Radboudumc

Contact

Facility	Dept. of Human Genetics
Head of the facility	Marcel Nelen

Expertise

Technologies	SangerSequencing NGS-Whole genome sequencing (WGS) NGS-Exome sequencing(WES) NGS-other Fluorescence in situ hybridization (FISH) Array comparative genomic hybridization (aCGH) Multiplex ligation-dependent probe amplification (MLPA) Genotyping qPCR Droplet Digital PCR (ddPCR)
Purposes	Research Clinical use Service
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Infection medicine Microbial Genomics Therapeutic development

Features

Collaboration with industry where the institute collaborated with Genomics expertise (in the last 5 years)	>10
% of TIME involved in technology/methods development/innovation/intellectual property related to Genomics	70%
Certifications	ISO15189

Track record

Key opinion leaders

Han Brunner (clinician, rare genetic diseases) Lisenka Vissers (Clinical utility and HTA) Christian Gilissen (Bioinformatics) Alex Hoischen (ImmunoGenetics and technology)

Publications

de Ligt J, Willemsen MH, van Bon BW, et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med. 2012;367(20):1921-1929. doi:10.1056/NEJMoa1206524 Vissers LELM, van Nimwegen KJM, Schieving JH, et al. A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Genet Med. 2017;19(9):1055-1063. doi:10.1038/gim.2017.1 Lelieveld SH, Reijnders MR, Pfundt R, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19(9):1194-1196. doi:10.1038/nn.4352 Arts P, Simons A, AlZahrani MS, et al. Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies. Genome Med. 2019;11(1):38. Published 2019 Jun 17. doi:10.1186/s13073-019-0649-3 Neveling K, Mensenkamp AR, Derks R, et al. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem. 2017;63(2):503-512. doi:10.1373/clinchem.2016.263897

Contact

Facility	Radboud Technology Center for Mass Spectrometry
Head of the facility	Jolein Gloerich

Expertise

Technologies	LC-MS Liquid chromatography (HPLC, UHPLC)
Purposes	Research Clinical use
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Expression proteomics

Features

Collaboration with industry where the institute collaborated with Proteomics expertise (in the last 5 years)	>10
% of TIME involved in technology/methods development/innovation/intellectual property related to Proteomics	100%

Track record

Key opinion leaders

Jolein Gloerich - targeted proteomics, expression proteomics Hans Wessels - glycopeptide profiling, intact protein analysis

Publications

Biosynthetic homeostasis and resilience of the complement system in health and infectious disease Willems E, Alkema W, Keizer-Garritsen J, Suppers A, van der Flier M, Philipsen RHLA, van den Heuvel LP, Volokhina E, van der Molen RG, Herberg JA, Levin M, Wright VJ, Ahout IML, Ferwerda G, Emonts M, Boeddha NP, Rivero-Calle I, Torres FM, Wessels HJCT, de Groot R, van Gool AJ, Gloerich J, de Jonge MI. EBioMedicine. 2019 Jul;45:303-313. doi: 10.1016/j.ebiom.2019.06.008 The future of protein biomarker research in type 2 diabetes mellitus. Tans R, Verschuren L, Wessels HJCT, Bakker SJL, Tack CJ, Gloerich J, van Gool, AJ Expert Rev Proteomics. 2019 Feb;16(2):105-115. doi: 10.1080/14789450.2018.1551134. Analysis of 953 human proteins from a mitochondrial HEK293 fraction by complexome profiling. Wessels HJCT, Vogel RO, Lightowlers RN, Spelbrink JN, Rodenburg RJ, Van den Heuvel LP, Van Gool AJ, Gloerich J, Smeitink JAM, Nijtmans LG, PLoS One 2013 Jul 23;8(7):e68340. doi: 10.1371/journal.pone.0068340 A comprehensive full factorial LC-MS/MS proteomics benchmark data set Wessels HJ, Bloemberg TG, van Dael M, Wehrens R, Buydens LM, van den Heuvel LP, Gloerich J. Proteomics. 2012 Aug;12(14):2276-81. doi: 10.1002/pmic.201100284 Bacterial Electron Transfer Chains Primed by Proteomics Wessels HJ, de Almeida NM, Kartal B, Keltjens JT. Adv Microb Physiol. 2016;68:219-352. doi: 10.1016/bs.ampbs.2016.02.006.

Contact

Head of the facility	Dr. Karlien Coene

Expertise

Technologies	High performance liquid chromatography (HPLC,UHPLC) LC-MS Nuclear magnetic resonance (NMR) Untargeted metabolomics assays Targeted metabolomic assays High Resolution QTOF mass spectrometry
Purposes	Research Clinical use
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research

Features

Collaboration with industry where the institute collaborated with Metabolomics expertise (in the last 5 years)	<10
% of TIME involved in technology/methods development/innovation/intellectual property related to Metabolomics	20%
Certifications	ISO15189

DATA ANALYSIS for

• Genomics
• Proteomics
• Metabolomics
• Omics data integration/systems biology
• Structural bioinformatics

DATA INTERPRETATION for

• Genomics
• Proteomics
• Metabolomics
• Omics data integration/systems biology
• Structural bioinformatics

 DATA MANAGEMENT for:

• FAIR data

DATA SUBMISSION in to public database

STATISTICS

• Molecular profiling (omics and others)
• Expertise in clinical design of experiments, clinical statistics
• Metadata (patient/sample information)
• Methods and policies for information infrastructure, including privacy and security

BIOINFORMATICS

• Genes proteins and metabolites annotation
• Expression profiling with omics and others (e.g. PCR) for RNAseq, microRNA, other RNA species, proteins and metabolites
• Data integration (“Systems biology”)
• Structural modeling
• Genetic analysis for Structural variation detection (Genome, Exome) and prediction of protein function from sequence information
• Drug-target interaction analysis
• Semantic analysis (“Bibliome analysis”, text mining)
• Imaging
• Development of new algorithms, e.g. new decision algorithms, new sequence aligners for NGS data, etc.
• Development of semantic analysis tools
• Informatics methods to support clinical decisions (diagnostic, predictive tests)

OMICS INTEGRATION METHODS

• Published tools – mixOmics; WGCNA; MOFA
• Own scripts/software