With the sharply decreased cost of sequencing and the
improvement of bioinformatics analyses (both the computer
power as well as the development of new algorithms to analyze
the big sequencing data), it is possible to conduct sequencing
analyses in large patient cohorts and systematically investigate
hundreds of target genes or even all genes. For instance, the land-
scape of somatic mutations in target 633 epigenetic regulator genes
across 1000 pediatric cancer genomes has been profiled, identifying
the most frequent mutations inH3F3A,PHF6,ATRX,KDM6A,
SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1,
NSD2,SETD2,SMC1A, andZMYM3. Not surprisingly, different
gene mutations tend to enrich in distinct subtypes of ALL [160].
According to the comprehensive investigation of ALL gen-
omes, their somatic mutation load is significantly lower than adult
solid tumors probably due to the limited time for mutation accu-
mulation, mostly with less than 10–20 non-silent mutations per
patients [164]. For instance, MLL-rearranged leukemia in infancy
has one of the lowest somatic mutation frequencies of any described
tumor [61, 165], while focal deletions that normally mediate the
process of lymphoid antigen receptor gene rearrangement are the
most common type of structural genetic alterations observed in
ALL [62, 158]. Of the most important findings for classification of
molecular subtypes, a comprehensive profiling has been conducted
in BCR-ABL1-like ALL (10–15% of pediatric ALL or over 25% of
adults ALL) and further divided these patients into several groups
in terms of their molecular features, which are screened in both
genomic and transcriptome levels. BCR-ABL1-like ALL is also
characterized by a diverse range of genetic alterations involving
CRLF2,IKZF1, andJAK. With NGS, a lot of novel druggable
target fusions were also found, including multiple ABL-class genes.
In this case, dasatinib is recommended to be used in patients with
fusion involvingABL1,ABL2,CSF1R, andPDGFRB,JAK2inhi-
bitors can be used in fusion involvingCRLF2,JAK2,EPOR, and
TSLP, while crizotinib and FAK inhibitor may be used in patients
with fusion involving NTRK3 and PTK2B, respectively
[69, 166]. Actually, such precious regimens have been fully consid-
ered to be translated into clinical practice, which highlights the
importance of high-throughput sequencing in precision
medicine era.
Another important usage of NGS in ALL genomic investiga-
tion is to find the relapse-related alteration. AlthoughCREBBP
mutations have been observed to be related to high risk of treat-
ment failure and relapse through sequencing 300 candidate genes
with Sanger methods [167], the single gene can’t explain all the
relapse cases. Thanks to NGS technology, many lesions novelly
acquired in relapse or selected from the initial subclones have
been identified, involvingIKZF1,TP53[168],CREBBP,SETD2
[169], and two more drug metabolism-related genes (i.e., NT5C2,404 Heng Xu and Yang Shu