Longitudinal Genome Wide Analysis of Chronic Lymphocytic Leukemia Reveals Complex Evolution of Clonal Architecture at Disease Progression and at the Time of Relapse

Little is known about the extent of intraclonal heterogeneity of CLL tumor cells. We performed longitudinal whole genome analysis in 22 CLL cases with evidence of clinical progression and/or clinical relapse post therapy. We demonstrate the striking and unanticipated presence of genetic clonal heterogeneity, with at least 27% of patients exhibiting clonal evolution and 18% showing evidence of multiple subclones. We show that CLL progression can occur with multiple genetic subclones evolving either in a linear or branching manner. The analysis reveals a shift in the relative dominance of subclones with the emergence of initially minor clones after therapy all of which were very resistant to secondary therapies. This study uncovers the clinical importance of tracking subclone diversity in CLL. All patients had genome wide genetic analysis performed by aCGH on at least two sequential tumor samples >6 months apart. For the purposes of this study, we classified samples as; time point 1 (TP1) collected >6 months before starting first-line treatment for disease progression; time point 2 (TP2) consisting of tumor samples at the time of progression requiring treatment; and time point 3 (TP3) consisting of tumor samples collected >6 months after initial treatment but prior to subsequent treatments. Overall, aCGH assay was performed in 54 samples from 22 patients (2 to 4 time points analyzed per patient). Thus, 6 patients were analyzed at TP1 and TP2, 8 patients at TP2 and TP3, 2 patients at TP1 and TP3, and the remaining 6 patients were analyzed at TP1, TP2 and TP3. Keyword : array comparative genomic hybridization