Clinical Workflow Guide

This guide walks through a typical clinical case workflow in CSA, which is usually carried out by the Variant Scientist and Lab Director user roles and includes the following steps, or workflow states:

Example Clinical Workflow

Workflow state	Actions	User role
QC Review	Review quality metrics of the sequencing data for participants in the study	Variant Scientist
Case Review	Review participants, phenotypes, and advanced report settings	Variant Scientist
Variant Review	Review variant listing, add variant curations, score variants, and draft clinical report	Variant Scientist
Report Review	Review and approve variant classification and clinical report	Variant Approver and/or Lab Director
Report Delivery	Approve clinical report, generate PDF and deliver to physician	Lab Director
Case Complete	Set the workflow state to Case Complete	Lab Manager

Note

Case workflows in CSA can be customized according to the lab’s needs and are configured by a CSA administrator (for more information, refer to the Administration manual).

This section covers the following topics:

• Clinical Workflow Quick Start
• Managing Studies
• Study Overview
• Query settings
• Reviewing Variant Listings
• Variant Curation
• Editing the Variant Summary
• Generating a Report