The Hartwig Medical Foundation database is growing with whole genome sequencing data of about 40 patients per week. Currently (March 2017) WGS data of ~900 patients with metastatic cancer are available. A distribution of tumor types present in the database is shown in Figure 1 below.
Data is obtained by tumor-normal pair WGS of tumor biopsies at a depth of 90-120x and blood at 30-40x. Data is analysed for germline variants (BWA-GATK pipeline on blood) and somatic variants (combination of 4 somatic variant callers: Strelka, Freebayes, Mutect and Varscan).
Patient data on tumor characteristics, treatment and treatment outcome are continuously collected for all patients. Biopsies for WGS are taken pre-treatment and to a limited extend post-treatment biopsies were collected and sequenced as well. An overview of treatment types present in the database is shown in Figure 2 below.
Figure 1: Distribution of tumor types in the Hartwig Medical Foundation whole genome sequencing database.
Figure 2: Overview of treatment types, numbers and percentages of total. Not filled in yet indicates patients for which local data entry is still in progress.
Figure 3: Analysis of mutational load distribution over samples and average mutational load per tumor type.