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Documentation for Registry NGS

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Last Modified Date10/11/2019 8:14 AM
SummaryDocumentation for Registry NGS
Content

The HD4DP application enables data providers to collect data.

Registers are accurately composed to be able to capture all the necessary specifications and data in HD4DP.

The specifications for NGS and more information to get started with the registration of data for NGS are explainded in this article.

Description 

 

Data Providers

 All laboratories executing Next Generation Sequencing tests who want a reimbursement for that test

Support

   For technical issues, contact support.healthdata@sciensano.be 
   For administrative questions about the reimbursment, contact ngs@riziv-inami.fgov.be

 

Specifications of the register

The powerpoint used at the information sessions on 3/5/18 and 7/5/18 at RIZIV-INAMI can be consulted by clicking the below images.

NL                                                             FR                
ppt ngs pitter used at riziv     ppt NGS PITTER

A technical session was organised for LIMS providers and IT responsibles of LABS on May 22nd 2018 to instruct on how to prepare the csv extractions.

  • Please find the video of this Webconference call here:

  • Please find the presentation that was used during this Technical Information session here.

Request an account

HD4DP is a local application that is accessible in a web browser, such as Internet Explorer or Chrome, which has a specific link in every organisation.
  • Open the link for the HD4DP application or contact healthdata.be at support.healthdata@sciensano.be to get the link for your organisation.

User-added image

  • Click on the Request account link on the login page 
  • Fill out the request form:
    • Enter a username, first name, last name and email address
    • Select the organization and data collection(s)
    • Fill in the Requester email field if a person requests an account for a third person
    • Submit the request user the Request button 
  • Confirmation emails are sent to the person for whom the account was requested as well as the requester, if the field 'Requester email' was filled
  • The approval or rejection for the user account is confirmed by mail. Depending on your orginazation, this could take a few hours.
    • This action will be done by an HD4DP administrator in your organisation 
    • The confirmation mail will include all the necessary information to log in
 

Start collecting data

The HD4DP application enables data providers to collect data

The medical and professional secret is protected at various levels and through principles such as encoding, encryption, and user-acces management. The combination of these elements guarantees so-called "end-to-end security". 

During the data collection process, which is done by this application, all data is securely (= anonymized) transferred to Sciensano, with the use of e-health box:

  • The data provider never receives the coded identifiers

  • eHealth has never access to medical data or metadata

  • Healthdata.be never receives the original identifier, but can reconcile different entries


An overview is given in the video:


We provide more documentation of the different functions and possibilities in the different phases of data collection in the HD4DP application.

 

NGS User Manual

You can find the NGS User Manual.

Transfer the VCF File via SFTP

For each patient record, you have to provide a VCF file.
You have to transfer the VCF file via File Transfer Protocol (SFTP).
You can request your credentials to the SFTP server of healthdata.be by contacting support.healthdata@sciensano.be and ngs.healthdata@sciensano.be .

Healthdata provides 2 options for using its SFTP transfer:
  • A manual file transfer using a web page
    • using a web page
    • using a SFTP client (e.g. Filezilla, Winscp etc.)
  • An automated file transfer using a script:
    • developed by the local Information Technology (IT) Department of your organization;
    • developed by Healthdata
Requirements of the VCF File
  • The file must not contain patient information within the VCF header
  • The VCF file content (the list of mutations) should reflect the select “NGS indication” put in the NGS registry and the biomarker put in PITTER
  • The VCF filename transferred though SFTP must be exactly the same as the filename filled out in the patient record
File Manual Transfer

Hereafter, find the 2 manual ways for transferring a VCF file using the HDUpload Webpage and a local SFTP client.
.
Find below the 4 steps for using the HDUpload Webpage
  • go to https://hdupload.healthdata.be
  • add your credentials by:
    • filling out the user name in the field SFTPUser
    • filling out the password in the field SFTPPassword
  • select the file to transfer by clicking on the button labelled Choose File
  • transfer the file to healthdata.be by cliking on the button labelled upload File
OR Find below the steps using a SFTP client
  • install a free-of-use SFTP client on your computer, the most popular ones are Filezilla and Winscp.
  • make sure to have the port 2222 opened (contact your local IT department to configure this)
  • connect to the healthdata.be SFTP Server using credentials provided by support.healthdata@sciensano.be, using the SFTP client you will choose by entering your credentials:
    • Host Name or Public Address IP of the healthdata.be SFTP server
    • User Name
    • Password
  • transfer your file from your local system to the healthdata.be SFTP server
  • move the files to the Finished Folder when the SFTP client will notify the completion of the file transfer. This last action indicates our system that the file transfer was successful, and that the subsequent files upload can be done. Then, the whole VCF file will be uploaded.

File Automated Transfer

For the automation of the file transfer, a collaboration between your IT Department and Healthdata is required.
We want to empahize the 2 requirements to meet for enabling a fully automated data flow from the sequencer to Healthdata.
That will create System-To-System communication of VCF files using the SFTP protocol.
This requires the automation of 2 flows:
  • from the sequencer (System 1) to a specific folder in the local infrastructure of your organization. This automation has to be implemented by your local IT department in collaboration with Healthdata.be
  • from a specific folder in the local infrastructure of your organization to Healthdata.be. This automation can be implemented by your local IT department or Healthdata.be



 

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