APC and Familial adenomatous polyposis: In order to enrich for tumours with LOH [2] and to reduce the frequency of confounding background events – such as copy number changes related to chromosomal instability in late lesions – we analysed early colorectal adenomas from FAP patients who harboured germline mutations close to codon 1300 of APC. Since these lesions were generally available as FFPE specimens, we set up a custom SNP array (see Additional File 2) using the Illumina Goldengate platform that has previously proved suitable for LOH analysis [11].