Sequencing of variants for celiac disease

Isis Ricaño Ponce

M.Sc. in Medical & Pharmaceutical Sciences, RUG

Practical work period: Sept. 2009-April 2010

I have always found the field of genetics very interesting and during my MSc program I had the opportunity to do a research internship in the group headed by Prof. Cisca Wijmenga. The group focuses on studying the genetics of complex immune-related diseases.

I joined a very challenging project: ‘Sequencing of variants for celiac disease’ . At that time (Sept. 2009), exome sequencing was a quite new technique and had not been applied to the study of complex diseases. We decided to use a family-based approach, sequencing the coding part of the DNA of affected members of the family, focusing on low frequency variants that may co-segregate with the disease. We prioritized our results by combining different strategies, such as linkage analysis and homozygosity mapping. The candidate variants were also analyzed using in silico prediction tools for single nucleotide polymorphisms (SNPs) and further validated in the laboratory using different techniques. The work led to a paper published in Clinical Genetics*.

One thing that I really liked about the time that I spent in the Dept. of Genetics was that you could always go to people and discuss your ideas, and if you do not know how to do something, there is always someone who can help you. The internship was initially for 6 months, but I was really enjoying the project and learning a lot, so I asked for an extension and stayed 8 months in total.

* Exome sequencing in a family segregating for celiac disease

Szperl AM, Ricaño-Ponce I, Li J K , Deelen P, Kanterakis A , Plagnol V,van Dijk F, Westra HJ, Trynka G, Mulder CJ , Swertz M, Wijmenga C and Zheng H Ch .
Clin Genet 2011: 80: 138–147.
© University Medical Center Groningen, NL, 2011

Abstract
Celiac disease is a multifactorial disorder caused by an unknown number of genetic factors interacting with an environmental factor. Hence, most patients are singletons and large families segregating with celiac disease are rare. We report on a three-generation family with six patients in which the inheritance pattern is consistent with an autosomal dominant model. To date, 27 loci explain up to 40% of the heritable disease risk. We hypothesized that part of the missing heritability is due to low frequency- or rare variants. Such causal variants could be more prominent in multi-generation families where private mutations might co-segregate with the disease. They can be identified by linkage analysis combined with whole exome sequencing. We found three linkage regions on 4q32.3-4q33, 8q24.13-8q24.21 and 10q23.1-10q23.32 that segregate with celiac disease in this family. We performed exome sequencing on two affected individuals to investigate the positional candidate regions and the remaining exome for causal nonsense variants. We identified 12 nonsense mutations with a low frequency (MAF < 10%) present in both individuals, but none mapped to the linkage regions. Two variants in the CSAG1 and KRT37 genes were present in all six affected individuals. Two nonsense variants in the MADD and GBGT1 genes were also present in 5/6 and 4/6 individuals, respectively; future studies should determine if any of these nonsense variants is causally related to celiac disease.

Key words: complex disease, rare variants, linkage study, exome sequencing