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.

中文翻译：

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海王星：提供基因组医学的环境

 目的

基因组医学对于改善医疗保健有着巨大的希望，但将可搜索和可操作的遗传数据整合到电子健康记录 (EHR) 中仍然是一个挑战。在这里，我们描述 Neptune，一个用于在临床报告过程中管理临床实验室和 EHR 系统之间交互的系统。

 方法

我们开发了 Neptune 并将其应用于两个需要报告定制、变异重新分析和 EHR 集成的临床测序项目。

 结果

Neptune 已用于生成和交付超过 15,000 份临床基因组报告。这项工作涵盖了基于分别包含 68 和 153 个基因的靶向基因组的两项临床测试。这些项目需要可定制的临床报告，其中包含各种遗传数据类型，包括单核苷酸变异（SNV）、拷贝数变异（CNV）、药物基因组学和多基因风险评分。还支持两项变体再分析活动，突出了这一重要的工作流程。

 结论

需要有方法将结构化遗传数据传递给电子病历。这种需求不仅限于开发数据格式，还包括提供管理报告流程本身的基础设施。 Neptune 已成功应用于两个高通量临床测序项目，以构建并向 EHR 系统提供临床报告。该软件是开源的，可从 https://gitlab.com/bcm-hgsc/neptune 获取。