High-throughput sequencing of clonal TCR alpha genes rearrangements in pediatric T-lineage acute lymphoblastic leukemia

Introduction:

Relapses are still the major cause of poor outcome in therapy of T-lineage acute lymphoblastic leukemia (T-ALL) in children. Over 30% cases of relapse in T-ALL are accompanied by changing of the main clones. At the present time the most reliable markers for analysis of clonal structure of T-ALL are rearrangements of T-cell receptors (TCR) genes: TCR beta, gamma and delta. The purpose of this study is identification and characterization a new type of clonal markers based on previously unanalyzed in ALL rearrangements of TCR alpha locus.

Material and Methods:

Detection of TCR alpha genes rearrangements was based on high-throughput sequencing of amplicons obtained in series of multiplex PCR with genomic DNA from bone marrow and primers for all major V- and J-genes combination of TCR alpha locus.

Results:

We analyzed 75 samples of T-ALL in which we identified over 90 clonal rearrangements of TCR alpha locus. 15 samples contained rearrangements with clonal rate more than 40%, 37 samples contained 1 – 4 rearrangements with lower clonal rate (5 – 35%), 23 samples didn't contain any leukemia specific TCR alpha rearrangements.

Conclusion:

For the first time we evaluated frequency of clonal rearrangements of TCR alpha locus in pediatric T-ALL. This type of markers is presented in more than half of T-ALL cases what makes them fully applicable for analysis of clonal structure of T-ALL in both onset and relapse.

Funding: Russian Science Foundation grant # 17 – 75 – 10113.