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DATA CATALOGUE

The database of Hartwig Medical Foundation is the world’s largest database of metastatic tumor data obtained through Whole Genome Sequencing (WGS) in combination with clinical data. The types and percentages of tumors recorded in the database represent the incidence of solid tumors in the Netherlands. In addition to molecular data, the database also contains a growing list of tumor characteristics and data on treatments and treatment outcome. The data in the database are of the highest quality thanks to the use of a completely uniform procedure that is applied to all samples, from the results of the biopsy to the bioinformatic analyses.

Data generation

The DNA (obtained from a biopsy of the tumor) and a blood sample of every patient are analyzed using Whole Genome Sequencing (WGS). Germline variants are determined using the blood sample and insight is gained into the tumor-specific variants by comparing the blood with the tumor biopsy. The tumor-specific variants include single nucleotide variants (SNVs), insertions and deletions (INDELs), structural variants (SVs), and copy-number alterations (CNAs), which are identified using state-of-the-art open-source bioinformatics tools. The blood DNA is read 30 to 40 times on average, while the tumor biopsy DNA is read between 90 and 120 times on average. It is standard practice to take biopsies immediately prior to treatment, but for a small group of patients a second biopsy was also  taken after the initial treatment.

Validation

More information on the technical details and the performance of WGS analyses, sample requirements and an overview of all validation experiments can be found in the Hartwig Medical OncoAct Technical Information document.

Bioinformatic analyses 

dna string

Hartwig Medical Foundation uses a state-of-the-art IT-pipeline for their bioinformatic analyses. 

Distribution of tumor types in the Hartwig Medical Database

 

Hartwig Medical Database

The figure below displays the distribution of tumor types in the database.

The database currently contains WGS data of over 4,500 metastatic tumor samples distributed across a broad range of tumor types. The database also contains a large amount of clinical data in addition to the WGS data. To request access to data in the database please visit this page.

A subset of data (somatic variants of 2,399 samples) extracted from the database can be viewed in a graphic interface (portal). This subset corresponds to the data used in the pan-cancer paper published in Nature by Priestley et al. (pre-print available). The portal allows users to browse through different levels of the data  (see the example queries on the right side of the portal webpage).

Watch this video: Genomic database of cancer patients in the Netherlands (in Dutch)