As soon as your purchase order is received by AgriPlex Genomics we will contact you directly to discuss any detailed information pertinent to your project. The following is some detailed information on our process.
SNP and Target Sequence Submission
The first step in a genotyping project is designing primers. To that end, please provide information about your target SNPS and surrounding DNA sequence using the SNP Submission Form. Download the form, complete it, and email it to Agriplex Genomics. Additional information about the types of information required and formatting can be found in that document.
PlexSeq™ Assay Design
The SNP and sequence information you provide is utilized to design and validate primers for our multiplexed PlexSeq™ assay.
Primers are designed, synthesized, and validated for your target SNPS using reference DNA for the species of interest. In some cases where the appropriate genomic DNA is not readily available, we may ask you for appropriate DNA for validation of the assay or utilize some of your provided sample DNA.
If there are SNPs for which we are unable to successfully design an assay, we will contact you to discuss options.
Submission of DNA Samples
Once the Plexseq assay has been designed and validated for your SNPs, it is time to submit your DNA samples.
DNA samples must be submitted in a specific manner so that the identity of the plate and samples and the exact location of the samples on each plate are known with certainty. Details on this process can be found in the DNA Sample Submission Guidelinesdocument. Please download, review, and comply with these guidelines. There you will find details on the volume and concentration of DNA samples, the type of plates, sealing methods, plate labeling, sample names, plate maps, and shipping.
As is described in the DNA Sample Submission Guidelines, sample names should be provided in plate column order using the Sample Name Submission & Platemap form. Sample volume and concentration should be provided there as well, and there is space to provide any other information you may want to associate with the sample name. The Excel sheet will generate a plate map. Please confirm carefully that all samples are in the correct positions.
Please review carefully the shipping guidelines and take any additional precautions to ensure that your samples arrive without damage to the plate, leaking of wells, contamination, etc.
PlexSeq™ Workflow and Turnaround Time
Processing of your samples will begin once the assay is validated and your samples have been received and approved.
Generally, sequencing libraries are prepared that include your target SNP. These libraries are then sequenced on an Illumina platform and the data analyzed using our PlexCall™ software. The process generates allele counts for each of the alleles of your SNP from which the genotype is called.
We aim for a turnaround time of 6 weeks from the time we have both the assay validated and the samples in hand. If there will be deviations from this, your project manager will discuss these with you.
Delivery of PlexSeq™ Results
The output from our Plexcall™software will be reviewed as a quality control measure before providing the results to the customer. Results will be organized and reported in an excel file with genotype calls for each sample / SNP combination. The PlexSeq™ genotype report will be sent to the customer as an email attachment.