Embracing the Diversity of Library Preparation Options on the Element AVITI™ System

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 over the last several years.

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 Element AVITI™ System's full commercial launch, 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 fifteen 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 as well as a new and comprehensive collection of applications means your team would need to replicate a decade of diverse development by academic and commercial contributors. Fortunately, the general concepts that are 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 size 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 sequencer 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. Element's platform is the first and only platform to utilize an amplification methodology and data quality that not only supports the diversity of applications and vendors across the field of genomics but delivers improved data accuracy and cost. Element launched with three categories of library preparation methods. The first is our Adept™ method. Adept extends the vast majority of existing library preparation kits and methods to the Element AVITI. The second is the Elevate™ method which creates libraries specific to the Element platform that leverage some of the unique chemistry features of the platform. The third is the Loop Genomics 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.

Element's unique amplification method allows the platform to use nearly any existing library type as a template for sequencing. Our Adept methods adapt 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 platform. 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 couple of cycles of PCR. Almost 30 kits and catalog numbers have been validated with the Adept method, with more being added. All our materials supporting the Adept option are summarized here. That includes a compatibility guide that describes the Adept process in detail, including a protocol and necessary reagents (Element Adept Library Compatibility Workflow Guide MA-00001). The list linked above is summarized in the table below. Please note that the list and table represent specific kits that have been empirically tested by Element. Many other kits are also compatible as noted below. Our early protocols required 0.5pmol of library material, but we've recently reduced that requirement to 0.2pmol library material, reducing the necessary input by 60%. This reduction in input amounts means most library pools prepared for another platform will be compatible with Element and save valuable library material. Once a library is created, the Element Adept Library Compatibility Kit (cat number 830-00003) is the key reagent to not only convert the library, but the kit also includes qPCR standard and primers for real-time PCR quantitation of the converted library material for QC before sequencing.

Please note that many other kits are compatible with the Adept workflow. Individual libraries or pools of libraries may be converted. Complexity of library and index distribution is maintained in the conversion. No additional PCR is used in the conversion process. 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.

Compatible Kits for the Element Adept™ Library Compatibility Workflow Tested by Element.

