As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storage and sharing is Ethereum smart contracts. Ethereum is a blockchain platform, and smart contracts are immutable pieces of code running on virtual machines in this platform that can be invoked by a user or another contract (in the blockchain network). The 2019 iDASH (Integrating Data for Analysis, Anonymization, and Sharing) competition for Secure Genome Analysis challenged participants to develop time- and space-efficient Ethereum smart contracts for gene-drug relationship data. Here we design a specific smart contract to store and query gene-drug interactions in Ethereum using an index-based, multi-mapping approach. Our contract stores each pharmacogenomics observation, a gene-variant-drug triplet with outcome, in a mapping searchable by a unique identifier, allowing for time and space efficient storage and query. This solution ranked in the top three at the 2019 IDASH competition. We further improve our ”challenge solution” and develop an alternate ”fastQuery” smart contract, which combines together identical gene-variant-drug combinations into a single storage entry, leading to significantly better scalability and query efficiency. On a private, proof-of-authority network, both our challenge and fastQuery solutions exhibit approximately linear memory and time usage for inserting into and querying small databases (<1,000 entries). For larger databases (1000 to 10,000 entries), fastQuery maintains this scaling. Furthermore, both solutions can query by a single field (”0-AND”) or a combination of fields (”1- or 2-AND”). Specifically, the challenge solution can complete a 2-AND query from a small database (100 entries) in 35ms using 0.1 MB of memory. For the same query, fastQuery has a 2-fold improvement in time and a 10-fold improvement in memory. We show that pharmacogenomics data can be stored and queried efficiently using Ethereum blockchain. Our solutions could potentially be used to store a range of clinical data and extended to other fields requiring high-integrity data storage and efficient access.

中文翻译：

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使用以太坊区块链通过智能合约存储和查询药物基因组学数据。

随着药物基因组学数据越来越成为临床治疗决策不可或缺的组成部分，需要采用适当的数据存储和共享协议。安全，高完整性的存储和共享的一种有希望的选择是以太坊智能合约。以太坊是一个区块链平台，智能合约是在该平台的虚拟机上运行的不可变代码段，可由用户或其他合约（在区块链网络中）调用。安全基因组分析的2019年iDASH（分析，匿名化和共享数据集成）竞赛要求参赛者开发省时，省空间的以太坊智能合约，用于基因-药物关系数据。在这里，我们设计了一种特定的智能合约，以使用基于索引的多映射方法在以太坊中存储和查询基因药物相互作用。我们的合同将每个药物基因组学观察结果（带有结果的基因变异药物三联体）存储在可通过唯一标识符搜索的映射中，从而实现时空高效的存储和查询。该解决方案在2019年IDASH竞赛中排名前三。我们进一步完善了“挑战解决方案”，并开发了另一种“ fastQuery”智能合约，该合约将相同的基因-变体-药物组合组合到单个存储条目中，从而显着提高了可扩展性和查询效率。在私有的权威证明网络上，我们的Challenge和fastQuery解决方案都显示出大约线性的内存和时间消耗，用于插入和查询小型数据库（小于1,000个条目）。对于较大的数据库（1000至10,000个条目），fastQuery保持此缩放比例。此外，两种解决方案都可以通过单个字段（“ 0-AND”）或字段组合（“ 1-或2-AND”）进行查询。具体来说，质询解决方案可以使用0.1 MB的内存在35毫秒内从小型数据库（100个条目）完成2-AND查询。对于相同的查询，fastQuery的时间缩短了2倍，内存减少了10倍。我们展示了可以使用以太坊区块链有效地存储和查询药物基因组学数据。我们的解决方案可以潜在地用于存储一系列临床数据，并扩展到需要高完整性数据存储和高效访问的其他领域。fastQuery在时间上提高了2倍，在内存方面提高了10倍。我们展示了可以使用以太坊区块链有效地存储和查询药物基因组学数据。我们的解决方案可以潜在地用于存储一系列临床数据，并扩展到需要高完整性数据存储和高效访问的其他领域。fastQuery在时间上提高了2倍，在内存方面提高了10倍。我们展示了可以使用以太坊区块链有效地存储和查询药物基因组学数据。我们的解决方案可以潜在地用于存储一系列临床数据，并扩展到需要高完整性数据存储和高效访问的其他领域。