Array based genetic profiling of chronic lymphocytic leukemia

University dissertation from Department of Laboratory Medicine, Lund University

Abstract: Although no common genetic defect has been described in chronic lymphocytic leukemia (CLL), recurrent genomic aberrations (i.e. deletions of chromosome 11q, 13q, 17p and trisomy 12) are important for prognostication. Deletion of 13q as single aberration is associated with the best prognosis, whereas del(11q) and del(17p) predict a poor outcome. Recent development of high-resolution genomic techniques, i.e. microarrays, provides effective detection of the known recurrent aberrations and simultaneous exploration of the whole genome. Hence, this thesis aimed to map genomic aberrations in CLL through application of high-resolution microarrays. In paper I, we investigated the pros and cons of four differently designed microarray platforms. All platforms readily detected the known recurrent aberrations in CLL as well as other large copy-number aberrations (CNAs). The difference in technical performance and discrepancies in detection of small CNAs were influenced by differential platform density, different reference sets, and platform-specific analysis. In paper II and IV, 250K single nucleotide polymorphism (SNP)-array screening of 203 and 370 samples, respectively, detected CNAs in >90% and the known recurrent aberrations in >70% of patients. Moreover, novel recurrent gains of chromosome 2p in combination with 11q deletion and copy-number neutral loss of heterozygosity on chromosome 13q were revealed. Furthermore, a high genomic complexity was correlated to worse survival, but also closely linked to poor-prognostic markers. In addition, study IV also included follow-up samples (n=43) to investigate clonal evolution, which showed that patients with unmutated immunoglobulin heavy chain variable (IGHV) genes and treated patients with mutated IGHV genes often gained novel aberrations. In paper III, high-density screening revealed a different spectrum of genomic aberrations in CLL patients with ‘stereotyped’ IGHV3-21 (poor-prognostic) versus IGHV4-34 (good-prognostic) B-cell receptors. IGHV3-21 subset #2 (n=29) showed a high frequency of samples carrying genomic aberrations, and a particularly high prevalence of del(13q) and del(11q), which may correspond to the adverse survival reported for these patients. In contrast, IGHV4-34 subset #4 (n=17) showed a lower frequency and complexity of CNAs, which may reflect an inherent low-proliferative disease, preventing accumulation of genomic alterations. In summary, the studies included in this thesis provided a greater insight of genomic aberrations in newly diagnosed patients, at follow-up and in different subgroups of CLL.