Bioinformatics

In large scale genotyping projects, the demands on all parts of the workflow increase. We have the expertise to aid our clients in many different kinds of genotyping related bioinformatics. Support can range from introductions to publicly available databases and genome browsers, to programming and custom databases to support automated SNP selection from very large datasets.

SNP selection

We can assist projects with SNP selection at various levels depending on the wishes of the clients. If the customer wants to perform selection themselves, we can supply source data such as design scores for specific systems, allele frequencies for populations of interest, conservation scores for SNP positions etc. Other possibilities are filtering of large datasets (often beyond the capabilities of excel) to make them more manageable.

We also have an in-house system to automate SNP selection for very large data sets with hundreds of thousands of SNPs in the source data.

This system allows customized selection based on the definition of a scoring model that combines pieces of information from different databases to rank the different markers in a region of interest such as a linkage peak. This allows the tailoring of the selection depending on the purpose and type of study.

For example, in a linkage study the most important factors could be the heterozygozity of the markers and their assay design score, whereas in a candidate gene study, there could be an interest specifically in SNPs that cause amino acid shifts, interfere with splice sites or are located in evolutionary conserved regions of the genome.

The system can easily be extended with additional types of data if the client has a specific interest or proprietary data.

Other types of information

We have experience in calculating linkage disequilibrium for genotyped markers and using different types of haplotype reconstruction algorithms to infer haplotypes in the analyzed samples, and can supply information about such things if desired.