Skip to Main Content
Welcome to the Marketplace

Go to Main Navigation

Netherlands Cancer Institute (NKI) Sequencing Core Facility

Year Established:
Amsterdam, , NL
Company Type:
Academic Core Facility


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 length.

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 primer.

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.

Mass spectrometer

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 PCR
Purification and single base extension
Dispensing PCR-products on SpectroCHIP
MALDI-TOF Mass spectrometer Analysis.
This entire workflow can be completed in two days.


- Custom made assay design

Panel for the clinical DNA-diagnostics laboratory (70 hotspot mutations in AKT, BRAF, DDR2, EGFR, KRAS, MEK1, NRAS, PIK3CA)
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 oncogenes.
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 (NSCLC).
GyneCarta: This panel is designed for epithelial ovarian, cervical and endometrial cancer profiling.
ColoCarta: This panel is designed for metastatic colorectal cancer.

Site Badges
Netherlands Cancer Institute (NKI) Sequencing Core Facility
Plesmanlaan 121 Amsterdam, , 1066 CX Netherlands
Netherlands Cancer Institute (NKI) Sequencing Core Facility
121 Plesmanlaan Amsterdam, NH, 1066 CX Netherlands

Get started

If your organization has a marketplace, you can log in here to order products and services directly.

If you're interested in ordering custom research services from suppliers in the network, book a meeting with our team here.

To order products instantly, request access below.

Password must:

• Be at least 12 characters in length

• Contain a lowercase letter (a-z)

• Contain an uppercase letter (A-Z)

• Contain a numeral (0-9)

• Contain a special character (%, $, !, @)

By signing up for this account you agree to the Terms of Service