Submit Genotype Data with Webforms and Excel Templates

The Submission Editor allows you to create a genotype submission using Excel templates to assemble the data. Submitting genotype data to PharmGKB via webforms and Excel templates can be broken down into these steps:

1. Assemble and complete the required Excel templates for your submission.
2. Go online to the Submission Editor.
3. Upload a completed Sample Set template or select from one of your group's existing sample sets.
4. Provide a reference sequence and accompanying information.
5. Upload the completed Assay and Results templates.
6. Validate your submission.
7. Verify the data on the PharmGKB Preview Site.
8. Approve (or reject) the submission.

Step 1: Assemble and complete the required Excel templates and reference sequence for your submission.

The first step in submitting genotype data to PharmGKB is to complete all of the necessary Excel templates. All templates and accompanying instructions are available online. Choose the appropriate Assay and Results template for the experiment you are reporting. If you are reporting genotypes for new samples, you should also fill out the Sample Set template. Additionally, you should have the reference sequence that you are reporting on prepared in a text file to cut and paste (see Step 4).

Step 2: Go online to the Submission Editor.

Login to the PharmGKB Preview Site and click on the "Submit" tab. Follow the option to submit genotype data using Excel templates and webforms. The first webform will ask you to give your submission a title and provide a one or two sentence description.

Step 3: Upload a completed Sample Set template or select from one of your group's existing sample sets.

The next form will ask you upload your sample set information using the Sample Set Excel Template, or select from one of your group's previously submitted sample sets.

You will only be given a choice to select from one of your group's existing sample sets if there are any, and this will only happen once you have approved a submission containing a sample set.

Note that when you upload a sample set via a template, it is considered to be a new sample set even though you may already have an existing sample set with an identical set of samples. If you have performed many experiments with the same sample set, it is highly recommended that you select the same sample set instead of resubmitting each time. This will enable you to easily find your data based on a single sample set.

Step 4: Provide a reference sequence and accompanying information.

This form collects data on the DNA sequence you are using with the following fields:

• Name (optional): Provide your name for this sequence.
• Gene Symbol (optional): Provide the HGNC symbol for the gene containing this reference sequence (if applicable).
• Source: The source of the sequence.
• Sequence: Paste the DNA sequence in this field. The sequence must be between 40 bp and 25,000 bp in length and can only contain IUPAC codes.

Coordinate System

You may also specify the coordinate system you will be using to report positions against the reference sequence. The default coordinate system numbers the first base in the reference sequence as "1". It is highly recommended that you use the default settings to avoid confusion; however, you may change these parameters as needed.

• Start Position: The position on the reference sequence from which to start counting with this coordinate system. The first base on the reference sequence is position 1 and there is no zero position on the reference sequence. For example, if the reference sequence is AGCTGTAACGT, and the start position is 5, then position 1 in this coordinate system is mapped to position 5 on the reference sequence, which is the second "G" in this reference sequence. If the start position is -4, then position 5 in this coordinate system is the first "A" in this reference sequence. Note that it would be an error to report anything that is off the reference sequence. In this example, anything before position 5 would be invalid.
• Has Zero: This flag indicates whether this coordinate system has a zero. For example, if the reference sequence is AGCTGTAACGT, the start position is 5, and "Has Zero" is set to true, then position -2 is mapped to position 2 on the reference sequence, which is the first "G" on the reference sequence. If "Has Zero" is set to false in the same scenario, then position -2 is mapped to position 3 on the reference sequence, which is the first "C" on the reference sequence.

A visual diagram of how this information is used is available here.

Step 5: Upload the completed Assay and Results templates.

In this step, you upload information on the assay you performed along with the results you obtained. It is best to have the appropriate Assay and Result Excel templates completed in advance.

Step 6: Validate your submission.

After uploading the Assay and Results templates, PharmGKB will run a preliminary validation of the data. At this time, the validator is checking for any empty fields that are required to be filled, etc. If any problems are found, they will be listed so that you may address them. If you have any questions regarding the output from this step, please contact us.

If there are no problems, your submission will be accepted and you will be provided with a link to view it on the the PharmGKB Preview Site. Once the PharmGKB has processed your submission, you will be notified via email to let you know that it is ready to be reviewed.

Step 7: Verify the data on the PharmGKB Preview Site.

Once you have been notified via email that your submission is available for review, follow the link to the PharmGKB Preview Site.

If you do not have the email link or it does not work for some reason, you may find your submission page one of the following ways:

• Click on the "Search" tab at the top of the page. Click on the "Submissions by project" link. Find your project and click on the number in the "Pending" column. Click on the submission ID (PS number) that you would like to review.
• If you know the submission ID of the submission you want to approve, type it into the search box at the top right corner of the page. A search page should come up listing that submission. Click that link to continue.

Please see our documentation regarding submission review.

Step 8: Approve (or reject) the submission.

After the data has been reviewed for accuracy, only project PIs and other pre-approved registered users are able to approve submissions. The user with approval permissions must login to the PharmGKB Preview Site and go to the submission page (see Step 4 above)

If the submission is satisfactory, click the "Approve Submission" button on the page. The submission will then be posted on the public PharmGKB website. If there is a problem with the submission, reject the submission by clicking on that button instead.

(Note that only project PIs and other pre-approved registered users are able to view the Approve and Reject buttons, because they are the only users allowed to approve or reject submissions.)