Copy number analysis of DCIS with and without recurrence

We analysed a cohort of pure DCIS cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included those without recurrence within 6 years (n=25) and with recurrence between 1-5 years after diagnosis (n=15). Additional cases were excluded for low grade (n=6) or non-clonal recurrence (n=2). Recurrence tumour was available for 8 cases. Pure DCIS were broadly similar in copy number changes compared to invasive breast cancer, with the consistent exception of a greater frequency of ERBB2 amplification in DCIS. There were no significant differences in age or ER status between the cases with a recurrence versus those without. Overall, the DCIS cases with recurrence had more copy number events than the DCIS without recurrence. The increased copy number appeared non-random with several genomic regions showing an increase in frequency in recurrent cases including 20q gain, ERBB2 amplification and 15q loss. Copy number changes may provide prognostic information for DCIS recurrence but validation in additional cohorts is required. 48 cases of synchronous DCIS and IDC were microdissected from FFPE tissue and analysed by molecular inversion probe (MIP) copy number arrays. The arrays were a mixture of early and later release OncoScan arrays and the data for early release cases in this submission are CN values for the ~300,000 probes common to two batches performed. Raw data is retained by Affymetrix.