Affymetrix SNP array data for chronic lymphoblastic leukemia samples

Ibrutinib (Ibr), an orally administered covalent inhibitor of Bruton’s kinase, has generated remarkable responses in CLL patients including those with an unfavorable cytogenetic profile. Once patients develop resistance to ibrutinib, the outcome is poor with few treatment options. To further understand the genomic mechanisms underlying Ibr resistance, we’ve performed genome wide copy number analysis of serial samples collected from nine ibrutinib-relapsed patients. Deletions of 18p often coincide with del(17p)/TP53 mutations, predispose patients to relapse. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from diagnostic bone marrow, peripheral blood or lymph node samples. Copy number analysis of Affymetrix CytoScan or OncoScan SNP arrays was performed on a total of 26 samples collected from 9 patients included in the study. Please note that OncoScan arrays produce 2 CEL files generated from 2 separate chips that are subsequently converted and combined into one OSCHP file.