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CARROLL, RAETZ, AND MEYER
KEY POINTS
The genetic landscape of childhood cancer is far less
complex than that of tumors that occur in adulthood.
Tumor profiling has revealed genetic alterations unique to
traditional histological tumor subtypes as well as changes
that are shared across seemingly disparate tumors.
With few exceptions, high-frequency shared genetic
alterations are not observed, but low frequency individual
genetic alterations may coalesce into biological pathways
that offer the possibility of novel treatment approaches.
The impact of precision medicine is best evaluated in the
context of carefully controlled clinical trials.
noprecipitation (ChIP) sequencing, which determines chemical
changes to the surrounding chromatin that are also likely
to affect gene expression. In some cases, data can be produced
on an individual in less than a day. Ideally, all platforms
would be used to create a full portrait of the genetic and
epigenetic landscape of an individual, and there are many examples
where combining data (e.g., copy number, gene
expression, methylation, and DNA sequencing) shows convergence
on alterations in pathways shared among patients
of an individual tumor type and/or pathways used by tumor
cells to evade therapy. However, the prohibitive cost of sequencing
and data analysis now prevents simultaneous deployment
of multiple strategies.
The details of these approaches vary but, in general, involve
the generation of single-stranded DNA (from genomic DNA,
hybridization captured [exome], cDNA [RNA sequencing],
bisulfıte treated DNA [methyl sequencing] or immunoprecipitated
DNA [ChIP sequencing]) with ligation of DNA
adapters. Rounds of amplifıcation on beads or glass slides allow
adequate coverage of the DNA, and strands can then be
sequenced by the sequential addition of fluorescently labeled
nucleotides. Varieties of bioinformatic approaches are used
to determine quality, align sequences to the genome, and
determine variations in sequence. Each approach has advantages
and disadvantages. For example, whole-exome sequencing
(WES) is less expensive than whole-genome
sequencing and focuses on somatic variants in protein coding
domains that are likely to contain critical lesions. However,
it can miss fusion transcripts and does not provide gene
expression information that may highlight activation of biologic
pathways.
The sequencing of an individual cancer genome in a short
period of time to allow integration into clinical practice is
now a reality. However, the cost of a single sequencing run,
including analysis and validation, is signifıcant, especially
since reimbursement of such assays is still uncertain in many
cases. The $1,000 genome has been often quoted as a holy
grail for clinical sequencing, and the recent development of
the HiSeq X Ten system (Illumina) has fınally laid claim to
this title. However, achieving this goal requires the purchase
of 10 systems costing approximately $10 million and operation
more than 4 years yielding about 72,000 genomes for a
total outlay of $82 million in capital and operational costs. 4
PEDIATRIC CANCER GENOMES AND
THERAPEUTIC TARGETS
The practical implementation of precision medicine is facilitated
by the identifıcation of somatic changes unique to the
tumor that fuel cancer initiation and progression. Moreover,
such drivers that are shared among and across tumor types
would increase the effect of agents that selectively target the
gene product and/or downstream pathway. Although there
are a few exceptions, in general, childhood tumors contain
far fewer mutations than adult tumors and within tumors
types, most mutations are not shared by the majority of
cases. 5,6 Overall, the number of nonsynonymous coding mutations
varies from one to 12 per pediatric tumor sample.
Outliers exist with higher mutation frequency in a small percent
of pediatric tumors that may harbor alterations in DNA
repair pathway genes. Despite the relatively low mutation
burden, there are many examples where actionable mutations
are likely to lead to novel therapeutic interventions in
the near future.
There are a handful of pediatric tumors where highfrequency
shared genomic alterations are characteristic. Examples
include malignant rhabdoid tumors in which
SMARCB1 mutations occur in 100% of cases and may be the
sole abnormality, as well as diffuse pontine gliomas where H3
histone mutations are observed in 78% of cases. 7,8 Such mutations
converge on epigenetic pathways, and although these
targets are not actionable at the present time, downstream
targets in which expression is affected have been identifıed.
More commonly, recurrent mutations are seen in smaller
subsets of samples within a given class of tumors. There was
great anticipation that deciphering the genetic landscape of
high-risk pediatric tumors, where clinical progress has been
stalled, would lead to catalytic advances in treatment. Improving
therapy for the most common extracranial solid tumor,
neuroblastoma, is a top priority in pediatric oncology.
Although the prognosis is favorable for low-stage disease,
most patients present with widely metastatic disease. Therapy
for stage IV neuroblastoma has improved somewhat, but
further progress is urgently needed. 9 In one of the largest sequencing
efforts directed at neuroblastoma, 240 cases were
examined. Individual samples had on average 14 nonsilent or
nonsynonymous mutations. 10 The most commonly seen alterations
were ALK mutations (9.2%, gain of function),
ATRX alterations (9.6%, deletions and loss of function mutations),
and PTPN11 mutations (2.9%). Thus, it is somewhat
disappointing that neuroblastomas do not contain highfrequency
variants suitable for targeted therapy; however, the
use of ALK inhibitors for the 10% of patients who carry ALKactivating
mutations is an important avenue to pursue. This
disappointment is tempered by new approaches to inhibit
MYCN and its downstream targets. Amplifıcation of the
MYCN oncogene is observed in 25% of cases but, to date, numerous
approaches to target transcription factors like MYC
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2015 ASCO EDUCATIONAL BOOK | asco.org/edbook