TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

Background: High-throughput genotyping microarrays assess both total DNA copy number and allelic composition, which makes them a tool of choice for copy number studies in cancer, including total copy number and loss of heterozygosity (LOH) analyses. Even after state of the art preprocessing methods, allelic signal estimates from genotyping arrays still suffer from systematic effects that make them difficult to use effectively for such downstream analyses. Results: We propose a method, TumorBoost, for normalizing allelic estimates of one tumor sample based on estimates from a single matched normal. The method applies to any paired tumor-normal estimates from any microarray-based technology, combined with any preprocessing method. We demonstrate that it increases the signal-to-noise ratio of allelic signals, making it significantly easier to detect allelic imbalances. Conclusions: TumorBoost increases the power to detect somatic copy-number events (including copy-neutral LOH) in the tum...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Henrik Bengtsson, Pierre Neuvial, Terence P. Speed
• Keywords: Allelic, Allelic Signal, BMCBI 2010, Copy Numbers