Step-by-step Guide: A Typical Genotyping Service Project
1. Request Quotation
The customer submits a request for a quotation that includes the number of DNA samples and the number of SNPs (or inDels). Agriplex will provide a quote for the project along with instructions for submitting SNP sequence and DNA samples.
2. Review Quote & Provide Purchase Order
After reviewing the quote, the customer will submit a Purchase Order to the provided Agriplex address.
3. SNP and Target Sequence Submission
The customer will utilize the SNP submission form to provide Agriplex with the sequences of interest, SNPS / Indels, RS#s where available, and positions of SNP / Indel marked within the sequence. Known nearby SNPs should also be marked.
4. Assay Design & Validation
Agriplex will utilize the supplied information to design the Plexseq assay. The assay will be validated using the resulting oligonucleotide primers and reference DNA from the organism of interest. In some instances we may request organism-specific DNA for validation purposes if it is not commonly available.
5. DNA Shipment to Agriplex
The customer will send their DNA samples along with platemaps to Agriplex following our guidelines on amount of DNA, concentration, volume, placement in plate, and plate type as well as guidelines for the shipment itself. Quantity of DNA required can vary if a large number of SNPs are being genotyped.
6. Sample Plate Approval
Agriplex will examine the plates upon arrival, evaluate for consistency with provided sample information, and determine whether any additional manipulation of the sample plate is required to prepare for the genotyping assay.
7. Genotyping Assays on Sample Plates
Once assay validation is complete and samples are on hand and prepared for the assay, the Plexseq assay will be run. Agriplex will include negative and positive controls on each plate. The resulting Plexseq libraries will be sequenced using the appropriate Illumina platform.
8. Genotyping Results Provided
Sequencing data will be analyzed and genotype calls will be made using our PlexCall software. The genotypes will be provided to the customer in an excel format.
A much more detailed description of this process and guidelines for sample and SNP submission can be found here.