How do you sequence over 240,000 whole human genomes?

Danni Weldon leads the team responsible for receiving the sample deliveries, unpacking them, scanning them into the laboratory information tracking systems (LIMS) and undertaking quality control checks on the plates, tubes and DNA.

“It was like a factory line, handling such large volumes all at once, and then quantifying the DNA in each sample, and cherry-picking the samples to adjust the concentrations – all in a very short space of time.”

The next step is library preparation, where the DNA is readied for the sequencing machines. Jamie Lovell started at the Sanger Institute as a ‘finisher’ on the Human Genome Project. He now leads the library preparation team in DNA Pipelines.

“Working on the Human Genome Project was amazing, everyone was all in the same boat; we were all looking for the same outcome. It was just such a social time. Plus, I was a lot younger then.”

“Obviously the biggest change since then is the sequencing machines, and I’m sure they will change again. They are so hungry for DNA. From the library preparation side, we are only just keeping up. But as more robotics are brought in – and I’ve half a mind to develop some systems myself – that will also change.”

Tom Whitely manages the Laboratory Information Management System (LIMS) team that tracks the samples through the Institute.

“The samples go through a complex and varied workflow, from reception, refrigerated storage, quality checks, to stamping robots, until eventually the samples are put into a sequencing machine. Depending on the results the whole process may have to be repeated to reach the gold standard sequence quality we require. We have to be able to track and report back on all of these lab processes to UK Biobank, and combine it with the final results. The reporting is a lot more rigorous than we’d done before. And definitely not something you can do manually when there are 240,000 samples.”

“The mindset is more like manufacturing. We have to do a set of operations consistently and repeatedly. It’s a slightly different approach to life, compared to research where you are trying to prove a hypothesis.”

The next laboratory step sees the DNA libraries loaded onto the Illumina Novaseq machines, overseen by Tristram Bellerby.

For UK Biobank, the team was able to reach multiplexing, or pooling, of 32 individual human genomes in a single flow cell, with two flow cells on each of the 17 machines.

“I liaise closely with the Sequencing Research and Development team, and Illumina, to make sure everything is optimised. For UK Biobank, we adjusted our loading concentrations to get the best results and the most data per run. We improved our processes over the course of the project.”

Each Novaseq produces 1.8 terabytes (TB) of data every day, as it turns the chemical structure of DNA into digital code. There is a huge computational task to turn the raw data from the machines into data that represents whole genome sequences. This includes running algorithms to de-multiplex the pooled data, and to join the billions of fragments of code together into contiguous pieces that represent a person’s genome.

Much of the process has been automated over the years, and software engineers, data managers and informaticians are essential to oversee and develop the data flows.

The data processing and analysis for all of the Illumina sequencing at the Sanger Institute are overseen by David Jackson and the Sequencing Informatics team.

For the main phase of the project, the team also constructed a data pipeline to transfer raw data to their analysis partner, Seven Bridges Genomics, and pull key metrics back, whilst the sequence data products were submitted to UK Biobank.

“Quality control was an important issue – there was more reporting than we’d done before. But this close monitoring drove improvements in the laboratory steps of the process, as we could quickly see any issues in the data, and feed these back, working together to find what the cause was and how to resolve it.”

After the data are transferred to UK Biobank, they are made available to researchers undertaking vital research into the most common and life-threatening diseases.

Professor Nicole Soranzo, Senior Group Leader at the Wellcome Sanger Institute, said: “UK Biobank data are so vast, and so detailed. It has changed the way we do research in human genetics.”