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Sequence submission
KASP™ chemistry can be used for the detection of the following polymorphism types: SNPs or indels, presence or absence of target DNA sequence (plus/minus assay).
KASP chemistry can be used for the detection of the following polymorphism types:
- Single nucleotide polymorphisms
- Insertions or deletions (indels)
- Presence or absence of target DNA sequence (plus/minus assay).
Sequence information for KASP assay design should be submitted to LGC, Biosearch Technologies using the SNP submission template (Excel format). Please do not change the formatting of this template as we import this directly into our laboratory information management system (LIMS).
Biosearch Technologies can design assays using reference SNP ID numbers (rs numbers); please submit the list of rs numbers directly to your project manager. It is, however, advisable to submit the sequence in addition to the rs number to ensure that we are using exactly the sequence that you require.
We can also accept sequence information in FASTA format; please email this directly to your project manager.
Submission guidelines
Order number
Please include your order number and/or your unique project number within the first worksheet of the SNP submission template.
SNP ID
Please use this field to provide a unique identifier for each assay. This assay name can be up to 20 characters in length, and should include alphanumeric and underscore characters only e.g ABCD1234_ab.
Sequence information
We require our customers to submit sequence information for each target SNP; this is to avoid any ambiguities that may persist between different databases, and to ensure that the assay is designed to the correct sequence. Biosearch Technologies takes no responsibility for submission of incorrect sequence.
If you are using a SNP assay from one of our panels, you do not need to include sequence information. Just complete the SNP ID column with the required assays IDs.
The ‘Examples’ worksheet in the SNP submission file details how to submit sequence for SNPs and indels.
- Enter the sequence in 5’ – 3’ orientation
- Use uppercase characters to enter sequence information e.g. ATCG
- Identify the target SNP using square brackets e.g. ATCG[A/C]ATCG
- Include 50 bp of sequence on either side of the target SNP
- Identify any surrounding SNPs using IUPAC codes e.g. R, S
- Use lowercase characters to identify any regions of sequence that are uncertain e.g. atgc
- If there are particular regions of sequence that should be completely avoided, replace these bases with an N.
If your target SNP and surrounding sequence has homology with other regions of the genome, please contact your project manager directly before submitting sequences.