14. VarSome Clinical Tokens


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.

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


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

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

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 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 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
  • 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 file

In case the distributor wants to set up a new assay from FASTQ file for an existing customer, it
must first send to the Saphetor Support team (support@saphetor.com) and Sales Operations
team (billing@saphetor.com). 
1. the BED file of the new assay;
2. for amplicon assays, the BEDPE file with the primers;
 3. the contact information of the end customer for whom the new assay is going to be implemented.
This information will be used by the support team to properly assign the new assay on VarSome
Clinical back end.
Once the Support team has completed the assay implementation on behalf of the distributor’s
end customer, they will notify the distributor and the Sales Ops team that this step has been
completed. Then the distributor will be able to issue new tokens.
This is normally not applicable to VCF files.
How to print a Token and see all past Token ordered
Once you have ordered a token, your token will appear, as well as all the tokens you have
ordered so far:
You can print your token certificates by selecting a token and pressing the “print” button. It will
look like this:
How to claim (activate) a Token
Claiming a token means activating it. A token must be claimed by the end customer in order for
an analysis to be run.
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”
Tokens can be claimed for up to a year after they have been issued. If a user tries to claim a
token after this period, the token will be lost and a “not found” error message will be displayed
on the screen
How to run an analysis in VarSome Clinical using a Token 
Single Sample Analyses
Once a token is claimed, no further action is needed in order to run analyses on VarSome
Clinical. The platform however will validate whether a user attempting to run an analysis
possesses non-expired tokens for the specific assay and sample type (germline FASTQ or VCF
file, or somatic FASTQ) to be run.
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.
Multi-sample Analyses
For multi-sample analyses, the same validation occurs as with single sample analyses. Once a
multi-sample analysis runs, the system will decrease the number of analyses a user can run by
the number of samples participating in the multi-sample analysis. For example, if a token allows
a user to run 10 germline analyses from FASTQ or VCF files and the user initiates a multi
sample analysis composed of 3 samples (2 parents + 1 child), 7 more 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 Tokens Usage
To find all the tokens that hace been claimed, along with the number of analyses purchased vs.
consumed, the account administrator (from the distributor) or any end user must log into
sso.varsome.com, and click on the Partners tab.
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.
Tokens expiry dates (for claims and fro samples analyses)
The tokens have 2 different expiry dates: one for the claim and one for the samples’ analyses.
 1. Token Claim 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.
 2. 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 token will be invoiced at the time it is issued
Tokens-supported pipelines
Tokens support FASTQ and VCF files. They can be issued for either somatic or germline
analyses for FASTQ files and germline only for VCF files.
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).
When a token is used, it cannot be converted to another assay or another version of the same
assay than the one it was already issued for. For example, if a customer has ordered a germline token, claimed it and started to use it, it can not be converted anymore into a somatic one,
even if the token was ordered by mistake
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
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
purchase 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.