B allele frequency (BAF) and log R ratio (LRR) plots for a region of LOH with changing tumor cellularity.
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posted on 2012-09-25, 00:09 authored by Sarah Song, Katia Nones, David Miller, Ivon Harliwong, Karin S. Kassahn, Mark Pinese, Marina Pajic, Anthony J. Gill, Amber L. Johns, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Felicity Newell, Mark J. Cowley, Jianmin Wu, Peter Wilson, Lynn Fink, Andrew V. Biankin, Nic Waddell, Sean M. Grimmond, John V. PearsonDNA from a cancer cell line and matched normal DNA were mixed in different proportions and assayed using SNP arrays. BAF and LRR plots were generated using GenomeStudio software (Illumina). For illustrative purposes a region of loss on the p arm of chromosome 7 in the cancer cell line is shown. In the 100 normal sample (0 tumor) the SNPs are either heterozygous (BAF 0.5) or homozygous (BAF = 0 or 1). In regions of single chromosome loss in the tumour there is LOH. In the 100 cell line the BAF is showing a homozygous state and there is clear loss in the LRR. As tumour cellularity decreases the separation of the BAF decreases.
