Neptune: an environment for the delivery of genomic medicine.

Journal Article (Journal Article)

PURPOSE: Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. METHODS: We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. RESULTS: Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. CONCLUSION: Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .

Full Text

Duke Authors

Cited Authors

  • Eric, V; Yi, V; Murdock, D; Kalla, SE; Wu, T-J; Sabo, A; Li, S; Meng, Q; Tian, X; Murugan, M; Cohen, M; Kovar, C; Wei, W-Q; Chung, WK; Weng, C; Wiesner, GL; Jarvik, GP; Muzny, D; Gibbs, RA; eMERGE Consortium,

Published Date

  • October 2021

Published In

Volume / Issue

  • 23 / 10

Start / End Page

  • 1838 - 1846

PubMed ID

  • 34257418

Pubmed Central ID

  • PMC8487966

Electronic International Standard Serial Number (EISSN)

  • 1530-0366

Digital Object Identifier (DOI)

  • 10.1038/s41436-021-01230-w

Language

  • eng

Conference Location

  • United States