Skip to main content

Neptune: an environment for the delivery of genomic medicine.

Publication ,  Journal Article
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 ...
Published in: Genet Med
October 2021

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 .

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genet Med

DOI

EISSN

1530-0366

Publication Date

October 2021

Volume

23

Issue

10

Start / End Page

1838 / 1846

Location

United States

Related Subject Headings

  • Software
  • Neptune
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Genetics & Heredity
  • Electronic Health Records
  • 3105 Genetics
  • 1103 Clinical Sciences
  • 0604 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Eric, V., Yi, V., Murdock, D., Kalla, S. E., Wu, T.-J., Sabo, A., … eMERGE Consortium, . (2021). Neptune: an environment for the delivery of genomic medicine. Genet Med, 23(10), 1838–1846. https://doi.org/10.1038/s41436-021-01230-w
Eric, Venner, Victoria Yi, David Murdock, Sara E. Kalla, Tsung-Jung Wu, Aniko Sabo, Shoudong Li, et al. “Neptune: an environment for the delivery of genomic medicine.Genet Med 23, no. 10 (October 2021): 1838–46. https://doi.org/10.1038/s41436-021-01230-w.
Eric V, Yi V, Murdock D, Kalla SE, Wu T-J, Sabo A, et al. Neptune: an environment for the delivery of genomic medicine. Genet Med. 2021 Oct;23(10):1838–46.
Eric, Venner, et al. “Neptune: an environment for the delivery of genomic medicine.Genet Med, vol. 23, no. 10, Oct. 2021, pp. 1838–46. Pubmed, doi:10.1038/s41436-021-01230-w.
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. Neptune: an environment for the delivery of genomic medicine. Genet Med. 2021 Oct;23(10):1838–1846.

Published In

Genet Med

DOI

EISSN

1530-0366

Publication Date

October 2021

Volume

23

Issue

10

Start / End Page

1838 / 1846

Location

United States

Related Subject Headings

  • Software
  • Neptune
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genomics
  • Genetics & Heredity
  • Electronic Health Records
  • 3105 Genetics
  • 1103 Clinical Sciences
  • 0604 Genetics