ICAR+ panel content
The Amp-Seq One industry standard pre-designed ICAR+ panel includes the 554 SNP ICAR panel which includes the 199 SNP ISAG panel.
The ICAR+ panel includes four additional traits: A2/A2, Coat color (Red/Black/Wild), Pompes E7, Horned/Polled (Celtic and Friesian).
Note: some of these traits are multi-allelic and the Amp-Seq One ICAR+ panel targets multiple SNPs/Sites per trait.
For details please see the SNP list for this panel.
Recommended sequencing depth and chemistry
125,000 reads per sample, 200 reads per locus. All SNPs were designed for recovery with a minimum of single end 100bp sequencing, longer read lengths or paired end sequence are fully compatible.
Breed validation
The panel was validated on Angus and Hereford background and 21 samples provided by ISAG (default qualification samples)
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.
Workflow and applications of Amp-Seq One
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.
Amp-Seq One has been developed for high-throughput genotyping applications including:
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.
For more information please see: Pre-designed panels
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:
Data analysis
The BiosearchCaller analysis pipeline is specifically optimized for genotype calling in Amp-Seq and Amp-Seq One, and is available to Amp-Seq customers without a license. The pipeline is flexible and can be configured to suit your requirements, handling multiple species and panels. The BiosearchCaller calls genotypes by considering read alignments after quality filtering, allele balance, and local haplotype structure, utilizing Bayesian models to detect polymorphisms from Amp-Seq sequencing data, thereby enabling the accurate detection of SNPs and indels. The BiosearchCaller genotypes are reported in multiple formats to facilitate downstream analysis, along with additional metrics that support troubleshooting.
NGS kits and workflows
Amp-Seq One is a targeted genotyping by sequencing workflow for industrial scale genotyping in agricultural biotechnology. The unprecedented workflow simplicity and scalabi…
Format
The sbeadex Lightning Nucleic Acid Purification Kit is a game-changing innovation in nucleic acid isolation - as it delivers high-quality DNA in high yield with a simple, u…
| 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 (please enquire via request form) |
| Ploidy compatibility | Applicable to diploid and polyploid organisms | Amp-Seq One application note #2 |
| Species compatibility | Applicable to plant and animal species | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Compatible with existing Amp-Seq panels3 | Existing panels can be validated for Amp-Seq One | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Compatibility with diverse sample materials | Works with biologically diverse input sample types | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Marker type compatibility | SNPs, InDels4, MNPs | Amp-Seq One application note #2 |
| Sequencing read length compatibility | Suitable for a range of read lengths | Amp-Seq One application note #2 |
| Sample preparation compatibility | Works with purified DNA, including sbeadex Lightning chemistry, and with crude5 DNA | Amp-Seq One application note #2 |
| Compatible with low input DNA amounts | Works with 5 ng DNA6 | Amp-Seq One application note #2 |
| Typical genotype call rate | >90% | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Typical evenness of coverage | >80% | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Sequencing efficiency7 | Percentage of reads on target >95% | Amp-Seq One app note: Making plant and livestock genotyping simple |
| Typical in silico design to functional assay conversion rate8 | >85% | Amp-Seq One app note: Making plant and livestock genotyping simple |
Need some support with placing an order, setting up an account, or finding the right protocol?
Contact us| Europe, Middle East, and Africa | |
|---|---|
| UK | +44 1992 470 757 |
| Germany | +49 30 5304 2200 |
| North America, Latin America | |
| Wisconsin, USA | +1 888 575 9695 |
| Asia Pacific | |
| China | +8621-22509000 |
| Singapore | +65 6734 4800 |
