Post-pandemic, PacBio were now able to host their first EMEA distributor meeting which was attended by Dr Oliver Preisig (Executive Director), Dr Hamilton Ganesan & Mr Acclaim Moila. The two day meeting (6-7 December, 2022), held at PacBio’s new EMEA headquarters at King’s Cross (London) was a high-powered meeting introducing the EMEA distributor network to PacBio’s latest game changing NGS instruments, the Revio and Onso.
However, before heading back to South Africa on the 8th, we were kindly invited by Dr ThankGod Ebenezer for an Africa BioGenome Project meeting at the Sanger Institute in Hinxton (Cambridge) and, to meet the Sanger Tree of Life programme team.
Leaving the hustle and bustle of King’s Cross behind on the evening of the 7th, we then slowly (London traffic is not unlike Pretoria’s N1) made our way North East up to the Wellcome Trust Genome Campus in Hinxton, near Cambridge. From the noisy concrete jungle of King’s Cross, we now found ourselves surrounded by the tranquil, nature-filled, impeccably manicured lawns of the beautiful Hinxton Campus.
Early on the morning of the 8th, we were met by ThankGod at the colorful foyer of the Sanger institute (https://www.sanger.ac.uk). This was our first in person meeting with ThankGod after a long stretch of virtual meetings. It was great to experience his effable, friendly, efficient character which was not unlike his online persona.
After a quick photo session (picture), taken by a complete stranger we enlisted there in the foyer, we got ready for our meeting with the Sanger Tree of Life (ToL; https://www.sanger.ac.uk/programme/tree-of-life/) team. We soon found ourselves in a modern, glass enclosed meeting room joined by friendly, welcoming Sanger ToL team leaders. The next hour or so was spent listening to each team leader provide an overview of their functions and how they contributed to the overall objectives of the Sanger ToL organisation. Several AfricaBP members also managed to join us online.
During the presentations we were repeatedly struck by the attention to detail. From accessing sample collection permits from land owners, to pre-sample collection and cataloging to sample handling, all the way to data processing and analysis, every process was overseen by a passionate, dedicated team leader who keenly understood their field and needless to say, were incredibly skilled. It was immediately recognizable, that if there was anyone that could accomplish the task of sequencing the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland (see https://www.darwintreeoflife.org/), this was the place and these were the people. It was made abundantly clear throughout the talks that the end goal was not just to produce data, but rather, to produce high-quality reference-grade genomes which was to be a resource for generations to come, not just in the UK but the world over.
After the talks we were then given a tour of the actual Genome Sequencing facility, the powerhouse that produces all the genome data. Before entering the data production facility, we were dutifully provided with fresh lab coats but nothing could prepare us for the massive fleet of NGS instruments we were confronted with. A mind-blowing number of Sequel IIe’s and illumina NovaSeq’s each running to capacity, in what certainly appeared to be a 24 hour operation. Never had we seen this number of high-end NGS instruments in one place before. Each being fed by a highly skilled lab tech who managed to always get the best out of their instruments. These were, no doubt, experts. Needless to say, we were and still are extremely impressed not just by the efficiency and coherency between the groups, but by the sheer scale of the operation.
Throughout the talks and throughout the tour, we of course had many questions, which were all proficiently answered and there was an overall atmosphere of knowledge sharing and transparency, which was very admirable. Naturally, we tried to soak up as much knowledge, insights and general tips that we could leverage back in South Africa in support of the AfricaBP and its efforts. One of the insights we found particularly useful was that a sample with a good library QC is not always a guarantee of a good sequencing output. There are sometimes ‘impurities’ co-extracted with gDNA that may interfere with the HiFi yield but, there are ways around this, as the Sanger ToL discovered. Also, contrary to popular belief, the entire genome building process is not always fully automatic. A keen eye and intervention by an experienced genome scientist is often needed to assess genome build qualities. Furthermore, it is going to be useful going forward to assign Tree of Life IDs (TOLID; https://id.tol.sanger.ac.uk/) to samples on collection, always ensuring a species name is assigned before further processing. These were just some of the helpful tips that we’re certainly keen on implementing within AfricaBP henceforth.
In traditional British fashion, we ended the day at a pub. In the quaint village of Hinxton just outside the gates of the Wellcome Genome Campus, stood the cozy, medieval styled, Red Lion pub. Here, at our large square table, we continued to engage in scientific (and some leisure) conversation accompanied by superb food. This concluded our visit to the Sanger Institute and our meeting with the Sanger ToL team.