Immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements provide clonal markers useful for diagnosis and measurement of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL). We analyzed the sequences of Ig and TCR gene rearrangements obtained at presentation and relapse in 41 children with ALL to study clonal stability, which has important implications for monitoring MRD, during the course of the disease. In 42%, all original Ig and/or TCR sequences were conserved. In 24%, one original sequence was preserved but the other lost, and in 14% the original sequences were conserved with new sequences identified at relapse. In 20% only new sequences were found at relapse. Using primers designed from the novel relapse sequences, the relapse clone could be identified as subdominant clones in the diagnostic sample in 8 of 14 patients. Alteration of these clonal gene rearrangements is a common feature in childhood ALL. MRD IntroductionAdvances in cytogenetic and immunophenotypic characterization have greatly improved the diagnostic accuracy and risk assignment of childhood acute lymphoblastic leukemia (ALL) 1 resulting in cure rates approaching 80%, 2,3 however relapse still occurs in about 20% of children. Monitoring of minimal residual disease (MRD) has proved useful for predicting which children will relapse. [4][5][6][7][8][9][10] Most studies of MRD detection in pediatric ALL have used polymerase chain reaction (PCR)-based techniques. 4,8,10,11 Immunoglobulin heavy chain (IgH) and T-cell receptor (TCR) gene rearrangements appear to be excellent patient-specific PCR targets for MRD detection, but, of concern, these rearrangements may be unstable due to clonal evolution during the course of the disease. [12][13][14][15][16][17] Rearranged Ig and TCR genes have been used as molecular markers for characterization of clonality of lymphoid cell population. 11,18,19 Generally, it is assumed that the relapses result from outgrowth of residual leukemic cells that persist in patients below the limits of detection of standard techniques. 19,20 It has also been postulated that the "original" leukemia may in some cases be cured, but a "new," therapy-related secondary leukemia can develop. 21 Discrimination between those cases that relapse because of the re-emergence of the initial ALL and the occurrence of secondary ALL might be clinically important to guide subsequent therapy. A number of studies using Southern blotting or PCR amplification have previously demonstrated diverse patterns of the antigen receptor gene rearrangements in a larger proportion (10%-40%) of relapsed childhood ALL. [22][23][24] Sequence analysis has provided some insight into the molecular mechanisms that account for altered rearrangement patterns, including ongoing rearrangements (eg, V H to D H J H joining, V H -V H replacement, and "open-and-shut" mechanism), disappearance of initial clone/subclones, and generation of new clone/subclones. [13][14][15][24][25][26] TCR and Ig kappa delete element (Ig-de) rearrangements have been...

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