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100K_RD_reports Project Requirements

Participants

- Product owner: all GMCs
- Team: Aled Jones
- Stakeholders: GMCs, Genomics England

Current Status

In Progress

Purpose

Probands are referred to the 100,000 genomes project by a Genomic Medicine Centre (GMC). Samples are sequenced and sent to a CIP (clinical interpretation partner) for analysis.

GMCs are informed when results are ready. If variants have been found the lab can confirm variants before issuing a report from the lab to the referring clinician.

If no variants have been found a report based on the original GEL negative report is issued, as no interpretation has been performed by the laboratory.

This project aims to take the information from the CIP-API, modify the report as required and create a PDF report which can be issued by the GMC.

Project Goals & Objectives

Code was designed to be modular with the hope minimal changes would be required by an GMC to implement this code.

The resulting Appshould:

  • Read the CIP-API
  • Download the clinical report for the desired proband (using the GEL Participant ID)
  • Modify the html report
  • Produce pdf that can be sent to referring Clinician

Requirements

This must be easily deployable within all GMCs (taking into account common operating systems and staff expertise)

Functional

  • Take a GEL participant ID
  • Able to differentiate between samples that have been interpreted and confirmed by the lab and where no variants have been found and no interpretation has been performed by the laboratory.

Technical

  • Able to run cross platform
  • Use widely supported tools/software where possible
  • Uses Python to enable easy adoption and development by any GMC

Usability

  • Modular so can be called by/integrated into other automated systems/user interfaces.