Integrated Genomic Analysis of Chromosomal Alterations and Mutations in B-Cell Acute Lymphoblastic Leukemia Reveals Distinct Genetic Profiles at Relapse

• Main Authors: Maribel Forero-Castro, Adrián Montaño, Cristina Robledo, Alfonso García de Coca, José Luis Fuster, Natalia de las Heras, José Antonio Queizán, María Hernández-Sánchez, Luis A. Corchete-Sánchez, Marta Martín-Izquierdo, Jordi Ribera, José-María Ribera, Rocío Benito, Jesús M. Hernández-Rivas
• Format: Article
• Language: English
• Published: MDPI AG 2020-07-01
• Series: Diagnostics
• Subjects: acute lymphoblastic leukemia (ALL); relapse; next-generation sequencing (NGS); array comparative genomic hybridization (aCGH); multiplex ligation-dependent probe amplification (MLPA); <i>IKZF1</i>
• Online Access: https://www.mdpi.com/2075-4418/10/7/455

The clonal basis of relapse in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is complex and not fully understood. Next-generation sequencing (NGS), array comparative genomic hybridization (aCGH), and multiplex ligation-dependent probe amplification (MLPA) were carried out in matched diagnosis–relapse samples from 13 BCP-ALL patients to identify patterns of genetic evolution that could account for the phenotypic changes associated with disease relapse. The integrative genomic analysis of aCGH, MLPA and NGS revealed that 100% of the BCP-ALL patients showed at least one genetic alteration at diagnosis and relapse. In addition, there was a significant increase in the frequency of chromosomal lesions at the time of relapse (<i>p</i> = 0.019). MLPA and aCGH techniques showed that <i>IKZF1</i> was the most frequently deleted gene. <i>TP53</i> was the most frequently mutated gene at relapse. Two <i>TP53</i> mutations were detected only at relapse, whereas the three others showed an increase in their mutational burden at relapse. Clonal evolution patterns were heterogeneous, involving the acquisition, loss and maintenance of lesions at relapse. Therefore, this study provides additional evidence that BCP-ALL is a genetically dynamic disease with distinct genetic profiles at diagnosis and relapse. Integrative NGS, aCGH and MLPA analysis enables better molecular characterization of the genetic profile in BCP-ALL patients during the evolution from diagnosis to relapse.