Automation of Cell Free DNA from Blood

Hazel Ingram
Sian Morgan
Joshua Jones
Antony Harris

Industry Partners: Antenatal Screening Wales Qiagen Ltd

Cardiff and Vale University Health Board

The project is to validate an automated method of extraction of cell free DNA from blood, to introduce into service for the Institute of Medical Genetics. The project is being carried out in collaboration with Qiagen, transferring from the current manual method using the QIAVac, to the automated system using the QIAsymphony.

Currently the extraction team at the All Wales Medical Genetics Service are undertaking manual extraction of these samples in a time consuming, difficult process that is open to error. In order to meet anticipated demands for this growing technology, an automated extraction method is required. The implementation of automated cell-free DNA extraction from blood would mean that more samples can be processed in a shorter time period, with less room for error.

Project Plan

February: Procure consumables from Qiagen

March-September: Sample Collection. Samples would be collected from 2 areas:

June-October: Training and extraction of samples.

September-October: Completion of validation paperwork, SOPs.

October: Introduce service into lab.

Recent developments in technology has shown that cell free DNA is a useful resource with vast potential for cancer patients (circulating tumour DNA) and in prenatal testing (free fetal DNA). As a laboratory we are expanding our services to offer genetic analysis to these categories of patients.

Analysis & Approach

A legal issue regarding the tendering process meant that there were delays to the initiation of the Non-Invasive Prenatal Testing (NIPT) validation project. This in turn impacted on this automation project, by the fact that there were no samples to extract.

This was added to by the lack of samples collected by the cancer teams, due to a mixture of consent, eligible patients and volume of sample received.

To date approximately 15 samples have been received that may be used for the automated extraction. This will increase in the next month to allow training to begin.

Goals & Targets

Improved healthcare outcomes:

Laboratory able to provide automated cell free DNA extraction service throughout Wales.

Improved patient experience/safety outcomes:

More patients will be able to reliably access non-invasive services for either personalised medicine (avoiding the need for tumour biopsy) or pre-natal diagnosis (avoiding the need for amniocentesis). This will allow our laboratory to expand our downstream testing repertoire, resulting in further benefits from cancer patients and allowing our NIPT service to thrive.

We can evaluate the output DNA using our standard quantification methods (Nanodrop and Qubit), and through downstream processing. This project would benefit two groups of patients: cancer patients with poor health who cannot undergo surgery can be genetically tested to elucidate effective treatments; it also reduces risk of miscarriage in pregnancies, by avoiding the commonly used amniocentesis test.

Resource efficiency:

Reduction in hands-on time.


We expect the accuracy of the extraction to be improved, processing a large number of samples would be impossible in the same time period, and with the same level of consistency.

Future State

At the current time, the project has not moved forward. Samples are currently being collected to initiate the project. This has resulted in a huge delay to the project, but the team is confident that an automated service is still possible and achievable. The project is vitally important to being able to offer patients the best healthcare, while ensuring the laboratory is the most efficient it can be!

This Project Supports Prudent Healthcare

Principle 1: This validation will ultimately providing a better Health Service for antenatal and oncology patients, allowing the Laboratory to provide a robust non-invasive genetic testing service, as a cost-effective and low-risk alternative to surgery, and therefore improving the patient experience.

Principle 2: Automating our extraction service will allow the Laboratory to increase the number of extractions we can currently perform from 24 in 6 hours to 96 in 6 hours. The amount of hands on time will be reduced significantly.

Principle 3: If the validation is successful, there will ultimately be a reduction in the number of invasive pre-natal testing and also the number of biopsies taken, as we are able to provide a non-invasive genetic testing service.

Principle 4: The QIAsymphony eliminates manual pipetting errors, ensures standardisation and avoids contamination with the use of tip guards and built-in UV lamps. The system has a barcode reading system to allow full sample tracking throughout the process. Publications from Qiagen have shown the automated system compared to manual produces a higher concentration better quality DNA, and this particular machine is being used in other laboratories, Great Ormond Street Hospital and Dundee Genetic Laboratories for cell free DNA extraction.

Part of Cohort Bevan Exemplars 2015-16