Life Science Discussions

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Stefan Schreiber

Professor of Medicine at the Christian-Albrechts University in Kiel,Germany

Application:

• SNP Genotyping

Applied Biosystems

Technology:

• ABI Prism® 7900HT SequenceDetection System

• Assays-on-Demand™ SNPGenotyping Products

• Assays-by-DesignSM Service

What is your main area of interest?

We are studying the pathophysiology and genetics of chronic inflammatory disorders and the way that these conditions may be induced by environmentalfactors. This might seem like a very broad subject, but inflammatory diseases thataffect the main organs that have barrier functions against the environment, such asthe skin, gut and lungs, often overlap in their clinical presentation. For example,individuals who suffer from bronchial asthma very often have a history of skinallergies and individuals suffering from psoriasis, an inflammatory skin disorder,will have an increased risk of developing some form of inflammatory boweldisease. One explanation for this common predisposition is that these differentdisorders may actually be caused by shared genetic abnormalities and this is alsosupported by the fact that these patients often have a family history of inflamma-tory diseases. A particular focus of our interest is inflammatory bowel disease, withits two forms of Crohn’s disease and ulcerative colitis.

How do you identify areas of interest in the genome?

Groups like ours first study the pattern of inheritance of chromosome-specificmicrosatellite markers using DNA samples from disease-affected nuclear families(i.e., affected sibling pairs). However, the problem with microsatellite mappingtechniques is that they provide only a very rough idea of where putative diseasegenes are located. Now commonly the method of choice is the use of singlenucleotide polymorphisms (SNPs) to detect linkage disequilibrium by high-density association mapping in disease susceptibility regions previously identified by the use of microsatellites.

Discovering How Genetic Susceptibility Influences Crohn's Disease and Ulcerative ColitisA Discussion with Stefan Schreiber

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What areas of the genome are you specifically looking at and how?

We are concentrating on two main hotspots that show linkage in Crohn’s disease,psoriasis, sarcoidosis, and asthma, one on chromosome 16q and the other on chromosome 6p. In these regions we can share the information from mappingexperiments between different disease-driven research approaches. Obviouslytyping thousands of polymorphisms in thousands of individuals means performinga lot of assays and we could spend quite some time optimizing assays for eachpolymorphism, so a high-throughput method with a high likelihood of experi-mental success is essential. Thankfully, new genomic assays products and servicesfrom Applied Biosystems provide us with validated, ready-to-use assays for SNPgenotyping and gene expression studies, saving us the trouble of developing and validating assays ourselves and allowing us to use fully automated analyticalplatforms such as the ABI PRISM® 7900HT Sequence Detection System. Thishigh-throughput PCR system uses 384-well plates, making it feasible to generateas many as 250,000 SNP genotypes per day.

How do these assays work?

There are two types of genomic assays: the Assays-on-Demand™ products, whichare off-the-shelf assays, and the Assays-by-DesignSM service, which allows us tocustom design the SNP genotyping assay we want. The easy selection of Assays-on-Demand products via the Internet site, www.allsnps.com, allows us to choosethe right set of SNPs according to physical location and allele frequency data. This definitely increases our efficiency and success rate in the first round of systematicassociation studies. Then, we have found it extremely useful to add in Assays-by-Design SNP products to fine tune the mapping strategy and increase the densityof SNPs in areas of interest. With this service, we simply provide a target DNAsequence to Applied Biosystems and, two to three weeks later, we receive a cus-tomized SNP genotyping assay. Since these genomic assays arrive as optimized,ready-to-use products, it allows us to focus our efforts and resources on the intellectual part of our research instead of optimizing technical procedures.

How have these assays helped your research to progress?

So far, we have used several thousand of these SNP assays to study samples fromthree and a half thousand people and more than three million SNP genotypeshave been completed since January 2002. We have also created chromosomal mapsthat help us to understand the haplotype structure in our regions. The work hasalready generated a number of promising leads in the association mapping ofdisease samples. We hope that in the next few years we will be able to close in on acouple of new disease genes in inflammatory conditions including Crohn’s disease.

“With Applied

Biosystems

approach, we can

begin performing

our association

studies within

days of ordering

these new

validated and

ready-to-use

Assays-on-

Demand™ SNP

Genotyping

Products.”Stefan Schreiber

And what of the future? Which path will your research now follow?

The most important question for the patient is how a genetic susceptibility influences his or her own disease. The data that is needed to answer these questions can only be obtained by analysis of a population representative sample.The next phase of this project will therefore apply automated tests for individualdisease genes in a population study, which is funded by the German government’sNational Genome Research Network (www.ngfn.de, www.PopGen.de). This willallow us to assess the genotype-attributed risk of developing a disease in up to 1.2million individuals. Prospective cohort studies have also been set up to see howdifferent genotypes are associated with various disease outcomes and subtypes.The ultimate and long-term aim of many of these studies is the development ofpersonalized medicine algorithms, where specific diagnostic procedures or thera-pies are particularly suitable if you have a certain genetic make-up. For example,would the advantages of aggressive early therapy with immunosuppressants toprevent the development of Crohn’s disease in genetically highly susceptible individuals outweigh the many side effects of this treatment? This question will be tackled using SNP genotyping techniques in prospective cohorts set up by theGerman nationwide competence network in inflammatory bowel disease.

Professor Schreiber is Frederik Paulsen Professor of Medicine and Gastroenterology at the Christian-Albrechts-University in Kiel, Germany. He is a member of severalprofessional societies and has been an invited lecturer and held chairmanships at manynational and international meetings. Professor Schreiber is also editor for the interna-tional Journal of Colorectal Disease, and a section editor of Inflammatory BowelDisease, as well as an editorial board member of Gut. In 1998, he was awarded theMartin Guelzow Prize by the German Gastroenterological Association and has morethan 130 original publications to his name, in journals such as The New EnglandJournal of Medicine, PNAS, Gastroenterology, J. Immunology, and The Lancet.

©2004 Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. ABI PRISM and Applied Biosystems are registered trademarks and AB (Design), iScience,iScience (Design), Applera, Assay-by-Design and Assays-on-Demand are trademarks of Applera Corporation or its subsidiaries in the US and/or certain other countries. Part Number 1017-01

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“With Assays-by-

DesignSM service,

we simply provide

a target DNA

sequence to

Applied

Biosystems and,

two or three

weeks later,

we receive a

customized SNP

genotyping

assay.”Stefan Schreiber