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Sequence submission

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 using the SNP submission template (Excel format). Please do not change the formatting of this template as LGC import this directly into our laboratory information management system (LIMS).

LGC 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 LGC are using exactly the sequence that you require.   

We can also accept sequence information in FASTA format; please e-mail 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. LGC 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. 

 

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Related downloads

file
Genotyping service SNP submission template 32KB

Use this form for submission of sequence information for genotyping service projects

file
Assay design 151KB

A fact sheet explaining how sequencing information should be submitted for KASP assay design