Comprehensive detection of childhood cancer predisposing genes using exome sequencing:
The next step towards personalized treatment and cancer prevention.

It has been estimated that up to 10% of all childhood malignancies result from
a genetic predisposition. This figure likely represents an underestimation
since it is primarily based on patients with a recognizable clinical syndrome
or a positive family history for cancer. Overall, it is difficult to discern
hereditary from non-hereditary cases, especially when cancer arises from de
novo or recessive germline mutations or when no recognizable clinical phenotype
is apparent.
Early recognition of a genetic predisposition in a child with cancer can be of
major benefit for the patient and its family, as it may lead to better
treatment choices and early detection of second primary tumors. Additionally,
family members can be advised about specific surveillance options. Until
recently, the identification of cancer predisposing genes was laborious. With
recent rapid technological developments in next generation sequencing (NGS)
including whole-exome sequencing, the identification of cancer predisposing
genes in single patients has become a reality, thus providing enormous
challenges as well as opportunities for patient care.
We hypothesize that a genetic predisposition for childhood cancer is more
likely to be present in children diagnosed with cancer and one ore more of the
following characteristics: intellectual disability, congenital anomalies, an
adult type of cancer in a child or a family history for the same type of
cancer.

To detect high-risk pathogenic mutations in germline DNA of children with
childhood cancer that are suggestive of genetic predisposition, using NGS-based
whole-exome sequencing, resulting in novel targets for future functional and
translational studies.

We will offer genetic counseling and exome sequencing on germline DNA of
individuals with childhood cancer who meet the inclusion criteria and their
parents. Exome sequencing data will be filtered by exclusion of common variants
from international databases and our continuously growing in-house Radboud
Genetics variant database, which is thus far assembled from 600 exome
sequences. Candidate causative variants (nonsense and frameshift mutations,
highly conserved nonsynonymous missense mutations and canonical splice site
mutations) will be selected for further analysis that will be performed in a
fixed order:
a) At first instance we will analyze those variants identified in a set of
approximately 150 genes with a known correlation with cancer predisposition. If
no pathogenic aberrations are found in this list of genes we will:
b) Screen for genes recurrently targeted by rare candidate variants in the
childhood cancer patient cohort. In the final stage of the project this
analysis will be expanded by dedicated pathway analysis based on the genes that
are known or identified at that time. DNA of the parents will be tested using
Sanger sequencing to determine whether the variant is de novo.
c) Test a recessive model by selecting candidate causative variants that are
present in a homozygous or compound heterozygous form in a single gene.
Parental origin of the biallelic configuration of each selected candidate
variant will be tested in DNA of the parents using Sanger sequencing.
d) Test a de novo model by comparing exome sequences of the child and its
parents.

For a detailed description of the study see the research protocol.

Coincidental findings
We will apply a strict order of analyzing the data to minimize the chance of
finding aberrations in genes not related to the malignancy. Moreover we will
keep these samples (and their analysis) separate from our in-house Radboud
Genetics variant database to prevent incidental findings in the future.
Incidental findings might still give information about susceptibility for
diseases later in life. In case such
coincidental findings are encountered despite all our preventive measures, we
have a protocol in place how to proceed. This protocol was previously approved
by the ethical review board of the UMC St Radboud for diagnostic exome
sequencing. As part of this protocol, a committee is in place in our hospital
to judge the health benefits of sharing any information from incidental
findings emanating from the sequencing procedure with the child and the
parents. Of course, the informed consent procedure for this study will
extensively address this subject by clinical geneticists, who will perform the
inclusion.

Venapuntures
Most often venapunctures will be combined with venapunctures as part of the
treatment process and will therefore not be an extra burden for the children.