Although multiple instances of chronic lymphocytic leukaemia in some families, and low frequency of the disease in individuals of Japanese origin, suggest that genetic effects might be stronger than environmental factors in the pathogenesis of chronic lymphocytic leukaemia, the nature of this genetic predisposition remains uncertain and different genes may be involved in different families. A recent paper has identified a family in which a single nucleotide polymorphism down-regulates the expression of DAPK1 transcription. The same polymorphism has been identified in one sporadic case of chronic lymphocytic leukaemia, but not in other familial cases. DAPK1 is a pro-apoptotic protein whose expression is also suppressed in sporadic cases of chronic lymphocytic leukaemia by an epigenetic mechanism.  The many unsuccessful attempts to establish genetic linkages have been reviewed by Goldin and Slager. None of the reported genetic aberrations is constant, and whether they constitute initial events or arise during evolution is presently unclear. By contrast with observations in other B-cell malignant diseases, which typically exhibit balanced chromosomal translocations, in chronic lymphocytic leukaemia the most frequent abnormalities are mutations, deletions, or trisomies. Translocations do arise but are usually unbalanced, resulting in loss of genetic material.
Early attempts at karyotyping chronic lymphocytic leukaemia cells identified trisomy 12 and deletions at 13q, but most laboratories were unable to satisfactorily bring chronic lymphocytic leukaemia cells into mitosis. Only in the past few years have cytogenetic techniques been developed that make this proposition feasible. and  Döhner and colleagues showed in a series of 325 patients with chronic lymphocytic leukaemia that chromosomal aberrations can be detected in interphase cells by fluorescence in-situ hybridisation (FISH) in 82% of cases. The most frequent alterations are a deletion on chromosome 13q (55%), trisomy 12 (18%), and a deletion on chromosome 11q (16%). A deletion on chromosome 17p, affecting the TP53 protein, is seen less frequently (7%). The presence of a 17p or 11q deletion is associated with poor prognosis and predominates in advanced stages of chronic lymphocytic leukaemia and in patients with unmutated IGHV genes, whereas the 13q deletion or a normal karyotype are associated with good prognosis, initial stages of the disease, and mutated IGHV genes. Controversy exists about whether trisomy 12 is associated with an unmutated status and poor prognosis. and  Patients with mutated and unmutated chronic lymphocytic leukaemia differ clearly in terms of prognosis.
Genetic lesions associated with deletions of the short arm of chromosome 17 (del17p13), which encodes the TP53 tumour-suppressor gene, and the long arm of chromosome 11 (del11q23), which encodes the ataxia telangiectasia mutated (ATM) gene, result in a loss of function of TP53. TP53 is a transcription factor activated by strand breaks in DNA. It can trigger apoptosis or cell-cycle arrest. Thus, by controlling repair or elimination of cells with damaged DNA, TP53 maintains the integrity of the genome and prevents clonal progression. ATM is a kinase that regulates TP53. Many cytotoxic drugs require the ATM/TP53 pathway to be intact for them to be effective. A simple screening test that assesses how intact this pathway is has been described. Defects in the ATM/TP53 pathway constitute the strongest independent predictors for disease that is resistant to standard treatment.
Deletions of the ATM gene do not produce such a severe syndrome as do deletions of TP53, with some patients having a fairly benign disease course. Possibly, for ATM function to be impaired, mutations are necessary on the other ATM allele. Conversely, Kalla and co-workers have identified other genes affecting regulation of the cell cycle and apoptosis—namely NPAT, CUL5, and PPP2R1B—in the commonly deleted 11q22-q23 segment, which might underlie the severity of the chronic lymphocytic leukaemia.
The pathogenic role of trisomy 12 in chronic lymphocytic leukaemia remains unresolved. CLLU1—the first disease-specific gene identified in people with chronic lymphocytic leukaemia—has been located to 12q22, but there seems to be no difference in protein expression in patients with or without trisomy 12.
MicroRNA molecules (miRNAs) have an important role in regulation of gene expression during human development. Using a microarray containing hundreds of human precursors and mature miRNA oligonucleotide probes, Calin and colleagues recorded significant differences in miRNA expression between chronic lymphocytic leukaemia B cells and normal CD5+ cells. They showed the absence of two miRNAs (miR15 and miR16) associated with mutations in expressed IGHV genes and with deletions in the 13q14 region. As part of normal control of gene expression, miR15 and miR16 seem to target BCL2, and their absence in chronic lymphocytic leukaemia could be a major factor in prevention of apoptosis. However, Fulci and coworkers  have been unable to confirm these findings. They reported low expression of these miRNAs in only 12% of patients, despite 58% having del13q14. All individuals with a deletion of both 13q14 alleles showed striking miR15a downregulation, but such pronounced downregulation of both miRNAs was not paralleled by any significant increase in BCL2 expression levels. Fulci's team also noted overexpression of miR150, miR223, and miR29b and miR29c in IGHV-mutated chronic lymphocytic leukaemia compared with unmutated cases.
