Introducing new Jenner facility
Do you have a large number of samples that require DNA or RNA extraction? The Jenner Institute’s QiaSymphony nucleic acid extraction robot has been used for 1000s of successful automated extractions of DNA and RNA and this facility is now available for other University projects, with minimum hands on time, excellent recovery, consistency, purity and effectively zero cross contamination risk. Nick Edwards explains more.
Tell us about the new facility at The Jenner Institute
As part of our Malaria vaccine programme and for over 15 years now, we have been testing the efficacy of new candidate vaccines (once they have passed all the initial safety and immunogenicity tests) by using controlled human infection with malaria (CHMI) challenge trials. Originally, volunteers taking part would be monitored for malaria by the classic thick blood film microscopy. While this works well at higher levels of infection and to score protected vs unprotected volunteers, it tells you very little about whether the growth rate of malaria parasites earlier in the infection has been affected by the test vaccine. Monitoring parasitaemia by doing qPCR on parasite DNA extracted from the blood samples is much more sensitive and informative. In larger Oxford trials, this means monitoring 40 – 60 volunteers twice per day and doing manual DNA extraction from that number twice daily is a significant workload.
Automating the DNA extraction process has transformed how we do the lab monitoring of our volunteers however. The QiaSymphony robot massively reduces the hands on time needed, virtually eliminates cross contamination and improves sample to sample consistently for up to 96 samples at a time. It helps us to do more efficient real time monitoring of our volunteers by qPCR and it is also suitable for larger scale nucleic acid extraction projects of 100s or even 1000s of extractions. A typical CHMI trial in Oxford will involve many 100s of individual extractions and our partner labs at the KEMRI-Wellcome Trust Research Programme in Kenya use their instrument on a regular basis for much larger malaria clinical trials. The JR Hospital has two-of these instruments for their bacterial and viral diagnostics testing, the Oxford Vaccine Group has also just acquired their own instrument and the QiaSymphony is used by Forensic Science labs and many other institutions world-wide, so this is a very well established and supported technology. As well as the QiaSymphony, we also have an Agilent Tapestation for bioanalysis as part of the same facility and this can also be booked separately.
How can the facility help researchers?
Our small research facility can assist with speed, reduce hands on time, offers virtually zero cross contamination risk once samples are on board the instrument and better quality eluted nucleic acids, at least equivalent to that of a highly skilled manual operator. The magnetic bead separation of the nucleic acids from lysed sample material is very efficient, yields are good and because of using freely suspended beads that can repeatedly be magnetically separated from liquid at the binding stages, wash stages and elution stages, the risk of carry-over of potentially inhibitory substances from buffers is reduced compared to silica column methods. DNA extraction is possible from a wide variety of sample types including whole blood, bacteria, swabs, culture cells and even PPE preserved tissue. Similarly for RNA, with the added advantage that as Qiagen own Paxgene, the QiaSymphony is optimised for that workflow and can automate this otherwise very exacting and time consuming protocol. Training can be given so that you can spend time in our labs processing your own samples at a reduced usage rate, or you can commission us to do the extractions for you from you own supplied consumables.
DNA quality is easily comparable with or better than manual extractions and RNA quality from Paxgene extraction is equivalent to that of a skilled operator with RINe values typically between 7 and 9 from properly prepared and stored samples – but you can do 24 at a time two or even three times in a working day, with quality sufficient for all transcriptomics downstream applications. We can also QC RNA samples on site with our Agilent Tapestation 2200 (this will also bioanalyse cDNA and PCR fragments <1Kb, genomic DNA and small proteins depending on your application needs.)
Rates and quotes for Purchase Orders can be generated on request so that you can easily decide if this facility is suitable for your needs and we are happy to discuss pilot projects and take bookings around our own use of the facility, but it is typically available for months at a time between studies. For studies with many 10s, 100s or 1000s of samples, extraction cost per sample can equal or be more cost effective (depending on protocol), with all the additional benefits of freeing up staff time, greater consistency and the other technical advantages, as well as increased simplicity and convenience.
Why is this technique better than others?
Not necessarily better – it depends on what you actually need to achieve, but it is usually very comparable with or an improvement on manual methods in terms of yield and quality. It is also significantly more consistent over a large sample set, reduces operator hands on time and in turn things like fatigue and RSI from 100s of pipetting operations. It’s more productive too, saving lab staff weeks doing extraction that can now be done in days.. The magnetic bead technology also helps improve sensitivity of downstream applications and reduces potential inhibitor carry-over into eluted material. Methods may be customised with assistance from Qiagen and the customer support is excellent. The versatility of the instrument makes it ideal for various medium to large scale projects that might previously have utilised time consuming and tedious manual extraction methods. We would really miss this facility if it we didn’t have it or have access to a similar instrument and we would like to share this incredibly useful bit of kit with other researchers
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