Over the last five years, we've only seen incremental improvements and advancements in sequencing platforms, with innovations and creativity focusing instead on new applications and library preparation methods. Certainly, advancements in proteomics, spatial biology, and single-cell platforms are notable areas of technological advancement in high-throughput biology, but sequencing has been relatively unchanged.
This year will undoubtedly be remembered for the greatest diversity of new platform launches in the history of genomics. The first half of the year saw the full commercial la sunch of the Element AVITI System and the release of data, specifications, and early shipments on two other platforms (Ultima's platform and Singular's G4 sequencer). Pacific Bioscience has described the preliminary capabilities of their recently acquired Omniome platform, with a launch expected in 2023.
The interesting thing about the last 15 years in genomics is that while the diversity of sequencing platforms has been relatively limited, the number of applications and methods used in library preparation has grown to hundreds of options and opportunities. The analysis methods and tools have also remained robustly diverse. This diversity presents new challenges to novel sequencing platforms. Launching a platform now comes with the expectation that the platform and its available applications will be an immediate step forward. Supporting anything short of the options available brings the risk of relegation to niche applications. However, launching a platform and a new and comprehensive collection of applications means your team needs to replicate a decade of diverse development by academic and commercial contributors. Fortunately, the general concepts used in the preparation of libraries for sequencing applications share the same basic principles. Nucleic acid samples are converted into a random collection of fragments with relatively uniform sizes and common sequencing elements that support amplification and detection on the sequencing platform.
Element Biosciences is passionate about developing new and disruptive solutions. The recently launched AVITI System is the first commercially available platform to embrace the creative and innovative solutions that have resulted in hundreds of library preparation options and applications over the last decade. Genomic applications have been introduced at a pace that no one in the field would have predicted, and we now find that the diversity of library preparation and data analysis options vastly outnumber sequencing options. The Element platform is the first and only platform to use an amplification methodology and data quality that not only support the diversity of applications and vendors across the field of genomics but deliver improved data accuracy and cost.
Library preparation methods
Element launched with three categories of library preparation methods. The first is our Element Adept™ Library Compatibility Workflow. Adept extends many existing library preparation kits and methods to the Element AVITI. The second is the Elevate™ Library Prep Workflow, which creates libraries specific to the Element platform that leverage some of the unique chemistry features of the platform. The third is the LoopSeq™ technology that brings long-read capabilities to the Element platform. The next post in the Element blog will cover the Loop methods in more detail. This post will summarize the Adept and Elevate options and explain how they are implemented.
Adept library compatibility
Our unique amplification method allows the AVITI System to use nearly any existing library as a template for sequencing. Adept adapts an existing library in a simple, amplification-free method that does not change the library complexity or proportions to a format that can be sequenced on the AVITI System. Even the rare library type that is not directly compatible due to modifications on the 5' or 3' end of the library, or that has truncations or other changes, can be supported with a few cycles of PCR. Almost 30 kits and catalog numbers have been validated with the Adept method, with more being added.
Materials that support the Adept option are summarized here. That includes a guide that describes the Adept process in detail, including a protocol and necessary reagents (Element Adept Library Compatibility Workflow Guide MA-00001). Our early protocols required 0.5 pmol of library material, and we have since reduced that requirement to 0.2 pmol library material, a 60% reduction.
This reduction in input amount means most library pools prepared for another platform are compatible with the AVITI System and save valuable library material. After a library is created, the Adept kit contains the reagents to adapt the library and qPCR standard and primers for real-time PCR quantitation of the converted library material for QC before sequencing.
Individual libraries or pools of libraries can be converted. The complexity of library and index distribution is maintained in the conversion and no additional PCR is used. If the following criteria are met, the libraries should be compatible:
- The final library is a double-stranded DNA fragment library.
- The library does not have any modifications such as biotin at the ends of the DNA strands.
- The P5 and P7 sequences are intact and full length.
- The standard sequencing priming sites are present. If custom primers are required, the conversion process will still be effective, but the final QC of the converted library will change. Contact us for more information.
Elevate library prep
In addition to supporting libraries created by existing methods, Element has also launched the Elevate method. Elevate uses the same fundamental tools and chemistry but adds Element-specific sequences using Element adapters and index primers that can be substituted into existing workflows at your discretion. Like the Adept Workflow, the Elevate Workflow resources are detailed on our website. The index and adapter kit can be used as a compatible component with third-party library preparation kits. When preparing a linear library, use the third-party reagents without the adapter and index kit with the Elevate index and adapter kit. Users simply follow the volumes and other parameters specified in the third-party vendor instructions. The finished library is then input for the Elevate Workflow and sequencing on AVITI System.
Element will continue to add to the diversity of kits supported with the Adept and Elevate Workflows. We recognize the need for and importance of embracing the diversity of methods in the field. Future Elevate kits will take further advantage of some of the unique features of the AVITI System to bring the same improvements in cost and efficiency to library preparation that the instrument brought to sequencing.