Abstract
Background SNP genotyping microarrays may be used to detect regions of loss-of-heterozygosity (LOH). Genotype array data are collected for tumor tissue and germline tissue samples from each subject. For each subject, an initial call of LOH or non-LOH is generated for each marker via straightforward comparison of the genotype call across each tissue sample pair [1]. The genotype calls are generated with some error. Therefore, statistical models are used to analyze the pattern of LOH calls to infer regions of LOH for each subject [1].
Highlights
SNP genotyping microarrays may be used to detect regions of loss-of-heterozygosity (LOH)
We propose call-based segmentation analysis (CBSA) as a permutation-based method to infer regions of LOH from this type of data
Chromosome endpoints and the positions of markers with initial LOH calls are used to divide the genomes of study subjects into a series of distinct segments that are indexed by subject and location
Summary
SNP genotyping microarrays may be used to detect regions of loss-of-heterozygosity (LOH). Genotype array data are collected for tumor tissue and germline tissue samples from each subject. An initial call of LOH or non-LOH is generated for each marker via straightforward comparison of the genotype call across each tissue sample pair [1]. The genotype calls are generated with some error. Statistical models are used to analyze the pattern of LOH calls to infer regions of LOH for each subject [1]
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