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By Jon Smith
If you’ve decided to take advantage of next generation sequencing (NGS) for HLA typing, your timing couldn’t be better. With the recent introduction of more affordable bench-top sequencers and targeted HLA sequencing panels, NGS is more accessible than ever. Of course, integration of a new technology into a busy lab takes careful planning to avoid teething problems, so now is the time to consider the impact an NGS system will have on your lab, and what you can do to make the transition as smooth as possible.
Be prepared. The next generation of HLA typing is here!
Here are 5 essentials for your integration checklist:
1. Upstream automation
When you’ve splashed out for cutting edge NGS equipment, it can be tempting to make that your sole focus, but chances are that increasing throughput with massively parallel sequencing will highlight upstream bottlenecks. Genomic DNA purification and HLA library preparation are laborious and time-consuming steps that will undoubtedly need to be automated to keep apace with the throughput of NGS.
2. Flexibility for the HLA environment
Automation solutions need to be ultra flexible to handle the vast amount of variation encountered in the HLA lab on a daily basis. Ideally, liquid handlers should give you the freedom to work directly with diverse plate types, primary sample containers and commercial kit reagent tubes. The right automation will simplify your work and minimize turn-around times by enabling you to multiplex many different samples at the same time and combine multiple protocol steps. Features like independent multi-channel pipetting, onboard temperature control, temperature-controlled shaking, magnetic bead separation, an open worktable and flexible operator interface are must-haves to enable you to adapt the platform and protocols to suit evolving requirements.
3. Compatibility with commercial kits
Commercial kits for gDNA purification, DNA quantification and targeted HLA library preparation can make for a more robust and reliable process, but developing and validating automation protocols to integrate these steps can be a major headache. Fortunately, automation providers and vendors are starting to work collaboratively to produce qualified protocols that save you time and effort, while minimizing the risk of human error. For example, Tecan has worked closely with Promega to automate high throughput gDNA extraction from blood and saliva samples with the ReliaPrepTM 96 miniprep kit. In collaboration with Illumina, Tecan has developed qualified protocols for HLA library preparation using the TruSight® V2 HLA sequencing panel on Freedom EVO® NGS workstation.
4. Training needs and error proofing
In a multi-user environment with high staff turnover, the training burden can be high. With the increased scale that NGS brings to HLA typing, mistakes at any stage during sample preparation can significantly reduce cost-effectiveness and delay vital results. In addition to commercial kits and pre-validated protocols, it’s worthwhile looking for automation solutions that have intuitive software with error proofing baked into the operator interface. Protocol wizards and visual displays for easy verification of the set-up can help catch errors before they cause problems, and make it much easier for staff to create and adapt protocols.
Even with the best preparation things can go wrong, so it pays to have frank conversations early on with equipment providers about the level of service and experience available to help you integrate new equipment and overcome any problems quickly. Fortunately there is no need to reinvent the wheel when adopting NGS technology. Tecan’s technical integration team has a wealth of experience working with major research centers and leading experts to integrate NGS platforms for genomics applications. They can help you overcome teething problems and tailor automation solutions to suit the specific needs of your lab.
With the above preparation checklist in hand, you’re well on the way to faster and more reliable HLA typing. Download our application note to see how automating Illumina’s TruSight® HLA library preparation protocol with the Freedom EVO® NGS workstation can enable you to produce high-throughput, sequence-ready HLA libraries in less than one working day.
Download the application not “Automated library prep for Illumina TruSight HLA v2 Sequencing Panel":
Evaluating the quality of DNA for Next Generation Sequencing, genotyping, and other downstream applications