Genotyping and Sequencing Facility
Since 1999 the UMCG exploits a central facility for DNA analyses like large-scale genotyping and sequencing. The Genotyping Facility is part of the Integrative Genomics research group of Medical Biology and is financially supported in part by Mibiton, is and has been involved in a large number of clinical projects with focus on unravelling the genetic components of complex diseases. Examples of past and present disease projects are asthma, breast cancer, cervical cancer, colon cancer, IBD (Crohn’s disease), SLE, rheumatic arthritis, various psychiatric disorders, diabetes, testis cancer, the large PREVEND study, and some renal and heart diseases. The role of the facility and its people varies from ‘service only’ to research partner or fellow project leader.
One of the services is performing large-scale DNA isolations from 20 ml blood samples for the establishment of the patient cohorts, varying in size between 350 and 3500 samples (including controls/relatives). For some projects DNA has been isolated from buccal swabs or FTA cards. By now, about 15,000 DNA samples have been collected and safely stored in duplicate -80°C freezers. Together with replicates of several large cohorts collected on other locations (e.g. some asthma cohorts, PREVEND, MERIT, and GENDER) the total amount of DNA samples adds up to 30,000 and is still growing. These DNA-banks, together with the even more important databases established by the clinical project leaders and containing all patient data and phenotypic characterizations, are invaluable tools for present and future studies on multifactorial diseases.
The main task of the genotyping facility is to perform large numbers of DNA-variant analyses for disease association studies. In the past four years over 1,2 million genotypes of various markers have been established, both for microsatellite markers, also known as VNTRs (variable number of tandem repeats), as well as SNPs (single nucleotide polymorphisms). Microsatellite markers are characterized by differences in repeat length between individuals (alleles), and therefore are analysed by PCR and subsequent separation of the PCR products on automated sequence analysers. Dedicated software is used to determine the alleles of a particular marker (allele calling). Two 96-wells MegaBACE capillary sequencers, as well as 4 PCR machines with in total twelve 384-wells plate PCR capacity, are present to generate enough throughput. These machines also serve the Sequencing Facility.