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Amp-Seq One Kit

Amp-Seq One Kit

Product Details

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The Amp-Seq One kits consist of the following components:

1. Amp-Seq One Reagent

2. Amp-Seq One Amplification Master Mix (5X)

3. Amp-Seq One Buffer

4. Amp-Seq One Bead Cleaning Solution

The kits are provided with a pre-dispensed dried down index plates (384-well format). The bead cleaning solution enables cost savings on beads.

Please select the desired index plates in the “kit items” section after selecting the appropriate kit format and number.

Amp-Seq One Kit

Amp-Seq One is a targeted genotyping by sequencing workflow for industrial scale genotyping in agricultural biotechnology. The unprecedented workflow simplicity and scalability enables a frameshift in throughput that can drive the pace of breeding programmes to exceed expectations in reducing time to bring new traits to the market.

Key features

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  • Unique simplicity - 1-stage workflow
  • Same-day-sequencing – 120-minute protocol
  • Consolidate workflows - target up to 5,000 markers per sample
  • High performance – industry leading SNP call rates and evenness of coverage
  • Compatible with a variety of sample types and DNA preparation methods
  • Reduced environmental impact with ambient temperature stable components

For ordering kits with pre-designed panels please contact your LGC representative

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Product information

Workflow and applications

The unique industry leading 1-stage workflow was co-developed with industry leaders in agricultural biotechnology to ensure it is optimised for industrial throughput and simplified to enable lab efficiency.

Picture 338655403, Picture

Amp-Seq One has been developed for high-throughput genotyping applications including:

  • Seed QC
  • Genomic selection
  • Parentage testing
  • Marker assisted selection (MAS) and back-crossing (MABC)
  • Other high-throughput genotyping applications

Custom targeting oligo libraries

We work with you to design a custom panel that meets your genotyping goals. With our proprietary design software, we design high-quality panels that result in high sequencing efficiency and typically have very high SNP call rates and evenness of coverage. These panels can be further refined and optimised for high priority markers.

A design service is available for custom targeting oligo panels. To initiate a custom panel design project, please contact your LGC Biosearch Technologies representative.

The design process includes custom panel design, panel production (per marker), panel validation and optimization (optional, recommended) and a test kit for in-house testing.

Description Part code Explanation
Custom panel design (in-silico) GEN-9910-001 In-silico design and optimization of a new Amp-Seq One panel. Does not require commitment for panel production.
Panel production (per marker) GEN-9910-002 Only charged for markers that pass approval during the design phase. Can be ordered separately from design.
Panel validation & optimization GEN-9910-003 Recommended for all new designs. Includes wet-lab validation and optimization on 384 samples (extraction, library preparation, sequencing, analysis)
Custom design test kit GEN-9910-004 Recommended for new Amp-Seq One users. Trial kit for in-house testing, including all required reagents (excl. template DNA)

Following the collaborative design process, your project manager will provide you with a design specific ‘Design ID’ number. Upon ordering your kits, the project specific targeting oligo library is added to your kit by your Biosearch Technologies representative. You will be contacted to confirm the ‘Design ID’ number for the desired targeting oligo library for the kit you have ordered

Online ordering: When ordering a kit with a custom panel online, please ensure to leave your Amp-Seq One targeting oligo design ID number (provided by your project manager) in the notes section upon checkout to ensure we add the correct panel to your kit.

Industry standard pre-designed panels

Amp-Seq One kits with pre-designed panels are available for fast, easy and cost-efficient validation of the technology and for production scale screening applications. These pre-designed panel kits do not require design, production, validation and optimization.

Description Part code Explanation
Pre-designed panel kit GEN-9910-005 Alternative to kits with custom designs. Pre-designed panel kits do not require design, production or validation.

Industry standard pre-designed Amp-Seq panels are currently available for bovine and maize, additional panels are in development. For more information about pre-designed panels or to develop your own custom panel, please contact your LGC representative.

Core reagent kits

Generic part codes for Amp-Seq One core reagent kits and index plates are in the table below.

Description Part code
Amp-Seq One kit incl. targeting oligo library (384 rxn) GEN-9910-384
Amp-Seq One kit incl. targeting oligo library (3840 rxn) GEN-9910-3840
LGC Nexar - Amp-Seq One kit incl. targeting oligo library (384 rxn) GEN-9910-384
LGC Nexar - Amp-Seq One kit incl. targeting oligo library (3840 rxn) GEN-9910-3840
Amp-Seq One dried down RT storage CDI (indexing) plate 1-96 GEN-9902-001 to -096

The kits are available in 384 and 3,840 reaction sizes that include sufficient coverage to accommodate the use of liquid handlers.

To order reagents for more than 3,840 reactions please order multiples of the relevant kits, for example: for processing 8,000 samples, please order 2 x 3,840 rxn kits and 1 x 384 kit. To determine the number of samples you can multiplex depending on your sequencing instrument and flow-cell type, please refer to the Amp-Seq One manual for an overview of multiplexing options on various sequencing instruments.

Online ordering: After selecting the desired kit format and number, please select the desired index plates from the “kit items” section.

Automation and implementation support

Amp-Seq One is compatible with most liquid handling systems, see technical specifications for details. Additionally, LGC can support implementation on your workflow.

