Our genotyping services

The SNP&SEQ Technology Platform can assist genotyping projects of varying size, from 1 to 5,000,000 SNPs and array based methylation profiling in a few to hundreds or thousands of samples using four different genotyping systems to cover the needs of all projects.

The platform offers semi automated SNP genotyping based on primer extension technology with fluorescence or mass detection, or by sequencing by synthesis in an accredited laboratory with highly skilled personnel. The platform has the following instruments; iScan (Illumina), MiSEQ (Illumina), MassARRAY (Agena Bioscience) and Hidex Sense (Hidex Oy) and our service includes:

  • Bioinformatics-assisted primer and assay design
  • Measurement of the DNA concentration of samples to be genotyped
  • Analysis of data using the analysis software of each genotyping system, e.g. genotype calling, analysis of copy number variation or DNA methylation
  • Delivery of quality assessed genotyping results in several formats using “GRUS”, a secure delivery resource hosted by SNIC-UPPMAX
  • Compilation of material and methods regarding assay design and genotyping for publications
  • Maintenance of database containing information on samples, genotypes, SNPs and primer sequences

Read more about the different instruments and methods below, or contact us to discuss the most suitable method for your project.

The iScan System

The iScan system (Illumina) is used for genotyping SNPs or DNA methylation analysis of CpG sites by the Infinium assay. Sets of SNPs are available for human, domestic animals and crops, for both custom and fixed sets. Appropriate for disease association studies, QTL analysis as well as for detecting copy number variation and loss of heterozygosity. Methylation changes can also be detected making it ideal for genome-wide DNA methylation analysis in the human genome.

Range: up to 5,000,000 SNPs
              up to 850,000 CpG sites

The infinium assay

Image: Courtesy of Illumina, Inc

The MiSeq

The MiSeq system (Illumina) is used for genotyping of SNPs and is based on genotyping-by-sequencing using the Illumina TruSeq Custom Amplicon method.

Range: 384 to 1,536 SNPs

TruSeq Custom Amplicon

Image: Courtesy of Illumina, Inc

The MassARRAY® system

The MassARRAY® system (Agena Bioscience) is used for genotyping of SNPs using the iPLEX® chemistry.

Range: a few to 384 SNPs

The Hidex Sense System

Hidex Sense (Hidex Oy) is used for genotyping SNP by single-base extension with fluorescence polarization detection.

Range: individual or a low number of SNPs

The Hidex Sense System


The cost for a sequencing or genotyping project varies according to the application and the number of samples. Please contact our project coordinators for the specific pricing for your project.

Accreditation by SWEDAC

To secure a high quality of the offered services, the SNP&SEQ Technology Platform works according to the European quality standard ISO/IEC 17025 and is accredited by SWEDAC as a testing laboratory for genotyping and sequencing. New methods and protocols are continuously validated and added to the collection of accredited methods. The quality of genotyping and sequencing is monitored by regular comparison of the performance of the methods against data from other laboratories. As an accredited laboratory the genotyping and sequencing process, user contacts and management of the SNP&SEQ Technology Platform are audited annually on-site by SWEDAC prior to continuation of the accreditation.

For genotyping inquiries

To request a meeting, please use the NGI Order portal.

For SNP genotyping and methylation analysis inquiries:

Tomas Axelsson, Head of Genotyping. Mobile: +46 (0) 70 167 94 58
E-mail: contact@genotyping.se