High resolution genotyping with immunochip in idiopathic retroperitoneal fibrosis patients

IRF is a rare disease with an estimated annual incidence of
1:100,000/inhabitants, most commonly affects between 40 and 60 years and more
frequently males (M:F=2:1).

To date, the pathogenesis of IRF is unknown, but is considered a multifactorial
disease in which genetic and environmental factors interact determining
susceptibility to the disease. Given the extreme rarity of the disease, the
genetics of IRF is still poorly investigated, for which the associated genes
are few; among them, there are genes related to major histocompatibility
complex, in particular HLA-DRB1*03 and HLA-B*27.
Because many patients are seen in two centers in Italy (Parma, Prof. Dr.
Vaglio; Milaan, Dr. Moroni) and in our center in the Netherlands, we
collectively wanted to study the possible genetic basis of iRPF.

The study is designed to evaluate the possible association between genetic
variants and susceptibility to IRF, based on previous studies in
autoimmune-inflammatory diseases (celiac disease, type 1 diabetes and
rheumatoid arthritis).

In this study, the method used involves the genotyping of polymorphic DNA
markers using case-control study to compare and evaluate allele frequencies of
the marker in patients and healthy controls. For healthy controls will be used
genotypes from data of 200 individuals of the Caucasian population deposited
anonymously in online databases (http://www.1000genomes.org/;
http://www.ncbi.nlm.nih.gov/;http://hapmap.ncbi.nlm.nih.gov/). There will not
be recruitment of healthy individuals.

The study involves the use of the Immunochip platform (Illumina), which can
simultaneously genotype 196,524 polymorphic markers, it includes 195.806 SNPs
and 718 small insertions and deletions. The polymorphic markers included in the
chip offer a high level of coverage in the region of the major
histocompatibility complex (MHC).

To perform a genetic study with rare diseases, it is necessary to design a
multicenter project; the entitycenter responsible for the sample recruitment is
the Unit of Nephrology of the University Hospital of Parma (Prof. Dr. Augusto
Vaglio, Dr. Palmisano, Dr. Maritati, Dr. Urban). The recruitment of samples
will also include University of Milano-Bicocca (Dr. Gabriella Moroni) and the
Albert Schweitzer hospital in the Netherlands ( Dr. Eric van Bommel). These
specialised centers follow patients in their clinical course and treatment.

Blood samples will be sent to the laboratory of Medical Genetics of the
University Hospital of Parma (Responsible for sample storage Dr. Davide
Martorana). DNA extraction (performed with QIAamp DNA Blood Mini Kit, Qiagen,
Valencia, CA) will be performed by Dr. Davide Martorana.
Once extracted, the DNA samples will be sent for genotyping at the Institute of
Parasitology and Biomedicine López Neyra, the Superior Council for Scientific
Investigations, Armilla, Granada, Spain). The responsible for the execution of
genetic testing is Prof Dr. Javier Martin.

Final bioinformatic and statistic analysis will be performed by Dr David
Carmona (Institute of Parasitology and Biomedicine López Neyra, the Superior
Council for Scientific Investigations, Armilla, Granada, Spain). The
statistical analysis includes a case-control association test using a standard
test Cochran-Armitage using PLINK v1.07.

At the end of the study, DNA samples will be destroyed.

There is no particular risk or burden for the patient when participating in
this study, hence, we think performing this study is justified. There is a
single extra collection of a 10 cc blood sample, which is not part of the
standard care of the patient. There is no other burden for the patient, other
than the regular visits to the outpatient department, blood sampling and
radiologic investigations as part of the standard care and as such depicted in
the 'Zorgpad RPF'.