MS von Bergwelt-Baildon 1,2 , A Shimabukuro-Vornhagen 1,2 , CM Wendtner 3 and E Kondo 4 1 Laboratory for Tumor and Transplantation Immunology, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; 2 Stem Cell Transplantation Program, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; 3 Laboratory for Molecular Biology and Immunology of CLL, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany and 4 Department of Hematology and Oncology, Okayama University Hospital, Okayama, Japan E-mail: michael.von-bergwelt-baildon@uk-koeln.de References 1 Wang M, Sun L, Qian J, Han X, Zhang L, Lin P et al. Cyclin D1 as a universally expressed mantle cell lymphoma- associated tumor antigen for immunotherapy. Leukemia 2009; 23: 1320–1328. 2 Kondo E, Maecker B, Weihrauch MR, Wickenhauser C, Zeng W, Nadler LM et al. Cyclin D1-specific cytotoxic T lymphocytes are present in the repertoire of cancer patients: implications for cancer immunotherapy. Clin Cancer Res 2008; 14: 6574–6579. 3 Kondo E, Gryschok L, Schultze JL, von Bergwelt-Baildon MS. Using CD40-activated B cells to efficiently identify epitopes of tumor antigens. J Immunother 2009; 32: 157–160. 4 Sadovnikova E, Jopling LA, Soo KS, Stauss HJ. Generation of human tumor-reactive cytotoxic T cells against peptides presented by non-self HLA class I molecules. Eur J Immunol 1998; 28: 193–200. 5 Kessler JH, Melief CJ. Identification of T-cell epitopes for cancer immunotherapy. Leukemia 2007; 21: 1859–1874. 6 Alexander-Miller MA, Leggatt GR, Berzofsky JA. Selective expan- sion of high- or low-avidity cytotoxic T lymphocytes and efficacy for adoptive immunotherapy. Proc Natl Acad Sci USA 1996; 93: 4102–4107. 7 Kondo E, Maecker B, Draube A, Klein-Gonzalez N, Shimabukuro- Vornhagen A, Schultze JL et al. The shared tumor associated antigen cyclin-A2 is recognized by high-avidity T-cells. Int J Cancer 2009, E-pub ahead of print 8 June 2009, DOI: 10.1002/ijc.24629. 8 Speiser DE, Baumgaertner P, Voelter V, Devevre E, Barbey C, Rufer N et al. Unmodified self antigen triggers human CD8T cells with stronger tumor reactivity than altered antigen. Proc Natl Acad Sci USA 2008; 105: 3849–3854. 9 Rubio V, Stuge TB, Singh N, Betts MR, Weber JS, Roederer M et al. Ex vivo identification, isolation and analysis of tumor-cytolytic T cells. Nat Med 2003; 9: 1377–1382. Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients Leukemia (2010) 24, 211–215; doi:10.1038/leu.2009.187; published online 10 September 2009 The known recurrent genomic aberrations, that is deletions of 11q, 13q, 17p and trisomy 12, are important prognostic markers, which reliably predict clinical outcome in chronic lymphocytic leukemia (CLL) patients. 1 Approximately 50% of CLL patients carry deletions of 13q, which is correlated with an indolent disease course when detected as a sole aberration. In contrast, deletions of 11q and 17p, which cover the ATM and TP53 gene, respectively, are associated with poor prognosis. Furthermore, trisomy 12 is related to an intermediate prognosis, whereas deletion of 6q has been identified as a recurrent CLL progression marker. 1,2 Genomic microarrays are widely used for screening of copy- number alterations (CNAs) in cancers. Several studies on CLL have provided additional information on genome-wide altera- tions, such as gain of 2p and deletion of 22q. 3,4 Recently, an SNP-array (50K) study showed an association between genomic complexity (X3 CNAs/sample) and time to first or second treatment as clinical end points. 5 To date, copy-number neutral loss of heterozygosity has been identified on chromosome 11p, 13q, and 17p in CLL, 3,6 although the biological or clinical significance remains unknown. In this study, we applied high-density SNP arrays for evaluation of genomic alterations and their clinical impact in 203 newly diagnosed CLL patients. All patients were selected from the Swedish part of a Scandinavian population-based case– control study called SCALE (Scandinavian Lymphoma Etiol- ogy). 7 Peripheral blood samples were collected during 1999– 2001, within a median of 3 months from diagnosis (range, 0–18 months) and follow-up was achieved in 2008 (median follow-up time 91 months). All samples showed a typical immunopheno- type and 470% tumor cells. Clinical data obtained from medical records is presented in Table 1. Genomic DNA was extracted and subjected to Affymetrix GeneChip Mapping 250K Nsp1 arrays as described earlier. 8 All raw and normalized data from the SNP arrays can be accessed through Gene Expression Omnibus (http://www.ncbi.nlm.nih. gov/geo, accession number: GSE16406). Copy-number analysis for detection of CNAs was performed in the BioDiscovery Nexus Copy Number 3.0 software (BioDiscovery Inc., El Segundo, CA, USA) using the built-in Rank Segmentation algorithm. We performed validation experiments with quantitative real-time PCR on genomic DNA to define the optimal setting for detection of CNAs in the copy-number analysis (primer sequences are available on request). A high number of verified alterations (23 of 27, 85%) was found for regions 4200 kbp, when applying P ¼ 1 Â 10 À6 in the copy-number analysis, thus applied for the detection of CNAs in all samples. Moreover, different cutoffs in log 2 ratio for regions 200–500 kb and regions 4500 kb were applied (log 2 ratio 0.2 and 0.15, respectively), as longer stretches of SNPs are less likely to be affected by technical fluctuations. Furthermore, to avoid inclusion of copy-number variations, which exist as genomic variants in the population, regions overlapping 450% with reported copy-number variations were removed from further analysis. We here report that 182 samples (90%) of the 203 CLL samples investigated carried CNAs, whereas 21 samples (10%) presented a normal karyotype. In total, 455 aberrations were identified and losses were more commonly detected than gains, 70% vs 30%, respectively. The majority of samples (75%) carried between 1 and 3 CNAs. Moreover, the known recurrent aberrations were detected in 74% of patients and constituted approximately one-third of the total CNAs in this cohort of Letters to the Editor 211 Leukemia