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1 Introduction

This chapter provides an introduction to Oracle Healthcare Precision Medicine (OHPM). It contains the following topics:

• Section 1.1, "Overview"

• Section 1.2, "Disclaimer"

• Section 1.3, "What Can I Do Using Oracle Healthcare Precision Medicine"

• Section 1.4, "User Roles"

• Section 1.5, "Known Issues"

1.1 Overview

Oracle Healthcare Precision Medicine is a software application designed to address the gap between treatments in the clinic and the knowledge in the research pipelines. It enables collaboration between the clinician, looking for the most appropriate treatment for his patient, and the molecular pathologist, learning patient's molecular profile and suggesting the most up-to-date treatment to follow.

The clinician orders diagnostic tests. After the specimen is collected and processed, the molecular pathologist analyzes test results and delivers treatment recommendations. OHPM helps optimize personalized patient care based on an individual's clinical and genomic profile. It also accelerates molecular laboratory testing throughput, while maintaining consistency and traceability of the generated reporting contents to fulfill compliance requirements.

1.2 Disclaimer

The Oracle Healthcare Precision Medicine software is only a search tool and is not intended to, and must not replace the clinician's judgment or experience. Furthermore, the healthcare professional using this search tool should employ their professional judgment concerning the reliability and accuracy of the information in the various knowledge databases that are employed or selected as content for reports generated using Oracle Healthcare Precision Medicine.

1.3 What Can I Do Using Oracle Healthcare Precision Medicine

The following lists the primary tasks that can be accomplished using OHPM:

• Filter through thousands of variants to identify ones which are clinically actionable or may be relevant

• Annotate variants that can be acted upon today or warrant further investigation based on sequenced data and reference information, both internal and external

• Publish a genomic report to be used in clinical practice (report can be published both to OHPM and EMR system) and therefore personalize treatment

• View the published report with full security settings, which are based on the user's access to patient records

1.4 User Roles

The following are the various user roles in OHPM:

• pm_reporter_group - for users who will be generating molecular reports and publishing them or browsing through genomic data. This includes molecular pathologists and clinical geneticists.

• pm_clinician_group - for doctors who are seeing patients and request the report to be done. This includes clinicians, physicians and nurses.

• pm_reporter_limited_group - for someone who can browse through data and do most of the reporting steps but cannot publish the report nor request report from third parties (example, Nof1). This includes molecular pathologists and clinical geneticists who may be training on the software.

• pm_admin_group - for users who can create groups of other users and manage roles of users.

Users may be given several of these roles but the roles take precedence in the order of precedence listed below:

• pm_reporter_group

• pm_reporter_limited_group

• pm_clinician_group

A user cannot have both clinician and either of the reporter roles. If this happens, the application displays an error.

The pm_admin_group role can be used in conjunction with any of the above roles.

1.5 Known Issues

Following are the known issues for this release of OHPM:

• When clicking View Patient from the Genomic Report window, the Patient Viewer does not perform. It can take several minutes to load.

• In the variant table, sorting based on chromosome position treats numbers as strings. For example, chr7 appears after chr11 when you select sorted by ascending.

• Certain variants which are present on MT or Y chromosome appear as linked to bogus ’No Gene' record.

• While filtering, certain variants are missing non-coding impact attribute when listed in the tabular view. This attribute appears correctly once the user looks at the Variant Detail screen.

• No warning or prompt is displayed before the application times out.

• Variant Effect calculations are incorrect for variants near CDS boundaries.

• There is no indication to display the default sorting and then change it.

• Mitochondrial chromosome variants are not labeled correctly when sent to Dalliance resulting in no data shown.

• The Patient Viewer tab does not load the relevant patient automatically.

• Patient Viewer only supports searching by patient ID, not patient name.

• After viewing patient details from the patient viewer, if you open another report and click Patient Viewer, you will still see the patient details from the previous report.

• Protein impact is missing from variant details in the published report and has to be added manually by the end user when publishing a report.

• Variants with chromosome position :CHRMT do not display the variant area in Dalliance.