’s WGG BeadChips for SNP-CGH is that these arrays are easily manufactured and possess intrinsic scalability. The feature density is now greater than 550,000 SNPs across the human genome.
The Infinium assay enables both unlimited multiplexing and relatively unconstrained SNP selection, allowing development of high density tag SNP arrays. Additionally, automation of the Infinium assay allows large numbers of samples to be robustly processed and analyzed. The combined measurement of both allelic ratios and normalized intensities provides enhanced detectability of aberrations and allows identification of copy-neutral genetic anomalies, such as uniparental disomy and mitotic recombination. SNP-CGH can also collect allelic information on deletions, duplications, and amplifications, which has significance to cancer therapeutics.