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The
SNP&SEQ Technology Platform performs genotyping of SNPs
(single nucleotide polymorphisms) and sequencing as a
service to academic researchers in Sweden and other
countries. Our aim is to make SNP genotyping and
sequencing of high quality, using the most modern
technology available to researchers at the lowest
possible cost. SNP genotyping has been offered since
2001 and from 2008 the platform also offers “next
generation” DNA sequencing as a service to researchers.
SNP genotyping is offered for large-scale association or
linkage studies, analysis of copy number variations and
chromosomal rearrangements and DNA methylation levels.
We can assist genotyping projects of varying size, from
1 SNP to >1,000,000 SNPs in hundreds or thousands of
samples using four different genotyping systems to cover
the needs of all projects.
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Illumina
iScan and BeadStation 500GX are used for genotyping of 384- >1,000,000
SNPs per sample using the GoldenGate and Infinium assays.
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Illumina BeadXpress is used for 48-384 SNPs.
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GenomeLab SNPstream is used
for projects with 12-96 SNPs per sample.
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Single-base extension with fluorescence polarization detection is used
when only few SNPs are to be analysed per sample.
Sequencing of genomic DNA, targeted
genomic regions, RNA (cDNA) and chromatin-immunoprecipitated
DNA is performed using two Illumina Genome AnalyzerIIx
systems.
The genotyping procedure at the SNP&SEQ Technology
Platform is accredited by SWEDAC (the Swedish Board for
Accreditation and Conformity Assessment) according to
the international SS-EN ISO/IEC 17025:2005 quality
standard. The sequencing procedure was included in the
quality system during the fall 2009 and accreditation of
the process will be sought in the fall of 2010.
Over 150 research projects, most of which have studied
human complex diseases, have received service from the
SNP&SEQ Technology Platform. Our services include
bioinformatics-assisted custom SNP assay design or large
fixed SNP panels followed by production scale genotyping
and quality control of the results.
We have a staff of eight research engineers or
laboratory technicians, four biocomputing engineers, one
scientist and a laboratory manager. The staff of the
SNP&SEQ Technology Platform is supported by Uppsala
University, Uppsala University Hospital and the Swedish
Research Council for Infrastructures.
Our computational infrastructure includes an “in-house”
developed laboratory data management system. A
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. Next generation sequence data is handled by
dedicated servers equipped with large capacity redundant
storage. For delivery of the large amounts of data
generated by next gen sequencing we are collaborating
with UPPMAX,
Uppsala University's resource of high-performance
computers, in the UPPNEX project.
For information on how to get access to our services,
please click HERE for contact information.
For information on how to get access to our services,
please click HERE for contact
information.
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