Cyto2.7M copy number analysis of eight diffuse large B-cell samples and one matched blood sample

We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the Cyto2.7M data. GEO submission, GSE37977 contains the SNP6.0 data. DNA was extracted from eight samples of diffuse-large B-cell lymphoma with complex genomic rearrangements using the DNeasy Blood & Tissue kit (Qiagen) following manufactures instructions. DNA was also included from one matched blood sample where mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific). Copy number analysis of Affymetrix cytogenetic 2.7M whole-genome arrays was performed on eight diffuse large B-cell samples and one matched blood sample.