Study description

Low-pass whole genome sequencing was performed on plasma cell-free DNA samples obtained from 114 colorectal cancer patients and 142 cancer-negative subjects. The samples were obtained from the previously reported Danish Endoscopy II study (PMIDs: 32884322 and 27935033). Libraries were prepared with 15 ng of cfDNA when available, or the entire purified amount under 15 ng, and paired-end sequenced at a median sequencing coverage of 1.17× (IQR: 0.31) per sample. Bioinformatics processing of raw fastq files included trimming of adapter sequences using Cutadapt v/3.0, mapping to the hg38 reference genome using BWA MEM v/1.10, sorting and indexing using Samtools v/1.21, and filtering duplicated reads using GATK4 MarkDuplicates v/4.1.9.0. The dataset contains bam files and their index files.

Original publication

Olsen et. al. Cross-dataset pan-cancer detection: Correlating cell-free DNA fragment coverage with open chromatin sites across cell types.

Data access

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 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).