Despite clinical and molecular differences, chronic lymphocytic leukaemia is characterised by a common gene-expression signature that differs from other lymphoid cancers and normal lymphoid subpopulations, suggesting that patients with the disease—in agreement with the monotonous phenotypic signature—share a common mechanism of transformation, cell of origin, or both.  However, despite sharing a common signature, chronic lymphocytic leukaemias expressing mutated and unmutated IGHV genes differentially express more than 100 genes. Of these, overexpression of genes encoding ZAP70, lipoprotein lipase (LPL), BCL7A, dystrophin (DMD), and gravin (AKAP12) are noted in individuals with aggressive unmutated disease, whereas people with stable mutated chronic lymphocytic leukaemia overexpress WNT3, CTLA4, the gene encoding nuclear receptor interacting protein 1 (NRIP1), ADAM29, and TCF7.,  and  Furthermore, evidence suggests that for particular IGHV genes, such as IGHV1-69 and IGHV3-21, different genomic aberrations might be associated with differential gene expression.,  and  These results indicate that indolent mutated and aggressive unmutated chronic lymphocytic leukaemias constitute two variants of the same disease. The reasons for these striking differences in clinical outcomes remain unsolved.
63 A Raval, SM Tanner and JC Byrd et al., Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia, Cell 129 (2007), pp. 879–890.
64 LR Goldin and SL Slager, Familial CLL: Genes and Environment, Hematology Am Soc Hematol Educ Program 2007 (2007), pp. 339–345.
65 F Dicker, S Schnittger, T Haferlach, W Kern and C Schoch, Immunostimulatory oligonucleotide-induced metaphase cytogenetics detect chromosomal aberrations in 80% of CLL patients: a study of 132 CLL cases with correlation to FISH, IgVH status, and CD38 expression, Blood 108 (2006), pp. 3152–3160.
66 G Juliusson, DG Oscier and M Fitchett et al., Prognostic subgroups in B-cell chronic lymphocytic leukemia defined by specific chromosomal abnormalities, N Engl J Med 323 (1990), pp. 720–724.
67 DG Oscier, AC Gardiner and SJ Mould et al., Multivariate analysis of prognostic factors in CLL: clinical stage, IGVH gene mutational status, and loss or mutation of the p53 gene are independent prognostic factors, Blood 100 (2002), pp. 1177–1184.
68 A Krober, T Seiler and A Benner et al., V(H) mutation status, CD38 expression level, genomic aberrations, and survival in chronic lymphocytic leukemia, Blood 100 (2002), pp. 1410–1416.
69 K Lin, PD Sherrington, M Dennis, Z Matrai, JC Cawley and AR Pettitt, Relationship between p53 dysfunction, CD38 expression, and IgV(H) mutation in chronic lymphocytic leukemia, Blood 100 (2002), pp. 1404–1409.
70 B Austen, JE Powell and A Alvi et al., Mutations in the ATM gene lead to impaired overall and treatment-free survival that is independent of IGVH mutation status in patients with B-CLL, Blood 106 (2005), pp. 3175–3182.
70 C Kalla, MO Scheuermann and I Kube et al., Analysis of 11q22-q23 deletion target genes in B-cell chronic lymphocytic leukaemia: evidence for a pathogenic role of NPAT, CUL5, and PPP2R1B, Eur J Cancer 43 (2007), pp. 1328–1335.
72 D Winkler, C Schneider and A Krober et al., Protein expression analysis of chromosome 12 candidate genes in chronic lymphocytic leukemia (CLL), Leukemia 19 (2005), pp. 1211–1215.
73 AM Buhl, J Jurlander and FS Jorgensen et al., Identification of a gene on chromosome 12q22 uniquely overexpressed in chronic lymphocytic leukemia, Blood 107 (2006), pp. 2904–2911.
74 GA Calin, CG Liu and C Sevignani et al., MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias, Proc Natl Acad Sci USA 101 (2004), pp. 11755–11760.
75 A Cimmino, GA Calin and M Fabbri et al., miR-15 and miR-16 induce apoptosis by targeting BCL2, Proc Natl Acad Sci USA 102 (2005), pp. 13944–13949.
76 V Fulci, S Chiaretti and M Goldoni et al., Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia, Blood 109 (2007), pp. 4944–4951.
77 U Klein, Y Tu and GA Stolovitzky et al., Gene expression profiling of B cell chronic lymphocytic leukemia reveals a homogeneous phenotype related to memory B cells, J Exp Med 194 (2001), pp. 1625–1638.
78 A Wiestner, A Rosenwald and TS Barry et al., ZAP-70 expression identifies a chronic lymphocytic leukemia subtype with unmutated immunoglobulin genes, inferior clinical outcome, and distinct gene expression profile, Blood 101 (2003), pp. 4944–4951.
79 Y Vasconcelos, J De Vos and L Vallat et al., Gene expression profiling of chronic lymphocytic leukemia can discriminate cases with stable disease and mutated Ig genes from those with progressive disease and unmutated Ig genes, Leukemia 19 (2005), pp. 2002–2005.
80 D Kienle, A Benner and A Krober et al., Distinct gene expression patterns in chronic lymphocytic leukemia defined by usage of specific VH genes, Blood 107 (2006), pp. 2090–2093.
81 DL Kienle, C Korz and B Hosch et al., Evidence for distinct pathomechanisms in genetic subgroups of chronic lymphocytic leukemia revealed by quantitative expression analysis of cell cycle, activation, and apoptosis-associated genes, J Clin Oncol 23 (2005), pp. 3780–3792.
82 C Haslinger, N Schweifer and S Stilgenbauer et al., Microarray gene expression profiling of B-cell chronic lymphocytic leukemia subgroups defined by genomic aberrations and VH mutation status, J Clin Oncol 22 (2004), pp. 3937–3949.