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CliveOME cfDNA dataset

By Chris Wright
Published in Data Releases
May 18, 2022
1 min read
CliveOME cfDNA dataset

We are pleased to release a cell free DNA (cfDNA) dataset to our s3://ont-open-data resource.

Normal blood plasma contains background amounts of short degraded extracellular DNA - these DNA fragments typically range from 50bp to 200bp in length. The DNA is of cellular origin but has been released into the blood during cell lysis. The fragments may be either of nuclear or mitochondrial origin and are collectively referred to as cfDNA. Much of the cfDNA circulates still packaged with nucleosomes; 147bp of DNA are wound around the nucleosome.

The concentration of cfDNA fragments correlate both with age and disease. Cancer patients often have elevated cfDNA levels that also reflect the mutations that have been acquired within a tumour’s genome. This observation has enabled the techniques of liquid biopsy. Isolated cfDNA may be used to non-invasively screen for genetic biomarkers associated with cancer types and stages.

Our recent updates to enable short-fragment sequencing on Nanopore devices open exciting new horizons for cfDNA sequencing. This cfDNA dataset release has been prepared from a blood sample provided by our CTO, Clive Brown. The cfDNA was isolated from 7 ml fresh plasma using then QIAGEN ccfDNA Midi Kit. The manufacturer’s instructions were followed. QC was performed using both the Agilent Bioanalyzer and the Qubit dsDNA high sensitivity assay. 30 ng of cfDNA was used to prepare sequencing libraries using the new SQK-LSK114 kit. The end prep SPRI concentrations were increased by 3x.

Kernel density estimate depicting the read length distribution for short fragment mode cfDNA sequencing.
Kernel density estimate depicting the read accuracy for short fragment mode cfDNA sequencing. Peaks in to plot correspond to 0, 1, 2, etc. errors per read.

The FAST5 files from the sequencing run have been placed within our Amazon S3 bucket publicly available at:

s3://ont-open-data/cliveome_kit14_2022.05/cfdna.

More information on downloading the data from s3://ont-open-data may be found on our Open datasets Tutorials page.

We aim to enhance this dataset in the coming days with a standard genomic DNA dataset, and provide 5mC basecalls.

We hope that you have some interesting explorations within this dataset.


Tags

#datasets#cfDNA#R10.4.1#basecalling
Chris Wright

Chris Wright

Director Customer Workflows

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