Low-pass whole genome sequencing was performed on plasma cell free DNA samples obtained from 331 prostate cancer patients and 18 men with cancer-negative prostate biopsies. Samples were collected at Aarhus University Hospital, Denmark, between 2006 and 2023. Libraries were prepared from up to 100ng cfDNA and paired-end sequenced at 0.5x coverage per sample. Bioinformatics processing of raw fastq files included trimming of adapter sequences using Cutadapt v/4.8, mapping to the hg38 reference genome using BWA MEM v/0.7.17, and sorting and indexing using Samtools v/1.20. The dataset contains bam files and their index files.
| Samples | Technology | Sequencing platform |
|---|---|---|
| Control_1, PC_1 … Control_18, PC_331 | Illumina NGS | IlluminaⓇ Novaseq |
Olsen et. al. Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types.
External researchers (academic or commercial) interested in analysing the prostate dataset will need to contact the Data Access Committee via email to kdso@clin.au.dk. The Data Access Committee is formed of Karina Dalsgaard Sørensen, Michael Borre, Britt Elmedal Laursen, and Ole Halfdan Larsen (Department of Clinical Medicine, Aarhus University). Due to Danish Law, for the authors to be allowed to share the data (pseudonymised) it will require prior approval from The Danish National Committee on Health Research Ethics (or similar) for the specific new research goal. The author (based in Denmark) has to submit the application for ethical approval, with the external researcher(s) as named collaborator(s). In addition to ethical approval, a Collaboration Agreement and a Data Processing Agreement is required, both of which must be approved by the legal office of the institution of the author (data owner) and the legal office of the institution of the external researcher (data processor).