By Enrique Neumann
It’s an exciting time to be working in genomics. The explosion of sequence data and library preparation methods along with big advances in areas like gene editing and bioinformatics, is paving the way for breakthroughs that seem more like science fiction than science fact. But behind the scenes, day-to-day activities in the genomics lab can be a real drain on your resources and your patience, leaving you little time or energy to focus on the things that really matter. We all have only 24 hours in the day, so how is it that some genomics scientists are chronically stressed out and barely managing to stay afloat, while others seem to produce the goods with ease?
We turned to one of Tecan’s own experts, Dr. Marilena Meloni, for some insight.
Tell us a little about your background as a genomics scientist, Marilena.I did my PhD at University of Insubria, in Italy, where I specialized in conservation genetics.
My work studying genetic diversity and plant adaptation has taken me all over the world, including the University of Zurich, where I used genotyping by sequencing (GBS) methods to investigate interactions among plant communities.
About 6 months ago, I joined Tecan as a genomics application specialist. One of the main things I’m working on is the automation of commercial kits that are used to prepare genomic libraries for next-generation sequencing (NGS).
Your work in conservation genetics is fascinating. What motivated you to work in industry?
Over the past decade or so, I’ve experienced first-hand the remarkable transformation that’s taking place in genomics. Powerful technologies like NGS are completely changing the way genomics scientists work in the lab. After years in the field, I was motivated to share all the practical knowledge I’d acquired about NGS methods. I wanted to help scientists in genomics work as efficiently as possible, and hopefully enable them to avoid some of the hurdles, inconveniences and sources of error that I’ve encountered along the way.
How have genomics labs changed over the past 10 years?
Everything is completely different! When I started my second post doc in Zurich about 10 years ago, NGS was still extremely expensive, so like most labs we couldn’t afford it. After 3 or 4 years, NGS quality improved, the process continued to become more affordable, and more kits became available, so a lot of us started doing NGS. It really felt like a revolution. Suddenly, a huge number of samples could be processed at once. We had mountains of sequence data, but we also had issues in analyzing this data. The sequences were quite short, with high error rates depending on the platform used, and therefore alignment was difficult, especially for non-model organisms for which a reference genome was not available. So although there was an abundance of data, you faced the problem of analyzing this data.
And what is like for the genomics scientist today?
Well, now we have much better and more affordable sequencing platforms, improved informatic analysis methods, and also kits that make the workflows simpler and more robust. Sequences are much longer, and you get very high coverage. All this makes it easier to study and understand genomes. There are kits for species that are known and commonly used in labs—like Arabidopsis, mouse, human—but also there is the opportunity to study organisms that are less well known. So today’s problems are quite different from those earlier on.
Wondering how to be a genomics rock star? Tecan genomics application specialist Dr. Marilena Meloni has some advice.
What sort of hassles and problems are prevalent in genomics labs now?
That depends on the study you are doing or the reason why you are doing NGS, but problems start well before you get to the actual sequencing – at the stage of nucleic acid isolation and library preparation. And many of the problems come from either doing things manually or not getting the automation right. For example, manual library preparation is a crazy job in terms of pipetting steps. You are typically processing a lot of samples at the same time.
From start to finish in NGS library preparation, there is a huge number of pipetting steps with very small volumes, and for each and every one you need to be precise, accurate and absolutely error-free to avoid cross-contamination and incorrect results. It’s still an expensive technique, so mistakes can cost you a lot of money – that can really add to the pressure. The process is not extremely complicated, but it’s very long. It can take days, depending on your requirements, so it can be tedious, and it can be boring…and of course that leads to mistakes. Machines are much better than humans at these repetitive tasks, so it’s really worth the investment to automate the sample preparation steps.
What about people doing NGS in a more regulated environment like a clinical lab. Do they encounter different problems?
Regulated labs have many of the same problems and needs as non-regulated ones, but the consequences of error can be much greater in terms of human health. Cross-contamination can be a major issue. With NGS we are able to process samples from lots of individuals at once and mix libraries together. The sequences are then differentiated on the basis of built in ‘barcoding’ or indexing. So if, for example, there is cross-contamination in the adapters used for indexing, you can easily end up attributing a particular result to the wrong individual, and that can have serious consequences for the patient.
Also, we work with extremely small volumes, so even tiny pipetting variations can end up leading to poor quality or a false result; there’s very little tolerance for imprecision. With such complexity it is very easy to miss one well, which could even lead to the loss of an irreplaceable sample. Again, good automation can address many of these problems. Compliance is another key aspect for regulated labs to consider when they are choosing automation solutions because they absolutely need to have full traceability of human samples.
Any advice about what sort of library preparation and NGS automation to go for?
Yes, the automation that you choose and the way it’s programmed make a big difference in productivity and the quality of your results:
- You need speed and quality to be truly productive – Clearly, sample throughput is important with NGS to avoid bottlenecks, but you also need to check the system specifications and make sure it will deliver the level of reliability, precision and accuracy that are essential for high-quality NGS library prep. The sequencing results you get will only be as good as the library that you start with.
- Flexibility - A platform that is compatible with common kits but also gives you plenty of flexibility will help you adapt quickly to changing protocols, requirements and applications. The number of kits is increasing and new technologies make them more effective, so it is key to be prepared to adopt new workflows and NGS methods.
- User-friendliness – Some systems are less intuitive and user friendly than others, and that can waste your time significantly. If a system is difficult to use, people spend far more time and effort than necessary gaining confidence with it, setting up and editing protocols, and training new users. Ideally, you want a smart and intuitive user interface that will guide people through the set-up and actually help them to avoid making mistakes. This way you can reduce the training needs of the operator to only a few hours.
- Compliance – Especially if you are working in a highly regulated environment, look for a system that has been designed by people who understand the compliance issues you face. A well-designed and compliant system can make qualification, validation, data traceability, documentation, auditing, etc. much easier.
Given that most genomics scientists are facing the same types of problems, what do you think differentiates the ‘competent’ genomics scientists from the real ‘rock stars’?
In a word? Perfectionism. But I mean perfectionism applied with intelligence. The ultimate genomics ‘rock stars’ recognize the need to be fast and productive, but they never take their focus off quality. Take library preparation for example: every single step in the process is fundamental. There is nothing that can be more or less good. Starting from DNA extraction through to the very end when the library is ready for sequencing, every step must be perfect. That doesn’t mean you have to be super-human to be a ‘rock star’ – you just need to be aware of where problems are likely to occur, and then put measures in place to make sure that mistakes don’t happen. This is where good automation comes in – the right solution enables you to be a perfectionist without a lot of wasted time and effort. It takes away most of the risk and worry and frustration, so you can concentrate on rocking the world with your results!
Wondering how to make your NGS data rock?
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About the author
Dr Enrique Neumann is Product and Application Manager, Genomics, at Tecan, Switzerland. He studied Biology at the University of Santiago de Compostela, Spain. During his PhD at the University of Edinburgh, he focused on the molecular processes in plant cells. He joined Tecan in 2015 and focuses on the development and support of genomic applications for Tecan’s liquid handling platforms.