Whole-methylome profiling was performed on plasma cell free DNA samples obtained from 120 prostate cancer (PC) patients and 18 men with cancer-negative prostate biopsies (NPCC). PC samples represent multiple disease stages, including localized PC (LPC), hormone-sensitive PC (HSPC), metastatic castration-resistant PC baseline (mCRPC_BL), mCRPC at 1st follow-up scan (mCRPC_sc1), mCRPC at 2nd follow-up scan (mCRPC_sc2). Plasma samples were collected at Aarhus University Hospital, Denmark, between 2006 and 2022. Libraries were prepared from up to 100ng cfDNA and split into immunoprecipitated (IP) for cfMeDIP-seq and input control (IC) for low-pass whole genome sequencing. All libraries were paired-end sequenced, IPs at 1.5x coverage and ICs at 0.5x coverage per sample. Bioinformatics processing of raw fastq files included demultiplexing using bcl2fastq v/2.20.0.422, trimming of adapter sequences using Cutadapt v/1.16, mapping to the hg19 reference genome using BWA MEM v/0.7.15, removal of PCR and optical duplicates using Samblaster v/0.1.24, and realignment using GATK v/3.8.1.0. The dataset contains bam files and their index files.
| Samples | Technology | Sequencing platform |
|---|---|---|
| NPCC_1_IP … NPCC_18_IP, | Illumina NGS | Illumina(R) Novaseq |
| LPC_1_IP … LPC_10_IP, | ||
| HSPC_1_IP … HSPC_40_IP, | ||
| mCRPC_1_BL_IP … | ||
| mCRPC_70_BL_IP, | ||
| mCRPC_49_Sc1_IP … | ||
| mCRPC_70_Sc1_IP, | ||
| mCRPC_49_Sc2_IP … | ||
| mCRPC_70_Sc2_IP, | ||
| NPCC_1_IC … NPCC_18_IC, | ||
| LPC_1_IC … LPC_10_IC, | ||
| HSPC_1_IC … HSPC_40_IC, | ||
| mCRPC_1_BL_IC … | ||
| mCRPC_BL_70_IC, | ||
| mCRPC_49_Sc1_IC … | ||
| mCRPC_70_Sc1_IC, | ||
| mCRPC_49_Sc2_IC … | ||
| mCRPC_70_Sc2_IC |
Kondrup et. al. Genome-wide methylome profiling of cell-free DNA enables prognostication of patients with castration-resistant prostate cancer.
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, 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)