Warner Jeremy L, Prasad Ishaan, Bennett Makiah, Arniella Monica, Beeghly-Fadiel Alicia, Mandl Kenneth D, Alterovitz Gil
Vanderbilt University.
Boston Children's Hospital/Harvard Medical School, Boston.
JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00292. Epub 2018 May 1.
Data standards and interoperability are critical for improving care for patients with cancer. Recent efforts by ASCO include the Data Standards and Interoperability Summit in 2016, which led to the Omics and Precision Oncology and Advancing Interoperability workshops. To facilitate improved patient care, several recommendations for data sharing and standardization were made to the community.
To address these recommendations, we developed SMART Cancer Navigator, a Web application that uses application programming interfaces to gather clinical and genomic data from 11 public knowledge bases ranging from basic to clinical content coverage; three (CIViC, ClinVar, and OncoKB) explicitly linked genomic variants to clinical factors such as prognosis and treatment selection. We illustrated the utility of this application by selecting one of the monthly case studies presented by the ASCO University Molecular Oncology Tumor Board: Ovarian Cancer (BRCA Mutation). We also performed analyses on information from the three clinico-genomic knowledge bases to corroborate previous work and illustrate the state of data sharing among publicly available resources.
SMART Cancer Navigator aggregates and contextualizes data from 11 different knowledge bases and stores user queries in a lightweight Web application that can link into Fast Healthcare Interoperability Resources-enabled electronic health records. Potentially relevant clinical trials and/or approved treatments were identified for three mutations found in a hypothetical patient with advanced ovarian cancer. A comparison of the three clinico-genomic knowledge bases indicated substantial differences in coverage at the gene and variant levels.
SMART Cancer Navigator has immediate relevance to practicing oncologists and others. Additional knowledge bases can be added without undue effort. As a first step toward utility, we generalized and disseminated the resulting implementation (https://smart-cancer-navigator.github.io) and data sets.
数据标准与互操作性对于改善癌症患者的护理至关重要。美国临床肿瘤学会（ASCO）近期开展了多项工作，包括2016年的数据标准与互操作性峰会，该峰会促成了组学与精准肿瘤学以及推进互操作性研讨会。为促进改善患者护理，向业界提出了多项关于数据共享和标准化的建议。
为落实这些建议，我们开发了SMART癌症导航器，这是一个网络应用程序，它使用应用程序编程接口从11个涵盖基础到临床内容的公共知识库收集临床和基因组数据；其中三个知识库（CIViC、ClinVar和OncoKB）明确将基因组变异与预后和治疗选择等临床因素联系起来。我们通过选择ASCO大学分子肿瘤学肿瘤委员会每月呈现的一个病例研究：卵巢癌（BRCA突变），来说明该应用程序的实用性。我们还对来自三个临床基因组知识库的信息进行了分析，以证实先前的工作，并说明公开可用资源之间的数据共享状况。
SMART癌症导航器汇总并整合了来自11个不同知识库的数据，并将用户查询存储在一个轻量级网络应用程序中，该应用程序可以链接到支持快速医疗互操作性资源的电子健康记录。对于一名晚期卵巢癌假设患者中发现的三种突变，确定了潜在相关的临床试验和/或获批治疗方法。对这三个临床基因组知识库的比较表明，在基因和变异水平上的覆盖范围存在显著差异。
SMART癌症导航器与执业肿瘤学家及其他人员直接相关。可以轻松添加更多知识库。作为迈向实用化的第一步，我们推广并发布了最终的实施方案（https://smart-cancer-navigator.github.io）和数据集。
