All the information you need to know about tokens and their management on VarSome Clinical
Definition
A token is an activation code for VarSome Clinical services, which upon claiming, permits the client to analyze a certain number of samples belonging to a certain NGS assay from either FASTQ or VCF files. It can then be seen as a form of VarSome Clinical analysis prepayment.
Below you will find some basic information about tokens:
- Tokens are set either for somatic analyses (in which case they will include the somatic supplement), or for germline analyses.
- Tokens can be bundled with physical assays in order for a distributor to sell both the assay and the analysis that goes with it.
- Tokens may include storage. If you are interested, please contact your Saphetor sales representative to discuss fixed storage pricing.
- If a token was purchased by a distributor without storage, or if the storage period included in the initial token has expired, storage fees will be charged directly to the distributor. Please note that you can request to automatically archive samples after this initial period, so that no additional storage fee will be charged.
- Once purchased, a token must be claimed (activated) within a year from the purchase date. Once claimed (activated), all the analyses that belong to a given token must be used within a year from the claim (activation) date. Otherwise, the token/analyses will be lost and not reimbursed.
Token management
SSO platform and Account Administrator
Saphetor has developed an SSO platform on VarSome (sso.varsome.com) that can be used by the Account administrator of the distributor to facilitate the usage of VarSome.
To use this application, one unique user from the distributor must be defined as the Account Administrator. This user is set up by the Saphetor Billing Department.
How to order a Token
To order a new token, the customer / distributor can either:
- Issue the token on VarSome Clinical
- Send a Purchase Order to Saphetor (mandatory for new assays / new customers)
In the latter case , the customer / distributor should send to Saphetor a Purchase Order containing:
1. PO number
2. Assay name
3. Number of samples for each token
4. Number of tokens
5. Type of samples (check applicable boxes):
- FASTQ germline
- FASTQ somatic
- VCF germline
- VCF somatic
6. Storage option selected:
- No storage included in the token
- xx months of storage included
- Storage option selected (1 to 5)
How to issue a Token
Here are instructions on how a distributor can issue a token in favor of an end customer. For a new end customer that has never used tokens before, or for a new assay, you will also find some additional steps to follow.
Existing end customer/existing assay
At first, the token specifications for the user group must be set up by the Saphetor Support team (e.g. implementation of the token and setting up the group’s account to access specific assays on the Clinical back-end). Also, the Account Administrator (Account Administrator) of the distributor ordering the token with specific assays should have access to VarSome Clinical, because assays are fetched from the Clinical platform.
Once all of the above actions are completed, the Account Administrator of the distributor needs to follow the steps below to issue a token on the sso.varsome.com :
Click on the "Partners" button and then select the screen “Issue tokens”,
- select the proper assay name
- select the type of sample (germline or somatic),
- enter the number of samples and the number of tokens you want to order
- select the storage that you potentially want to include with the analysis (valued in
months) - In the reference field, type your P.O. # as your reference.
- Then, press order!
New indirect end customer
In case a distributor would like to purchase a token for a new end customer, it must first send to its Saphetor sales contact (copy billing@saphetor.com) an Account Opening Form (AOF) for VarSome Clinical token-based account, signed by the distributor. The Saphetor Sales Operations team will set up the new end customer account and will inform the distributor once the account has been created.
If the end customer is already using VarSome Clinical as a direct customer, the distributor still needs to go through that process above. The Saphetor Sales Operations team will set it up as an indirect customer, under the distributor account, so that the distributor (and not the end customer) gets invoiced for the token.
New assay from FASTQ or VCF
How to print a Token and see all past Tokens ordered
On this screen, you will also be able to see all your token orders listed and filtered by assay.
How to claim (activate) a Token
A) Claim a Token in SSO
Any user from the end customer needs to log into sso.varsome.com, and click on Labs. The system will display any tokens that have already been claimed. New tokens can be claimed by entering the token code on the Claim token window (on the right of the page) and hit the “Claim” button:
B) Claim a Token in VarSome Clinical platform
Any user needs to log into VarSome Clinical platform and click on the arrow that is next to the profiles' name and after that to choose the Claim Assay Token option.
Once you receive the token, you need to claim it, in order to activate VarSome Clinical for corresponding analysis.
How to run an analysis in VarSome Clinical using a Token
Once an analysis has been launched, the system will deduct from the token the number of analyses initiated by the user. For example if a token allows a user to run 10 germline analyses from FASTQ and the user runs 6 analyses, 4 more germline analyses will be available for future use of the token.
The 50% discount that we normally apply to multi-sample analysis does not apply to tokens. Tokens can not be used when the user wants to initiate a merge analysis from existing samples. Only new multi-sample analyses from FASTQ or VCF files can use tokens. Therefore, merging analyses from existing samples require that the end user holds some available billing balance, otherwise merging is not possible.
How to track Token's Usage
A) Token Tracking in SSO
All the tokens that have been purchased will show on this page together with the actual remaining analyses (not consumed yet), the price of the token/sample, the issue date, the claim date and the expiration date. You will also find there a price list per sample for all assays.
B) Token Tracking in VarSome Clinical
Tokens expiry dates (claim and samples analyses)
The tokens have 2 different expiry dates: one for the claim and one for the samples’ analyses.
- Token Claiming date: 12 months after the date of issue. This means that the end customer must claim the token within 12 months from the token’s issue date. If a token has not been claimed within 12 months after it was purchased, it will be lost.
- Analyses Expiry date: 12 months after the claiming date. This means that the token is valid for 12 months after it has been claimed. If some analyses linked to a token have not been used within 12 months after the token was claimed, they will be lost.A billing entry is generated upon token issuing, regardless of whether the token will be claimed by the client or not.
Token-supported pipelines
Somatic tokens include a supplement for somatic samples, which does not apply to germline samples. As a result, tokens cannot be issued as combined pipelines (somatic and germline).
Combined token analyses
Tumor normal analysis (token for paired analyses)
Tumor-normal analysis definition
The user has two different samples obtained from the same patient: a tumor sample and a "normal" (healthy) sample. The pipeline will report somatic variants observed only in the tumor sample.
For a tumor normal analysis, 2 tokens of the same assay must be used (a somatic token and a germline token) in conjunction, in order to obtain the desired results. The customer must buy both tokens (germline/somatic) of the same assay.
The tokens system was developed to answer distributors specific needs to bundle assays and analyses. If used outside the specific scope or when edge cases arise, problems to all parties may occur