How to start a genotyping project

Use the step-by-step guide to set up a genotyping project. Our service incl. labour,consumables,all reagents,data analysis & reporting

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).

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DNA sample plate data

LGC needs to know the layouts of your DNA sample plates; please submit DNA sample plate data using the appropriate DNA submission template.

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Result reporting

Once your genotyping project is complete, you will receive results. The results file will be in an Excel .csv (comma-separated text file) format.

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Step-by-step guide: A typical genotyping service project

Request quotation
The customer submits a request for a quotation or a general request for pricing information. When requesting this, please include details regarding the number of SNPs (or InDels) and number of DNA samples that you wish to genotype. LGC will email the customer with a quotation for their genotyping project and will include a sequence submission form and a DNA sample submission form.

Review quote & provide purchase order
The customer reviews their quotation and if happy, submits a purchase order to the provided address.

Project manager assigned
At this stage LGC will assign a project manager to act as the customers’ primary contact for this and any subsequent genotyping projects.

Provide sample and SNP submission forms
Next, the customer should complete and return the sequence submission form with sequence(s) of interest and polymorphism(s) marked to identify the SNPs/InDels that they are interested in. The completed sequence submission form can be e-mailed directly to the project manager.

Assay design & preparation
LGC use the sequence information submitted by the customer to design the KASP assays; for this, we use our proprietary Kraken software. The oligos are ordered, and KASP assays are prepared. These assays are validated against our panel of DNA samples where applicable (human assays only).

DNA shipment to LGC
Meanwhile, the customer will send their DNA samples to LGC, following our guidelines on sample shipment. Customers must ensure that they have completed a DNA sample submission form to identify their samples and e-mailed it to the project manager.

Sample plate preparation
Once DNA has been received, LGC prepare sample plates for genotyping using either 384-well or 1536-well format plates depending on the number of SNPs/Indels and samples being genotyped.

Assays run on sample plates
When all of the sample plates have been prepared and the assays have been made (and validated) the assays will be dispensed into the genotyping sample plates. The plates are then sealed, and thermally cycled in one of our Hydrocycler instruments. Plates are then read to obtain fluorescence data.

Genotyping cluster data scored and results provided
The fluorescence data read from the sample plates is plotted and genotypes are assigned to samples based on clusters.

Finally, the project manager will send the analysed results to the customer. Results are typically provided in two formats, one that can be viewed graphically using our SNPViewer software and the other that displays the results in a simple grid format.

For more information regarding the amount of DNA required for a genotyping project, please click here.  

All our service project costs include:

  • Labour
  • Consumables
  • Reformatting of DNA where necessary
  • Data analysis and reporting
  • All reagents required for genotyping.