HMF Whole Genome Sequencing database catalog

The Hartwig Medical Foundation database is growing with whole genome sequencing data of about 40 patients per week. Currently (summer 2018) WGS data of more than 3.000 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 variation (SNV/Indels via Strelka, SVs via Manta and copy numbers, purity and ploidy using a custom-built tool called Purple). 

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.