12 July, 2023
Hello! My name is Chris Fox, and I’m a sequencing specialist working within the Genomics facility housed in the Michael Wakelam building. I’ve been at the Babraham Institute for four months, which is just long enough to have settled into a routine but not so long that I’ve finished learning about the many facets of working in the facility.
In the Genomics facility, we perform library preparation and quality control (QC) on samples sent to us to ensure they are suitable for our other main offering, DNA sequencing. Library preparation involves attaching identifying ‘barcodes’ to DNA samples which is important for identifying sequences after data has been generated. QC allows us to work out concentration and size of the resulting DNA fragments, and spot any contamination. Sequencing is then performed; DNA sample fragments are loaded into the machines which are read by fluorescence chemistry as a series of bases. This sequence is then recorded and compared against other sequenced fragments like a jigsaw piece to recompile a complete image of that sample’s genetic code for use by researchers.
My previous job involved a lot of high throughput and similar sequencing and QC work, however my interest in research led me to the Institute where I could work more closely with academics to support science answering key questions about health and ageing. For me, the Institute users’ fast-paced and differing needs make this a fantastic place to work, as I am surrounded by so many interesting new projects each day. I enjoy working in a smaller, more coherent team and having frontline access to the cool and diverse topics that pass through our facility!
The Genomics facility is comprised of me and the facility manager Megan Hamilton, who is here an hour before me and greets me when I walk in from the bus at 9am. From the time she arrives, Meg will have first checked the quality of any overnight sequencing runs, entered relevant data into our records and filled in the associated paperwork. A large part of sequencing is tracing results from one run to the next to get an understanding of how particular DNA libraries using different preparation methods from specific users can be better sequenced, so this record keeping is very important.
When I arrive, we check our sequencing run tracking system to see what quality control procedures and sequencing will need to be done that day. This will influence the reagents we need to use and help us plan the day. I will then go and get out any reagents that may need to defrost: some of our kits can take upwards of three hours to defrost in a water bath before we can use them!
The morning is also a good time to perform any maintenance washes the sequencers may require, and head to stores if we have any samples that need sending to the NovaSeq sequencers on the Addenbrookes CRUK campus. On days when we are preparing DNA libraries for somebody my morning can look very different, as library prep protocols can be very long (potentially three days) and tend to take over a whole person’s schedule for that time.
To make sure our sequencers can give the best results possible we quantify samples sent to us before we run them on the sequencers themselves, via use of a BioAnalyser and qPCR which I will tend to run after the morning checks are done. This data is sent back to the sample owners before we begin the sequencing run so that they can double-check the sample quality and give us the OK to start.
Machine maintenance, investigating the quality of previous runs and preparing reagents, combined with checking and following up with emails, can take a good part of our day-to-day. Planning our time is important to meet deadlines - we have two sequencers in the facility and some sequencing runs take 40+ hours to complete. When deadlines are tight for projects we make ourselves available for questions and feedback from users any time throughout the day, by email or a quick chat, until around 12 when we’ll have lunch. This is almost always with members of the Flow Cytometry facility next door, and if we have an ongoing library prep might need to start a little later, but is a much-appreciated break!
Next on to the loading plan. Once a sample has been assessed for quality and concentration and the type of run selected, we can begin work on a loading plan. Each sequencer has very different requirements for concentration and volume when being loaded, and all sorts of other factors from DNA sequence to library prep method can change how we load samples.
I begin by looking through our records for samples with the same traits or from the same methods, preferably from the same user, and collaborate with Meg on a plan that gives the best quality and quantity of data. Too much sample, the quality of sequence reads drops dramatically. Too little and the surface of the flow cell will be underpopulated resulting in far less data generated. This tightrope can be frustrating to walk at times with all the variables mentioned prior, but coming in to see a perfect run makes it all worth it!
Upon finding and agreeing on a good loading plan, and with any special requests like custom read lengths/primers considered, we can begin the process of loading the sequencers. This is generally done in the afternoon and is my favourite part of the day, as the loading of a sequencer is very methodical in contrast to the many variables of a loading plan. Some people may not find quite as much joy in obsessively pipetting the exact amounts needed in the same way each time, but there’s a nice peace in getting more and more consistent that I find satisfying. As we use incredibly specific and small volumes for sequencing, generally µl of nM concentration liquids, the pipette work must be very precise, and reagents must be prepared just so to get the best yield possible.
Once the run is on, the lab space must be tidied up and reagent usage catalogued: not my favourite task but an ordered lab is a happy lab, and I’m glad for this step the next day when looking for a specific pipette or reagent. Most of our afternoon is spent reorganising and finishing tasks, and again corresponding with researchers on their samples and sequencing runs. Recently I’ve been devoting office-time to understanding upcoming library prep and sequencing technologies so that we might be able to offer them as options in future, and troubleshooting any anomalies we might notice in sequencing data. After Meg leaves I’m here for about an hour to receive samples, return emails and perform any remaining runs or analysis we might have left over.
On Wednesday morning, if I have time I will attend weekly meetings with our Epigenetics programme to get insight into their experiments, ideas and needs from our facility. Occasionally, I attend conferences as part of evaluating which technologies we could adopt next. This level of investigation and understanding across so many topics is why I’ve enjoyed working here so much, as I can (at least try to) learn and bring all of this information to researchers and postdocs who can use it to advance their work. I’m very appreciative of this opportunity to gain a great amount of understanding within my field in terms of both the abstract science and the physical real-world applications and excited to continue!
At the end of a day I’ll hop on the bus to Cambridge and head back home, then watch some TV and do a bit of meal prep ready to bring in for tomorrow. So, that’s a representative day in the Genomics facility!
12 July 2023
By Alumni Blogger