Low-pass whole genome sequencing was performed on plasma cell-free DNA samples obtained from 134 colorectal cancer patients from the GECOCA cohort (Dataset A) and 34 cancer-negative subjects from the Blood Bank at Aarhus University Hospital, Denmark (Dataset B). Libraries were prepared with up to 80 ng of cfDNA and paired-end sequenced to a median sequencing coverage of 2.23× (IQR: 0.33) 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.
| Dataset ID | Sample Type | Technology | Sequencing platform |
|---|---|---|---|
| A | cfDNA from CRC patients | Illumina NGS | IlluminaⓇ NovaSeq 6000 |
| B | cfDNA from individuals with no cancer | Illumina NGS | IlluminaⓇ NovaSeq 6000 |
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 colorectal cancer dataset will need to contact the Data Access Committee via email to cla@clin.au.dk. The Data Access Committee is formed of Claus Lindbjerg Andersen, Mads Heilskov Rasmussen, 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).