*IBDome; Identification of rare variants in candidate genes and regulatory elements in familiar and sporadic early-onset IBD (inflammatory bowel disease) patients*

Crohn*s disease (CD) and ulcerative colitis (UC) are inflammatory bowel
diseases (IBD) affecting 1 in 250 individuals of European ancestry. IBD is a
chronic relapsing and remitting disease. Although the exact etiology of IBD is
unknown, it is speculated that IBD occurs in genetically susceptible
individuals as a result of dysregulated immune responses to gut flora after
exposure to an as yet unidentified environmental stimulus.

The advances in science and technology now permit large scale genome-wide
association studies (GWAS) to identify genetic risk factors for disease in a
population and assess gene-environment interactions that can influence outcomes
in disease. Furthermore, with the results of different genetic studies,
functional studies of genetic risk factors have identified new pathways
involved in the pathogenesis of IBD.

Recent IBD GWAS showed that single nucleotide polymorphisms (SNP) in the IL10
locus are associated with ulcerative colitis and to a lesser extent Crohn*s
disease. Functional studies in patients with ulcerative colitis showed
physiologically important defects in IL10 signalling in lamina propria
mononuclear cells. These results imply that IL10 signalling plays an important
role in regulation of intestinal inflammation.

GWAS published in last 2-3 years revealed numerous other candidate genomic loci
involved in IBD. Nevertheless, the results of GWAS only explained part
(~10-20%) of the inheritability. In upcoming years a lot of effort will be put
into further analysis and sequencing of identified candidate loci to unravel
causative rare variants and genes. Since most of these studies are performed on
adult-onset IBD patients we will take advantage from our cohort of
familiar/sporadic cases of early onset IBD patients, while approximately 1/10
to 1/5 of IBD patients are diagnosed or have onset of their symptoms under the
age of 18. Due to a larger familial component and differences in phenotypic
manifestation and severity compared to late onset adult IBD we expect a larger
genetic component in pathogenesis of our cohort. In addition, we plan to
sequence the whole coding part of 300 candidate genes which allows us to
discover rare variants. Finally, we will take advantage from our flexible and
cost-effective deep sequencing setup which allows us to sequence large numbers
of candidate genes in numerous individuals for only small fraction of costs
needed for Sanger sequencing or whole exome/genome deep sequencing. This gives
us logistical advantage over competitors.

Primary Objective: Identification of rare variants in candidate genes and
regulatory elements in pediatric IBD patients.
Secondary Objective(s): To determine the functional consequences of identified
genetic variants in IBD, we will correlate clinical information (age of onset,
clinical data, associated diseases) with observed variants of candidate genes
and examine pathways involved in the pathophysiology of specific intestinal
inflammatory diseases.

Patients with IBD diagnosed in childhood will be recruited in two academic
centres, UMC Utrecht and Erasmus MC Rotterdam. Clinical data are already
available. We will collect blood from the patients that were diagnosed as a
child since 2005. We will also include newly diagnosed pediatric patients and
phenotype these according to the EUROKIDS protocol.

All patients diagnosed as a child will be asked for participation, particularly
patients with familial IBD and patients with a diagnosis before the age of 5
years. A venipuncture is one of the usual diagnostic procedures during
periodical check up for IBD. We will ask for a sample of extra blood (max 10
ml) during this diagnostic venipuncture after informed consent is obtained.
Affected and non-affected family members will be asked for participation and
provide max 10ml blood. In case obtaining a blood sample from non-affected
family members is a problem, DNA can also be extracted from sputum. Blood
samples are max 10 ml from individuals of 5 years and older, 4-10 ml from
children 1-5 years of age, and 2-5 ml from children < 1 year of age. This will
be coordinated during routine blood draws where possible.

A follow up questionnaire will be used to complete data on patient*s disease
progression that may have developed since diagnosis of IBD. Participating
family members are also asked to fill out a questionnaire.

The objective of the present study is sequencing ~300 candidate genes in
maximal 400 individuals, with the possibility to extend the range of sequencing
to regulatory regions and whole exomes, this possible future extension will not
require additional venipuncture.

The total duration of the study will be 3,5 years. After obtaining informed
consent, DNA from patients and family members will be collected in our
diagnostic DNA-lab followed by sequencing of ~300 candidate genes in maximal
400 individuals, with the possibility to extend range of sequencing to
regulatory regions and whole exomes. Even though we pick up 300 candidate
genes, there is a possibility that causative mutations are present elsewhere.
Therefore in patients where we can't explain the disease by mutations in one of
the 300 candidate genes, we'll perform whole exome sequencing (sequencing of
all genes) and sequencing of regulatory elements to find the causative mutation.
DNA and medical information will be stored for a maximum of 20 years.

Venous blood investigation is one of the usual diagnostic procedures during
periodical check up for IBD. We will ask for some extra blood (max. 10 ml)
during this diagnostic venipuncture. Affected and non-affected family members
will be asked for max 10ml blood. In case obtaining a blood sample from
non-affected family members is a problem, DNA can also be extracted from
sputum. No increased risk is to be expected, however venipuncture can be an
undesirable experience to a child, especially when the venipuncture is
difficult to perform e.g. because of small vessels. This can be inconvenient
for the patient. Therefore, we will refrain from taking the extra blood
necessary for our research if the venipuncture is difficult to perform and/or
the child is distressed.