Clinical Impact of Genomic Information in Pediatric Leukemia

Abstract

Pediatric leukemia remains a significant contributor to childhood lethality rates. However, recent development of new technologies including next-generation sequencing (NGS) has increased our understanding of the biological and genetic underpinnings of leukemia, resulting in novel diagnostic and treatment paradigms. The most prevalent pediatric leukemias include B-cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). These leukemias are highly heterogeneous, both clinically and genetically. There are multiple genetic subgroups defined by the World Health Organization, each with distinct clinical management. Clinical laboratories have started adopting genomic testing strategies to include high-throughput sequencing assays which, together with conventional cytogenetic techniques, enable optimal patient care. This review summarizes genetic and genomic techniques used in clinical laboratories to support management of pediatric leukemia, highlighting technical, biological, and clinical advances. We illustrate clinical utilities of comprehensive genomic evaluation of leukemia genomes through clinical case examples, which includes the interrogations of hundreds of genes and multiple mutation mechanisms using NGS technologies. Finally, we provide a future perspective on clinical genomics and precision medicine.

Keywords: diagnosis; genomic profiling; pediatric leukemia; prognosis; therapy.

Figure 1

Representations of different genomic alterations identified by CHOP Comprehensive Hematological Cancer Panel. (A) a PAX2–JAK2 fusion detected in an 11-month-old patient with residual/recurrent B-cell lymphoblastic leukemia. Double arrowed line indicates exon 5 of PAX2 is fused to exon 19 of JAK2, gray area indicates reading depth, red and blue horizontal bars are representative reads. (B) Copy number analysis using next-generation sequencing data from a patient with iAMP ALL. (B-1) Copy number variations analysis based on reading depth; red arrow indicates four copies of RUNX1 genomic region. (B-2) B-allele frequency analysis demonstrating SNP separation due to triplication of one allele; red arrows indicate genotype information of AAAB and ABBB (the genotype would be AABB if it were duplication of both allele). (B-3) FISH showing two ETV6 signals (green) and 4 RUNX1 signals (red). (C) IGV view showing a FLT3 ITD in an 11-year-old patient with acute myeloid leukemia.

Figure 2

A novel GOLGA5–JAK2 fusion was identified in an 11-year-old boy with very high-risk acute lymphoblastic leukemia. (A) Schematic representation of protein domains of the GOLGA5–JAK2 fusion protein. (B) Sanger confirmation of the GOLGA5–JAK2 fusion. The red arrow indicates the breakpoint of the fusion transcript. (C) Gel electrophoresis of nested polymerase chain reaction (PCR) products from the diagnostic bone marrow sample; F1R1—PCR product of inner forward and reverse primers; F2R2—PCR product of outer forward and reverse primers.