Copy-neutral Loss of Heterozygosity in Cancer

Loss of heterozygosity (LOH) is a common contributor to tumorigenesis, leading to the loss of a wild-type allele and the unmasking of a recessive mutation. Scans of genomic copy number (CN) can reveal LOH due to hemizygous deletions, but LOH can also occur independently of CN change, where one chromosome or chromosomal region has been duplicated and its homologue has been deleted. When LOH occurs without CN change, it is commonly termed copy neutral LOH. This Application Note describes the frequency and relevance of copy-neutral LOH in a variety of cancer samples, and presents a review of recent publications in which Affymetrix SNP arrays were used to simultaneously study CN and LOH. These publications identify significant and common chromosomal aberrations that cannot be identified when examining CN alone.