Neptune: an environment for the delivery of genomic medicine.

TitleNeptune: an environment for the delivery of genomic medicine.
Publication TypeJournal Article
Year of Publication2021
AuthorsEric, 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, DM, Gibbs, RA
Corporate AuthorseMERGE Consortium
JournalGenet Med
Volume23
Issue10
Pagination1838-1846
Date Published2021 10
ISSN1530-0366
KeywordsElectronic Health Records, Genomics, High-Throughput Nucleotide Sequencing, Humans, Neptune, Software
Abstract

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 .

DOI10.1038/s41436-021-01230-w
Alternate JournalGenet Med
PubMed ID34257418
PubMed Central IDPMC8487966
Grant ListU01 HG008676 / HG / NHGRI NIH HHS / United States
U01 HG008657 / HG / NHGRI NIH HHS / United States
U01 HG008672 / HG / NHGRI NIH HHS / United States
U01 HG008684 / HG / NHGRI NIH HHS / United States
U01 HG008679 / HG / NHGRI NIH HHS / United States
U01 HG008666 / HG / NHGRI NIH HHS / United States
U01 HG008680 / HG / NHGRI NIH HHS / United States
U01 HG008673 / HG / NHGRI NIH HHS / United States
U01 HG008685 / HG / NHGRI NIH HHS / United States
U01 HG006379 / HG / NHGRI NIH HHS / United States
U01 HG008664 / HG / NHGRI NIH HHS / United States
U01 HG008701 / HG / NHGRI NIH HHS / United States