10X GenomicsChromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1, 16 rxns1000175
10X GenomicsChromium Next GEM Single Cell ATAC Kit v2, 16 rxns1000390
10X GenomicsDual Index Kit NN Set A (for Sample Multiplexing)1000243
10X GenomicsSingle Index Kit N Set A1000212
10X GenomicsChromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.11000121
10X GenomicsDual Index Kit TT Set A1000215
10X GenomicsSingle Index Kit T Set A1000213
10X GenomicsVisium Spatial Gene Expression Slide & Reagent Kit1000184
AgilentSURESELECT XT HS2 Reagent Kit with Index Primer PairsG9983A
(pairs 1-96)
AgilentSURESELECT XT HS2 Reagent Kit with Index Primer PairsG9983B
(pairs 97-192)
AgilentSURESELECT XT HS2 Reagent Kit with Index Primer PairsG9983C
(pairs 193-288)
AgilentSURESELECT XT HS2 Reagent Kit with Index Primer PairsG9983D*
(pairs 289-384)
AgilentSSELXT HS Human All Exon V8, 16 Rxns5191-6873
AgilentSSELXT Human All Exon V8, 16 Rxns5191-6879
BD BiosciencesWhole Transcriptome Analysis (WTA) Amplification Kit633801
Bio-RadSEQuoia Complete Stranded RNA Library Prep Kit17005726
BioRadSureCell ATAC-Seq Library Prep Kit17004620
Dovetail GenomicsDovetail® Micro-C Kit21006
Dovetail GenomicsDovetail® Omni-C® Kit21005
IDTxGen™ DNA Lib Prep EZ 16rxn10009863
IDTxGen™ cfDNA & FFPE DNA Library Prep MC, 16 rxn10006202
IDTxGen™ Stubby Adapter-UDI Primers, 96 rxn10005921
IDTxGen™ Exome Hyb Panel v2, 4 rxn10005151
IlluminaNextera XT DNA Library Preparation Kit* (24 samples)FC-131-1024
JumpcodeCRISPRclean Plus Stranded Total RNA Prep with rRNA Depletion (Human, Mouse, Rat, Pan Bacteria)KIT1016
New England BioLabsNEBNext® Multiplex Oligos for Illumina® (Unique Dual Index UMI Adaptors DNA Set 1)E7395S
New England BioLabsNEBNext Ultra II FS DNA Library Prep Kit for Illumina, 96 reactionsE7805L
New England BioLabsNEBNext Ultra II DNA Library Prep Kit for Illumina, 96 reactionsE7645L
New England BioLabsNEBNext Ultra II Directional RNA Library Prep Kit for Illumina, 24 reactionsE7760S
New England BioLabsNEBNext Multiplex Oligos for Illumina (Index Primers Set 1)E7335
Parse BiosciencesEvercode™ Whole Transcriptome8098115702
PerkinElmerNEXTFLEX Variant-Seq SARS-CoV-2 V2 Kit v1NOVA-5350-096
QiagenQIAseq FX DNA Library KitVarious
RocheKAPA mRNA HyperPrep Kit, 24 libraries8098115702
RocheKAPA HyperPlus Kit With Library Amplification, 96 reactions7962428001
RocheKAPA HyperPrep Kit without amplification module, 96 reactions7962371001
RocheKAPA EvoPlus Kit, 96 rxn9420053001
RocheKAPA Unique Dual-Indexed Adapter PlateKK8726
SeqWellplexWell™ 384PW384
TakaraBioSMARTer Stranded RNA-Seq Kit, 12 Rxns634836
TakaraBioSMARTer RNA Unique Dual Index Kit – 24U, 96 Rxns634451
Twist BioscienceTwist SARS-CoV-2 Research Panel, 12 Reactions, Kit102017
Watchmaker GenomicsGenomics, Watchmaker DNA Library Prep Kit with Fragmentation (PCR-free)7K0013-096
Watchmaker GenomicsWatchmaker DNA Library Prep Kit with Fragmentation incl. Equinox Library Amplification Master Mix (2X) and P5/P7 Primer Mix (10X)7K0019-096

*Excluding any Nextera XT Index Kit v2 and bead-based normalization.
Above list is up-to-date as of June 29, 2022.

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 through the use of Element adapters and indexed primers that can be substituted into existing workflows at the user's discretion. Like the Adept option, the Elevate workflow resources are detailed on our website here. The Element Elevate 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 adapter/index module) 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 used as input for the Element Elevate Library Circularization workflow and sequenced on Element AVITI.

Compatible Kits for the Element Elevate™ Library Prep Workflow

The following table lists example library prep components compatible with Elevate Index and Adapter Kit.

VendorWorkflowCatalog #
WatchmakerWatchmaker DNA Library Prep Kits7K0019, 7K0013,
9K0030
WatchmakerWatchmaker RNA Library Prep Kits9K0078/ 7K0078,
9K0079/ 7K0079
NEBNEBNext Ultra II FS DNA Library Prep Kit for Illumina, 96 reactionsE7805L
NEBNEBNext Ultra II DNA Library Prep Kit for IlluminaE7645L
Roche-KAPAKAPA HyperPlus Kit with Library Amplification, 96 reactions7962428001
Roche-KAPAKAPA HyperPrep Kit with Library Amplification, 96 reactions7962363001

Above list is up-to-date as of June 29, 2022.

Like the Adept kit, the key reagents for the Elevate process are the Element Elevate Index and Adapter Kit (cat number 830-00005) and the Element Elevate Library Circularization Kit (cat number 830-00001). These reagents combined with the library preparation kit of choice will produce Element-specific libraries from any sample.

Element will continue to add to the diversity of kits supported with the Adept and Elevate workflow options. 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 platform to bring the same improvements in cost and efficiency to library preparation that AVITI brought to sequencing.