We generated high-density genotyping data for the 18 samples using both Sentrix® Human-1 Genotyping (∼1 09 000 SNPs) and Sentrix® Humanhap300 (∼3 17 000 SNPs) (Illumina, San Diego, USA). After scanning, the data were uploaded into BeadStudio and analysed using the BeadStudio LOH+ module with the default window size (1.1 Mb for Human-1 and 0.46 Mb for HumanHap300), the automatic bookmark system (Version 1.0) and a p-value cutoff <0.005. In BeadStudio (version 2.3.43), data from the same Infinium® assay can be combined, but at present this is not applicable to different types of arrays, such as Infinium® I and II. Therefore we performed a parallel analysis of the two array platforms (detailed output in Supplementary Table S1).
