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Abstract Background Based on the site of breakpoint in t(9;22) (q34;q11), <it>bcr-abl </it>fusion in leukemia patients is associated with different types of transcript proteins. In this study we have seen the association of HLA genes with different types of <it>bcr-abl </it>transcripts. The association could predict the <it>bcr-abl </it>peptide presentation by particular HLA molecules. Methods The study included a total of 189 patients of mixed ethnicity with chronic myelogenous leukemia and acute lymphocytic leukemia who were being considered for bone marrow transplantation. Typing of <it>bcr-abl </it>transcripts was done by reverse transcriptase PCR method. HLA typing was performed by molecular methods. The <it>bcr-abl </it>and HLA association was studied by calculating the relative risks and chi-square test. Results Significant negative associations (<it>p </it>< 0.05) were observed with HLA-A*02 (b2a2, e1a2), -A*68 (b2a2, b3a2, e1a2), -B*14 (b2a2, b3a2, e1a2), -B*15 (b2a2, b3a2), -B*40 (b2a2), -DQB1*0303 (b2a2, b3a2), -DQB1*0603 (b2a2), -DRB1*0401 (e1a2), -DRB1*0701 (b3a2), and -DRB1*1101 (b2a2). Conclusions The negative associations of a particular <it>bcr-abl </it>transcript with specific HLA alleles suggests that these alleles play a critical role in presenting peptides derived from the chimeric proteins and eliciting a successful T-cell cytotoxic response. Knowledge of differential associations between HLA phenotypes and <it>bcr-abl </it>fusion transcript types would help in developing better strategies for immunization with the <it>bcr-abl </it>peptides against t(9;22) (q34;q11)-positive leukemia.</p

Association of HLA Class I and Class II genes with bcr-abl transcripts in leukemia patients with t(9;22) (q34;q11)