- Dr Anneke Seller, formerly Director of Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust
- Penny Clouston, Consultant Clinical Scientist, Oxford University Hospitals NHS Foundation Trust
- Julie Evans, Registered Clinical Scientist, Oxford University Hospitals NHS Foundation Trust
In this film, we will outline the processes for receipt of blood samples for whole genome sequencing for both rare disease and cancer.
Samples must be received within six hours of being taken and ideally processed promptly. So transport logistics need to be optimised and the laboratory should be informed in advance of specimen arrival.
Julie Evans: It’s important that we process the samples correctly so that we don’t have to go back and get another blood sample from the patient.
This table, taken from the current NHS England specification, shows the preferred volume of blood and the number of tubes expected for each participant in the rare diseases programme. In cases where only small volumes of blood are obtained, for example in neonates and acutely ill children, laboratory workloads could be altered so that plasma is collected prior to the extraction of DNA from the EDTA sample.
Open all packages carefully in your designated specimen reception area following your usual protocols for unpacking clinical samples. The Genomics England sample linkage form should accompany all referrals for the 100,000 Genomes project. Depending on your local protocols, you may also receive other relevant patient information, such as copies of the 100,000 Genomes consent forms.
Penny Clouston: The requirements for trios for the rare disease part of the testing is to have three samples. The first is from the affected proband and the remaining two samples are usually from close relatives, ideally from the parents.
DNA will be extracted from both tumour tissue and from peripheral blood for the cancer programme. Patients should have their blood samples taken prior to biopsy or resection and before any anaesthesia is administered.
This table shows the recommended sample requirements for DNA extraction and for omics investigations. Note that an additional EDTA tube is required for the future extraction of circulating cell-free tumour DNA. In cases where it is not possible to collect sufficient blood for all of the investigations, priority will be given to the collection of the EDTA samples for DNA and for circulating cell-free tumour DNA. FFP tumour samples are stable at room temperature. However, ideally, fresh frozen samples should not be allowed to thaw prior to commencing DNA extraction procedures. Seek advice from Genomics England if necessary.
Dr Anneke Seller: Obtaining DNA of sufficient quality to consistently yield good whole genome sequencing results is really difficult and processes will continue to evolve as new evidence emerges. You will need liaise closely with your histopathologist or your oncologist to know exactly which samples you’re expecting to receive and when they might arrive in the laboratory.
Using your standard protocols for sample verification, check that all samples are correctly barcoded and the name, date of birth and hospital number match the information on the sample linkage form, or specimen referral form, and the consent form. If there is a discrepancy, speak to your supervisor or GMC project manager, or follow your standard protocols. It’s good practice to separate your tubes into different racks so that you can easily tell which samples are for DNA extraction or for plasma preparation, for example. You will need to log your samples onto your lab’s information management system before you start to process them.
Penny Clouston: The samples for the 100,000 genomes project are really important and they need to be prioritised. It’s absolutely vital that they are treated and processed immediately and that the relevant people are informed of their arrival in the laboratory. This means that we can produce high-quality samples which can go forward for whole genome sequencing.