PhD Scientific Days 2021

PO_II_L: Pathology and Oncology II. Lectures

Comprehensive Profiling of DNA Copy Number Aberrations with Digital Multiplex Ligation-dependent Probe Amplification in Pediatric B-cell Acute Lymphoblastic Leukemia

Text of the abstract

Acute lymphoblastic leukemia (ALL) is the most common malignant disease of childhood. The genomic landscape of pediatric ALL is heterogeneous with various copy number aberrations being detectable in vast majority of the cases. Several of these unbalanced alterations define genetic subtypes and provide prognostic and predictive information. To assess DNA copy number aberration profile in the Hungarian pediatric ALL population, we comprehensively investigated the disease-relevant copy number aberrations using a recently introduced next-generation sequencing based technique on a large cohort of patients with pediatric ALL. Diagnostic bone marrow samples from 215 children with B-cell ALL and 18 additional matching samples drawn at relapse were profiled by digital multiplex ligation-dependent probe amplification (digitalMLPA) using the ALL-specific D007 probemix. DigitalMLPA libraries were sequenced on an Illumina MiSeq platform, the bioinformatic analysis was performed using the Coffalyser digitalMLPA software. Whole chromosome gains and losses, subchromosomal copy number changes and unbalanced aberrations conferring intrachromosomal gene fusions were simultaneously identified. Copy number aberrations were detected in 89.3% of the samples. Subtype-defining alterations were identified in 30.5% of the patients with hyperdiploidy and internal amplification of chromosome 21 detected in 28.3% and 2.2% of the cases, respectively. Beyond that, numerous copy number changes in disease-relevant genes were identified (e.g. CDKN2A 25.3%, ETV6 23.2%, CDKN2B 21.9%, IKZF1 21.5% and PAX5 14.6%). Comparative analysis of diagnostic and matching relapse samples revealed characteristic temporal changes of copy number profiles with (i) additional aberrations, (ii) lost copy number aberrations, (iii) both emerging and disappearing copy number aberrations detected at relapse as compared to diagnosis, or (iv) the diagnostic and relapse sample pairs displayed identical copy number profiles. Comprehensive copy number aberration profiling with digitalMLPA revealed subtype-defining gross-chromosomal change status, and other disease-relevant sub-chromosomal copy number alterations in a large Hungarian pediatric ALL population. This technique may offer a fast and affordable copy number analysis implementable in the diagnostic workflow of ALL.
EFOP-3.6.3-VEKOP-16-2017-00009, NKFIH FK134253

University and Doctoral School

Semmelweis University, Doctoral School of Pathological Sciences