Assay design for KASP chemistry

Once your project manager has received your SNP submission template, KASP genotyping assays will be designed using our Kraken™ software.

LGC use the sequence information submitted by the customer to design KASP assays for genotyping. Sequence information should be submitted to your project manager using the SNP submission form.

Sequence information is imported into our proprietary Kraken™ software and assays are designed using our primer design parameters. KASP chemistry requires the design of two allele-specific primers and one common primer. The required primers are ordered, and KASP assays are prepared. All KASP assay aliquots are barcoded and tracked within Kraken.

KASP assays are validated across our human panel of DNA samples (where applicable). If your study species is not human, the KASP assays will be validated on a subset of your submitted DNA samples (does not apply to all-inclusive services).

Validated assays should meet the following criteria:

  • No template control (NTC) samples should be negative i.e. no amplification
  • Three distinct genotyping clusters should be observable
  • The call rate for samples should be greater than 90%
  • Minor allele frequency should be greater than 2%, unless the allele is known to be very low frequency.

If any assays fail during the design or validation process, your project manager will liaise with you to determine the most appropriate way to proceed.

Once LGC are happy that the assay(s) are functioning correctly, your project manager will proceed with your genotyping project.

Use of TaqMan assays

If you already have TaqMan® assays from ABI for your target SNP, we can run these on your DNA samples in our service laboratory as part of your genotyping service project.

TaqMan® is a registered trademark of Life Technologies Inc.

snp submission form

how to submit sequences

kasp assay design for highly similar sequences