Additional services include:

  • Optimisation for specific input material (species and sample types)
  • Wet-lab implementation support
  • Automation compatibility and scale up support
  • BiosearchCaller data analysis pipeline installation and support
  • Customisation of wet-lab chemistry, automation and analysis pipeline

Data analysis

The BiosearchCaller analysis pipeline is specifically designed for Amp-Seq and is available license free for Amp-Seq One users, the pipeline is open-source and universally applicable to all Amp-Seq One panels.

Data analysis can be performed with the most openly available and custom in-house built SNP calling pipelines as well.

Feature Specification Reference
Amplification time 50 minutes, one PCR stage Amp-Seq One datasheet
Protocol turnaround time1 120 min Amp-Seq One datasheet
Sample transfer2 None required Amp-Seq One datasheet
Number of 384 reaction well-plates used 1 x 384-well plate Amp-Seq One datasheet
Maximum marker density >5000 markers Amp-Seq One: Making plant and livestock genotyping simple
Automation compatibility Suitable for high-throughput automation including SNPline and Nexar Amp-Seq One SNPline manual
Amp-Seq One Nexar manual
Ploidy compatibility Applicable to diploid and polyploid organisms Amp-Seq One application note #2 - coming soon
Species compatibility Applicable to plant and animal species Amp-Seq One: Making plant and livestock genotyping simple
Compatible with existing Amp-Seq panels3 Existing panels can be validated for Amp-Seq One Amp-Seq One: Making plant and livestock genotyping simple
Compatibility with diverse sample materials Works with biologically diverse input sample types Amp-Seq One: Making plant and livestock genotyping simple
Marker type compatibility SNPs, InDels4, MNPs Amp-Seq One application note #2 - coming soon
Sequencing read length compatibility Suitable for a range of read lengths Amp-Seq One application note #2 - coming soon
Sample preparation compatibility Works with purified DNA, including sbeadex Lightning chemistry, and with crude5 DNA Amp-Seq One application note #2 - coming soon
Compatible with low input DNA amounts Works with 5 ng DNA6 Amp-Seq One application note #2 - coming soon
Typical genotype call rate >90% Amp-Seq One: Making plant and livestock genotyping simple
Typical evenness of coverage >80% Amp-Seq One: Making plant and livestock genotyping simple
Sequencing efficiency7 Percentage of reads on target >95% Amp-Seq One: Making plant and livestock genotyping simple
Typical in silico design to functional assay conversion rate8 >85% Amp-Seq One: Making plant and livestock genotyping simple
  1. Turnaround time defined by processing one plate from extracted DNA to sequencing-ready library as prepared on standardly available liquid handling platforms.
  2. Referring to sample transfer from PCR 1 plate to PCR 2 plate
  3. Amp-Seq One chemisty is typically compatible with original Amp-Seq design but some optimization may be required,.tested on three panels across two different crops.
  4. InDels up to 10bp are supported by default, larger indels may require manual design processing
  5. Typically compatible with specific crude extraction methods, may require optimization
  6. Input DNA amount is dependent on genome size, panel and several other factors - for typical panels and medium sized genomes (Maize) Amp-Seq One is compatible with 5ng DNA input amount
  7. Dependent on flowcell type, demultiplexed reads (barcoded)
  8. Testing based on 1000-2000 marker panels

SDS

Product information sheets

Additional resources

Please select the items required

For a more detailed review of the quality, robustness and performance of the Amp-Seq One method please see the application notes in the documentation section or start your custom evaluation .

Design compatibility and high-quality sequencing data

Across both plant and livestock panels, design compatibility is clearly demonstrated with panels developed for original Amp-Seq performing comparably when utilised with Amp-Seq One. Figure 1 illustrates an example of this comparable performance between methods for a 1920 marker panel for maize. Table 1 summarises high quality sequencing data from four panels, illustrating typical genotyping call rates of greater than 90% and typical genotyping efficiencies of greater than 95% (on target genotyping rate).

PictureFigure 1. Dataset for 1,920 marker panel for maize, illustrating comparable performance between Amp-Seq One and original Amp-Seq. For both protocols, percentage of reads mapped to the reference genome was greater than 98.5% and the percentage of reads mapped to the target SNP location was greater than 95%. Genotyping call rates and uniformity (read depth consistency across markers) were also comparable between both methods

 

PictureTable 1. Summary of high-quality sequencing data obtained for four Amp-Seq One panels.

Compatible with diverse sample materials

Results obtained with the 1,100-marker soy panel demonstrate almost identical performance between Amp-Seq One and original Amp-Seq when using biologically diverse soy leaf samples (figure 2).

 

PictureFigure 2. Dataset for 1,100 marker panel for soy, illustrating almost identical performance between Amp-Seq One and original Amp-Seq. DNA was purified from 384 individual soy leaf punch samples using sbeadex™ plant chemistry.

Marker density

Amp-Seq One is suitable for genotyping large numbers of SNPs (>5000) per reaction. Figure 3 illustrates high-quality sequencing data obtained for a high-density maize 5,200 marker panel.

 

PictureFigure 3. Dataset for 5,200 marker panel for maize illustrating high-quality sequencing results obtained with Amp-Seq One and a high-density panel. Overall genotyping call rate for this panel was >99% and 97% of reads were mapped to the reference genome.

Access support

Need some support with placing an order, setting up an account, or finding the right protocol?

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