We recently acquired Sequenom’s MassARRAY technology, which is an innovative platform for high-throughput genotyping according to a candidate gene-approach. We are currently using our Sequenom system for the following applications:

- SNP genotyping: Sequenom’s iPLEX technology efficiently multiplexes between 25 to 40 different SNP assays in one PCR reaction and thereby provides very flexible, effective, rapid and accurate SNP genotypes. Current set-up allows us to genotype 768 patients a day, thereby generating up to 30,000 genotypes/day. Currently, we are analysing 250 chips per year.

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- Oncogene profiling: We have recently optimized a high-throughput genotyping system to query >100 oncogene mutations in KRAS, PI3K and P53. These mutations can be genotyped in 5 genotyping assays. The advantage of using Sequenom for oncogene profiling experiments is that it uses only little amounts of DNA (±-10 ng DNA per reaction) and provides reliable results on paraffine-extracted tumor DNA. It is thus the preferred method to determine oncogene mutations in large sets of tumor extracted DNAs.

- Methylation profiling: We have recently also optimized the methylation protocol on our Sequenom system. It delivers individual methylation ratios for CpGs within a target sequence. Relative methylation ratios can be assessed in a range between 10-90%. It is scalable for long reads up to 600 bp in one reaction enabling the discovery of differential methylation patterns within large promoter regions. It is robust since it is efficient on a range of samples, including Formalin Fixed Parraffin Embedded (FFPE) samples. 

Members of the lab:
Joke Reumers, PhD, Postdoctoral Fellow
Ian Buysschaert, MD, PhD student
Bart Claes, Ir, PhD student
Joke Dhondt, PhD student
Betul Yesilgurt, PhD student
Gilian Peuteman, Research Assistant
Dominiek Smeets, Research Assistant
Sofie Van Soest, Research Assistant