Since 1999 the Netherlands Cancer Institute facilitates the
Sequence Core where DNA sequencing and fragment analysis for
research and diagnostic purposes is done.
The 3730 DNA Analyzer with 48 capillaries and the 3500xL Genetic
Analyzer with 24 capillaries (both Life technologies) are used for
analyzing DNA samples. Both systems are based on polymer
capillary electrophorese, with a maximum of 1,000 base read
The reagent used for sequencing is BigDyeTerminator
V3.1/V1.1. The BDT sequencing reaction has to be performed by users
themselves. The Sequence Core Facility will purify and analyze the
samples on one of the sequencers. Beside DNA sequencing it is also
possible to analyze PCR-products with Fragment analysis. The length
of PCR-products is determined using a fluorescent labeled
The Sequence Core Facility has a throughput of 110.000 samples a
year. Within 24 hours, 90 percent of the samples is analyzed. The
sequence data is available on a central server and will be stored
after 6 months.
The Mass-Array system by Agena Bioscience is a detection
platform utilizing mass spectrometry to accurately measure
PCR-derived amplicons. It combines the benefits of a multiplexed
primer extension reaction with MALDI-TOF mass spectrometry to
characterize genotypes. The system is ideal for panels from 10 to
400 single nucleotide polymorphisms.
Primers for PCR and single base extension for the SNP of
interest are designed with the assay software. DNA is provided by
the user and will be processed by the Sequence Core Facility:
- Amplification of the region of interest with
- Purification and single base extension
- Dispensing PCR-products on SpectroCHIP
- MALDI-TOF Mass spectrometer Analysis.
This entire workflow can be completed in two
- Custom made assay design
- Panel for the clinical DNA-diagnostics laboratory (70
hotspot mutations in AKT, BRAF, DDR2, EGFR, KRAS, MEK1, NRAS,
- Your own panel for SNP/mutation detection
- Pre-designed panels
- Oncocarta: This panel includes more than 230 somatic
mutations across 19 oncogenes.
- Melacarta: This panel is designed specifically for
metastatic melanoma profiling and offers 70 somatic mutations in 20
- Lungcarta: This panel provides a highly sensitive panel
for evaluating more than 250 somatic mutations in 26 genes for
targeted profiling in non-small cell lung cancer
- GyneCarta: This panel is designed for epithelial ovarian,
cervical and endometrial cancer profiling.
- ColoCarta: This panel is designed for metastatic