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Data analyses
Harmen van de Werken
Head Bioinformatics
We have a team of experienced bioinformaticians to run advanced analysis pipelines. Our services include specialised data analysis for genotyping arrays, methylation arrays, Olink proteomics, and sequencing. We also offer consultancy and support if you choose to analyse the data yourself.
Additional analyses for sequencing.
We have developed and optimised data analysis pipelines for both bulk and single-cell sequencing applications. Additionally, we offer custom bioinformatics solutions for projects that fall outside the scope of our standard analysis pipelines.
Additional analyses for Olink proteomics.
If you have previously run Olink proteomics panels that provide relative results and are processing a new batch, adding bridging samples is essential. Bridging samples enable assay-specific adjustments between datasets. We offer Olink bridging services, including the selection of bridging samples, comparison of their data within the new dataset and bridging normalisation.
Additional analyses for methylation arrays.
If your study requires more than technical QC, we offer extended quality control of your methylation data. This includes cell type proportions, epigenetic age estimation, and both functional and quantile normalisation. Our extended QC also features epigenetic clocks such as Horvath, Hannum, PhenoAge, and GrimAge.
After genotyping, your data routinely undergoes technical quality control. Pipelines for a range of additional data analysis services are available.
Creating an optimal dataset.
We offer extended QC, imputation - using HRC or 1000 Genomes on a secure Erasmus MC server - and SNP extraction to prepare your data for further analysis. For small batch sizes, an adapted and automated extended QC is available. Merging datasets or creating new ones is offered as an optional service, either standalone or in combination with other services.
Genome Wide Association Studies.
Genome-wide association studies are commonly used to identify genomic variants associated with diseases or traits. We offer GWAS services, along with SNP annotation and meta-analysis.
About our CNV services.
Is your study focused on copy number variation? Our CNV services may be the solution. Our pipelines include PennCNV, duplicate checks and, if needed, comparison and kinship analyses.
A pipeline for HLA imputation.
We offer extended quality control and HLA imputation to predict human leukocyte antigen genotypes from your genotype data.
Let's talk about your project.
We recommend reaching out to us as soon as possible to discuss your project. This will allow us to better tailor our services and applications to meet your needs.
Are you looking for a custom solution?
If your project requires a customised service, we are happy to discuss potential solutions and develop or optimise a service that meets your specific needs.
Predicting disease risk with polygenic risk scores.
If you need predictive genetic risk scores from your genotype data, we can extract selected SNPs for downstream processing. We also offer support and advice for calculating risk scores. Since PRS calculations are tailored to each study, please contact us to discuss available service options.
Pharmacogenetics
Our new data analysis pipeline translates genotype data into star allele genotypes for 20 key pharmacogenetic genes, enabling precise and efficient identification of PGx variants. We currently use genotype data from Illumina’s Infinium Global Diversity Array with enhanced PGx. In the future, pipelines for GCRA and GSA arrays with enhanced PGx data will be available.
Related services.
Genotyping arrays
Linking genetic variation and genetic variants to diseases or traits. We offer a variety of high-throughput arrays.
RNA sequencing
Comprehensive RNA sequencing services to explore gene expression and transcript profiles.
Olink proteomics
Measuring a broad range of proteins for large-scale biomarker discovery and targeted approaches.
Get in touch
For general inquiries or more information about our services, please contact us.