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Flype: Software for enabling personalized medicine
American Journal of Medical Genetics Seminars in Medical Genetics, Part C ( IF 2.8 ) Pub Date : 2020-12-03 , DOI: 10.1002/ajmg.c.31867
Donald L Helseth 1 , Kamalakar Gulukota 1 , Nicholas Miller 1 , Mathew Yang 1 , Tom Werth 2 , Linda M Sabatini 3 , Mike Bouma 3 , Henry M Dunnenberger 1 , Dyson T Wake 1 , Peter J Hulick 1, 4 , Karen L Kaul 3 , Janaradan D Khandekar 1, 5
Affiliation  

The advent of next generation DNA sequencing (NGS) has revolutionized clinical medicine by enabling wide‐spread testing for genomic anomalies and polymorphisms. With that explosion in testing, however, come several informatics challenges including managing large amounts of data, interpreting the results and providing clinical decision support. We present Flype, a web‐based bioinformatics platform built by a small group of bioinformaticians working in a community hospital setting, to address these challenges by allowing us to: (a) securely accept data from a variety of sources, (b) send orders to a variety of destinations, (c) perform secondary analysis and annotation of NGS data, (d) provide a central repository for all genomic variants, (e) assist with tertiary analysis and clinical interpretation, (f) send signed out data to our EHR as both PDF and discrete data elements, (g) allow population frequency analysis and (h) update variant annotation when literature knowledge evolves. We discuss the multiple use cases Flype supports such as (a) in‐house NGS tests, (b) in‐house pharmacogenomics (PGX) tests, (c) dramatic scale‐up of genomic testing using an external lab, (d) consumer genomics using two external partners, and (e) a variety of reporting tools. The source code for Flype is available upon request to the authors.

中文翻译:

Flype:实现个性化医疗的软件

下一代 DNA 测序 (NGS) 的出现使基因组异常和多态性的广泛检测成为可能,从而彻底改变了临床医学。然而,随着测试的爆炸式增长,带来了一些信息学挑战,包括管理大量数据、解释结果和提供临床决策支持。我们展示了 Flype,这是一个由在社区医院环境中工作的一小群生物信息学家构建的基于网络的生物信息学平台,通过允许我们:(a) 安全地接受来自各种来源的数据,(b) 发送订单来应对这些挑战到各种目的地,(c) 对 NGS 数据进行二级分析和注释,(d) 为所有基因组变异提供一个中央存储库,(e) 协助三级分析和临床解释,(f) 将签出数据作为 PDF 和离散数据元素发送到我们的 EHR,(g) 允许人口频率分析和 (h) 在文献知识发展时更新变体注释。我们讨论了 Flype 支持的多个用例,例如 (a) 内部 NGS 测试,(b) 内部药物基因组学 (PGX) 测试,(c) 使用外部实验室进行基因组测试的显着扩展,(d) 消费者使用两个外部合作伙伴的基因组学,以及 (e) 各种报告工具。Flype 的源代码可向作者索取。(d) 使用两个外部合作伙伴的消费者基因组学,以及 (e) 各种报告工具。Flype 的源代码可向作者索取。(d) 使用两个外部合作伙伴的消费者基因组学,以及 (e) 各种报告工具。Flype 的源代码可向作者索取。
更新日期:2020-12-03
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