SNP Uppsala

 

Facility/Node
SNP genotyping platform at Uppsala University

Contact person
Tomas Axelsson or Ann-Christine Syvänen

Facility website: www.genotyping.se 

Summary of service
The SNP Technology Platform performs high-through-put genotyping of SNPs (single nucleotide polymorphisms) as a service to academic researchers in Sweden and other countries. Our aim is to make SNP genotyping of high quality, using the most modern technology available to researchers at lowest possible cost. We can assist genotyping projects of varying size, from 1 SNP to 1,000,000 SNPs in hundreds or thousands of samples using three different genotyping systems to cover the needs of all projects.
The platform also organizes training courses/workshops and accepts visiting scientists for training and offers consulting assistance related to SNP genotyping.

Technologies/Methods
Genotyping is performed by minisequencing single nucleotide primer extension utilizing three different genotyping systems:

• Illumina BeadStation 500GX is used for genotyping of 384-1,000,000 SNPs per sample using the GoldenGate and Infinium assays.
• GenomeLab SNPstream is used for projects with 12-384 SNPs per sample.
• Single-base extension with fluorescence polarization detection is used when only few SNPs are to be analysed per sample

An “in-house” developed relational MS SQL database is used for handling and storing information on samples, SNP-assays and produced genotypes, and for quality assessment of the genotype data.
Over 75 research projects, most of which have studied human complex diseases, have received service from the SNP Technology Platform. Our services include bioinformatics-assisted SNP assay design, SNP assay development, followed by production scale genotyping and quality control of the results.
The SNP Technology facility is accredited by the Swedish accreditation agency SWEDAC, and works according to a quality system based on the international SS-EN ISO/IEC 17025 standard.

Practical information
We have a staff of five research engineers or laboratory technicians, four biocomputing engineers, one scientist and a laboratory manager.
The SNP Technology facility is supported by Uppsala University and the Uppsala University Hospital, and thus the research projects are only charged for marginal running costs for the SNP analyses.

Details/theories of technology