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ANSWER: Annotation Software for Electronic Reporting.

Chelsea Raulerson1, Guillaume Jimenez1, Benjamin Wakeland1

  • 1Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX.

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|January 13, 2022
PubMed
Summary
This summary is machine-generated.

A new tool called ANSWER helps clinical oncology next-generation sequencing (NGS) laboratories generate comprehensive genetic testing reports. This software facilitates variant filtering, annotation, and reporting for improved clinical actionability and electronic health record integration.

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Area of Science:

  • Genomics and Bioinformatics
  • Clinical Pathology
  • Health Informatics

Background:

  • Clinical genetic testing, particularly next-generation sequencing (NGS), is crucial for understanding disease mechanisms and guiding treatment.
  • Current reporting methods for NGS face challenges due to the vast number of genes and variants analyzed, unlike traditional tests.
  • Existing reporting tools for oncology genomics often lack essential features for comprehensive clinical reporting.

Purpose of the Study:

  • To develop a specialized tool for clinical oncology NGS laboratories to improve the reporting of genetic test results.
  • To address the limitations of current reporting systems by providing features for variant filtering, annotation, and data integration.
  • To facilitate the electronic transfer of genetic testing reports to electronic health records.

Main Methods:

  • Development of a tool named Annotation SoftWare for Electronic Reporting (ANSWER).
  • Utilized software for data storage (MySQL, MongoDB), database querying (Python), and a web-based user application (JAVA, JAVA script).
  • Incorporated features for manual data curation and report generation by users.

Main Results:

  • ANSWER enables molecular pathologists to filter variants based on quality control and clinical actionability.
  • The tool allows for variant visualization, creation of reusable annotations, and selection of relevant variants for reporting.
  • ANSWER generates comprehensive reports including demographics, variants, annotations, and references, exportable to PDF or HL7 formats for EHR integration.

Conclusions:

  • ANSWER is a locally installable tool designed to meet the specific clinical reporting requirements of oncology NGS laboratories.
  • The software enhances the utility of genetic testing by providing structured and actionable genomic information.
  • ANSWER supports efficient data management and reporting, crucial for personalized medicine in oncology.