Genotyping solutions for large and small projects

We are available to help you select the technology and price point best suited to your scientific question and budget

Our high-throughput lab generates data using any of the current the Illumina arrays

Off-the-shelf arrays for specific purposes are offered by Illumina and ThermoFisher

Validate your unique SNPs via Illumina, TaqMan assays, Pyrosequencing or traditional STR/VNTR methods

Whether using an Illumina non-human array or looking at individual SNPs, we are happy to assist you

Start Your Project Today!

Begin the consultation process by emailing Roxann Ashworth. Once the details of your project have been finalized, the project process is as follows:

1) Set up the order in iLab, including payment information (GRCF staff can help with this)
2) Send your Sample Information File (SIF) to your project manager for approval
3) Provide an address for shipment of your plates. Your project manager will supply a manifest file at the time of shipment
4) Plate your DNA
5) Send your completed manifest file to your project manager for approval
6) Ship your DNA
7) If pre-testing is included in your project, results will be returned to you and the project will be on hold until you return the results
8) Your samples will be processed in the lab
9) Data will be analyzed and samples which fail to meet QC standards will be rerun
10) Data will be cleaned and problems identified
11) Data release!

Frequently asked questions

Do you accept projects from entities outside of Johns Hopkins?

Yes, we accept samples from any outside entity, as long as minimum sample numbers are met.  Quotes are available and payment may be made via check, electronic funds transfer or credit card.  All external billing is done through our iLab ordering system.

What is included in your GWAS pricing?
For GWAS projects with more than 94 samples, the pricing includes:
  • [Pretesting with the ability to replace/drop poor performing samples–if this price option is selected]
  • Two controls per plate
  • Study duplicates (one per every other plate) at no additional cost
  • Individual sample reruns in the lab for poor performance (repeated 1X)
  • Full data release, which includes: hapmap concordance, reproducibility of genotype calculations broken down by MAF bin for each sample pair, GenomeStudio project, SNP and samples tables, full SNP technical filter applied, samples reclustered on own data, final reports, PLINK file and README docs explaining the data in each directory
Where should I ship my samples?

Shipment Instructions for Illumina genotyping:

DNA samples must be sent in bar-coded plates provided by the GRCF, 92 samples per plate. Plates will be provided only after arrangements for payment have been made, a sample information file (SIF) has been approved and a a duplicates file has been approved.

A DNA manifest template will be sent to you. Please read the instructions provided with the manifest carefully and follow them precisely. The manifest is our only record tying sample ID to plate and well location so please take care to ensure the accuracy of this document.Please return the completed manifest file to project manager prior to shipping plates to the GRCF. Plates must be shipped on dry ice for arrival on Tuesday through Friday.

Internal customers drop off locations:

     Illumina genotyping samples: Blalock 1004 or at 1812 Ashland (with prior arrangement)  

     Individual Taqman assay projects: G20

     OpenArray projects: Blalock 1004

Shipping address for Illumina genotyping (external customers):

      Johns Hopkins Genomics – CIDR

     1812 Ashland Avenue

     Room 245

     Baltimore, MD 21205

     Phone: 410-614-0702

Email the tracking number to  Roxann Ashworth.

Shipping address for plating services or individual Taqman assay genotyping (external customers):

      Laura Kasch – GRCF,

     Fragment Analysis Facility

     Johns Hopkins University

    725 N. Wolfe Street, PCTB G20

    Baltimore, MD 21224

    Phone (443) 287-7948

Email the courier tracking number and GeneSifter order number to

How much DNA should I send?

That depends on the chemistry.

  • Illumina Infinium Chemistry: 25 µl @ 50 ng/µl genomic DNA; WGA DNA is not recommended
  • Taqman OpenArray Chemistry: 10 ul @ 50 ng/ul genomic DNA; 200-300 ng/ul WGA sample
  • Individual Assays: Amount required depends on assay. Please  contact us for details.
Can I send Whole Genome Amplified (WGA) samples?

WGA samples will always preform worse than whole genomic DNA. They are usually somewhat successful for Golden Gate and Taqman chemistries, but they do not preform well with the Infinium chemistry. This means that for GWAS products, we would prefer to work with you on lower volumes and/or concentration and avoid using WGA samples if at all possible.

Will the entire amount of DNA be used?

Under normal circumstances, no. Excess DNA will be returned.

May I use my own plates for DNA transport?

For Illumina genotyping, no. We will provide plates for DNA transport. These plates will be provided along with individual tube caps and labels.  Please plate samples in column order (A1, B1, C1, etc.)

For other types of genotyping, yes. Samples should be sent in conical bottom PCR plates.  Make sure to discuss control placement and row vs. column order with your project manager.  Plate maps can be created for these projects to assist with control placement.

What is the best method to send our samples?

DNA samples must be frozen prior to boxing and shipping. Verify that the rack is locked (Illumina projects). Place each rack in a separate bubble bag. Place the racks in a shipment container and fill all empty space in the shipment container with dry ice so that the plates stay frozen and do not move during shipment. Ship all packages overnight for delivery on Tuesday, Wednesday, Thursday, or Friday. Send tracking number to your Project Coordinator. We cannot accept samples until all necessary documents and/or order forms have been filled out. Do not ship samples until all necessary documentation has been received and reviewed by the Project Coordinator.

Do you verify DNA concentration? Do you adjust volumes to achieve correct concentration?

We do not typically verify concentration. For large GWAS projects we do spot check DNA quality by running a small portion of the project on an eGel. For other projects, we do not check what you provide.  If you have concerns about DNA quantity or quality, please let your project manager know.  We can provide DNA quantitation, dilution and plating services for an additional fee.   Contact us for more information on these services.

Do we need to provide our own internal controls?

Yes, for human and mouse genotyping projects. All plates processed have HapMap controls on them. These spots will be reserved in the DNA manifest. We use these positive controls to: 1) Monitor assay performance 2) Evaluate experimental DNA quality 3) Aid in definition of cluster boundaries for each SNP locus 3) To assess marker performance and quality assurance 4) Evaluate plate to plate performance variation. For non-human projects, the investigator must supply their own controls.

Do you provide DNA controls for GWAS projects?

Yes. We recommend cross plate duplicates on each plate.

What is the timeline for my project’s data to be released?

This is dependent on the size and complexity of the project. Generally, for moderately sized GWAS projects without pretesting can be completed in 8-12 weeks, but this can vary with lab workload and your precise project details. Ask your Project Coordinator for a time estimate specific to your project.  

Who do we contact for information about our project?

Each study will be assigned a Project Coordinator who will be your primary contact for information about the project and will let you know if there are any issues with the samples, DNA manifest, etc. that need to be resolved.

I am uncertain about the quality and identity of all of my samples and would like some sort of QC done before committing to the full study?

If you are uncertain about your DNA, you can pay to add on pre-testing to your GWAS project.  This service uses the Illumina QC array, which has 15,000 SNPs that are included on every Illumina array.  This service allows for gender and relationship verification, as well as testing DNA quality.

Can we visit the GRCF?

Yes. We welcome all project PIs to visit the lab. Talk to your Project Coordinator to arrange a visit.