What are the genetic modifiers that explain the phenotypic variability in Lynch syndrome?

Lynch syndrome (LS) is the most common form of heritable colorectal cancer
(CRC). The genetic basis of LS has been traced back to mutations in the
mismatch repair (MMR) genes, MLH1, MSH2, MSH6, PMS2 and the EPCAM gene through
inactivation of MSH2. Although these genes are responsible for LS, there is a
wide range in phenotype amongst patients. We hypothesise that this variation
can be explained by both environmental factors and/or genetic modifiers. These
modifiers might alter the risk for cancer posed by the MMR defect alone and
thus result in a variation in penetrance of disease.

We aim to recognise potential genetic modifiers for mutations in PMS2. This
will be approached through comparing a selection of CRC-related genes in the
exome of members of a PMS2 family who differ in age of onset and severity of
disease.

We have designed this project as a case-control study. Confirmed carriers of
mutations in the MMR genes will be compared to unaffected or less severely
affected family members with regard to the clinical phenotype and genetic
composition. The genetic information will be obtained through a next generation
sequencing (NGS) based analysis of oncogenes and results will be derived from
statistical modelling. NGS will be carried out on DNA that has previously been
stored for research purposes with patient consent. The DNA of some individuals
has not been stored previously or is of unsufficient quality or quantity to
perform NGS. We will need to ask these individuals to donate blood for DNA
extraction and their consent for the use of this DNA for research purposes. We
will ask for informed consent specifically for the NGS in both groups as there
is a chance of finding genetic variants that may have clinical implications.

The people participating in this study will be requested a maximum of one
sample of blood for DNA extraction, only if the DNA currently stored is
inadequate for NGS. This is a mildly intrusive procedure and from which we do
not expect serious adverse effects.

The participants do need to be fully informed about the possibility of finding
germline oncogene mutations beside the well-known MMR defect. Through NGS,
their whole expressed genetic composition can be accessed. In this study we
will, however, only access a pre-determined set of 30-50 genes. Still, a small
chance remains that pathogenic mutations will be found that otherwise would not
have been identified. These mutations can encompass abnormalities that are
known to be related to CRC, which will always be reported to the patients.
Other mutations that can be found in CRC-related genes will be variants of
unknown significance (VUS), which are classified according to their assumed
pathogenicity. VUS*s of category 4 will also be reported to patients, as these
are the very likely to be pathogenic. Lastly, findings in genes not directly
associated with cancer can be found. These will be included in the study for
research purposes and not reported to the patients because of the uncertain
clinical significance.

The possible clinical implications of identifying a pathogenic mutation will to
be discussed with the participant before they give consent for NGS. Finding
mutations that underlie preventable diseases, although not a goal of this
study, will be beneficial for those individuals whom it concerns. Also, we
believe that the small chance of finding variants will be outweighed by the
added LS cancer risk knowledge. The current knowledge on the MMR gene defects
provides an inadequate answer to the variability of LS phenotype. An extended
genetic model needs to be established in order to allow better risk assessment
for LS patients in the future. This study will contribute to the generation of
this polygenic model.