Whole-Exome Sequencing of ETV6/RUNX1 in Four Childhood Acute Lymphoblastic Leukaemia Cases

Background: ETV6/RUNX1 gene fusion is the most frequently seen chromosomal abnormality in childhood acute
lymphobastic leukamia (ALL). However, additional genetic changes are known to be required for the development of
this type of leukaemia. Therefore, we here aimed to assess the somatic mutational profile of four ALL cases carrying the
ETV6/RUNX1 fusion gene using whole-exome sequencing. Methods: DNA was isolated from bone marrow samples
using a QIAmp DNA Blood Mini kit and subsequently sequenced using the Illumina MiSeq system. Results: We
identified 12,960 to17,601 mutations in each sample, with a total of 16,466 somatic mutations in total. Some 15,533
variants were single nucleotide polymorphisms (SNPs), 129 were substitutions, 415 were insertions and 389 were
deletions. When taking into account the coding region and protein impact, 1,875 variants were synonymous and 1,956
were non-synonymous SNPs. Among non-synonymous SNPs, 1,862 were missense, 13 nonsense, 35 frameshifts, 11
nonstop, 3 misstart, 15 splices disrupt and 17 in-frame indels. A total of 86 variants were located in leukaemia-related
genes of which 32 variants were located in the coding regions of GLI2, SP140, GATA2, SMAD5, KMT2C, CDH17,
CDX2, FLT3, PML and MOV10L1. Conclusions: Detection and identification of secondary genetic alterations are
important in identifying new therapeutic targets and developing rationally designed treatment regimens with less
toxicity in ALL patients.