Genotyping Service Details
As part of this service, the Facility will purchase the necessary assays, reformat your genomic DNA from 96-well plates to 384-well plates, set up individual SNP assay plates, perform the PCRs, obtain the data, assess quality and convert the data to an Excel format. For large studies, assays can be validated with your DNA to ensure each assay is working well with your DNA.
Turn around time varies depending on the size of the project. A project timetable will be assessed during the project consultation. For basic plate reading service, data is usually obtained within 48 hours.
Files are uploaded to our Amazon cloud. Users will be notified when their data is uploaded.
For large projects, the addition of Facility provided Coriell controls are an option. These control samples have known genotypes and are used to ensure that the data collected from your project is reliable.
Users need to register their project through iLab. Please go to the Customer Portal and make your request. However, sample templates are tailored to individual projects. These are not available through iLab but can be uploaded once the GEGF creates and sends them to you after your consultation.
There are 2 options for sample delivery: Users can bring genomic DNA for the Facility to plate, or they can plate the DNA themselves.
Facility Plates the DNA
Users should bring their genomic DNA in deep well or U-bottom 96-well plates provided by the Facility. We require at least 2 ng of DNA for each SNP being interrogated and DNA should be in water at a minimum of 1 ng/ul. Ideally, samples should be around 5ng/ul. A minimum of 200 ul of sample is required for robotic plating. larger projects require more volume.
User Plates the DNA
Alternatively, the user can plate their own DNA in 384-well plates, dry it down and the Facility will set-up and run the SNP assays. Contact the Facility to obtain the types of plate we can accept. In any case, the User will need to fill out a customized registration form available at the project consultation meeting.
DNA samples must be at approximately the same concentration. If concentrations differ widely, it is difficult for the algorithm to make a call.
We offer a full service where the facility will plate your DNA, run the assays and QC the data. Additional, we offer a partial service where we will run plates that are already plated.
The User can order their own assays or we can order them. Assays come in various sizes and are either custom or off-the-shelf.
Many safeguards have been implemented to ensure that the data generated is reliable and accurately reflects the sample genotype. Other quality control features have been implemented at the wet bench level to insure that the generated data is reliable, including customary equipment maintenance and calibration.
Quality Control Safeguards:
Prior to running an entire project, each assay is evaluated on a subset of samples to ensure that the assay functions properly and that the User's samples are in a detectable concentration range.
User's are provided with preconfigured plate layouts which assure that each layout is unique and contains water blanks to detect any contamination during the assay plating process.
Assays are plated robotically from left to right, in a quadrant by quadrant basis, ending with water blanks. Tips are changed after each quadrant.
Barcodes are scanned by the robot to verify the correct plate is being accessed.
In addition, Users are encouraged to include samples with known genotypes (if possible) and duplicate samples on the same plate, and across all plates, to aid in plate identification and call accuracy.
Data Quality Monitoring:
Data quality is monitored after each plate run to: assess any presence of contamination, assure the assay is working properly and clusters are assigned, and that the data coincides with the plate configuration and the positive controls are generating the correct genotypes.