Producing personalized statin treatment plans to optimize clinical outcomes using big data and machine learning.

Almost half of Americans 65 years of age and older take statins, which are highly effective in lowering low-density lipoprotein cholesterol, preventing atherosclerotic cardiovascular disease (ASCVD), and reducing all-cause mortality. Unfortunately, ∼50% of patients prescribed statins do not obtain these critical benefits because they discontinue use within one year of treatment initiation. Therefore, statin discontinuation has been identified as a major public health concern due to the increased morbidity, mortality, and healthcare costs associated with ASCVD. In clinical practice, statin-associated symptoms (SAS) often result in dose reduction or discontinuation of these life-saving medications. Currently, physician decision-making in statin prescribing typically relies on only a few patient data elements. Physicians then employ reactive strategies to manage SAS concerns after they manifest (e.g., offering an alternative statin treatment plan or a statin holiday). A preferred approach would be a proactive strategy to identify the optimal treatment plan (statin agent + dosage) to prevent/minimize SAS and statin discontinuation risks for a particular individual prior to initiating treatment. Given that using a single patient's data to identify the optimal statin regimen is inadequate to ensure that the harms of statin use are minimized, alternative tactics must be used to address this problem. In this proof-of-concept study, we explore the use of a machine-learning personalized statin treatment plan (PSTP) platform to assess the numerous statin treatment plans available and identify the optimal treatment plan to prevent/minimize harms (SAS and statin discontinuation) for an individual. Our study leveraged de-identified administrative insurance claims data from the OptumLabs® Data Warehouse, which includes medical and pharmacy claims, laboratory results, and enrollment records for more than 130 million commercial and Medicare Advantage (MA) enrollees, to successfully develop the PSTP platform. In this study, we found three results: (1) the PSTP platform recommends statin prescription with significantly lower risks of SAS and discontinuation compared with standard-practice, (2) because machine learning can consider many more dimensions of data, the performance of the proactive prescription strategy with machine-learning support is better, especially the artificial neural network approach, and (3) we demonstrate a method of incorporating optimization constraints for individualized patient-centered medicine and shared decision making. However, more research into its clinical use is needed. These promising results show the feasibility of using machine learning and big data approaches to produce personalized healthcare treatment plans and support the precision-health agenda.

Scalable and cost-effective NGS genotyping in the cloud.

BACKGROUND: While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. RESULTS: We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. CONCLUSIONS: Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

Biomedical cloud computing with Amazon Web Services.

In this overview to biomedical computing in the cloud, we discussed two primary ways to use the cloud (a single instance or cluster), provided a detailed example using NGS mapping, and highlighted the associated costs. While many users new to the cloud may assume that entry is as straightforward as uploading an application and selecting an instance type and storage options, we illustrated that there is substantial up-front effort required before an application can make full use of the cloud's vast resources. Our intention was to provide a set of best practices and to illustrate how those apply to a typical application pipeline for biomedical informatics, but also general enough for extrapolation to other types of computational problems. Our mapping example was intended to illustrate how to develop a scalable project and not to compare and contrast alignment algorithms for read mapping and genome assembly. Indeed, with a newer aligner such as Bowtie, it is possible to map the entire African genome using one m2.2xlarge instance in 48 hours for a total cost of approximately $48 in computation time. In our example, we were not concerned with data transfer rates, which are heavily influenced by the amount of available bandwidth, connection latency, and network availability. When transferring large amounts of data to the cloud, bandwidth limitations can be a major bottleneck, and in some cases it is more efficient to simply mail a storage device containing the data to AWS (http://aws.amazon.com/importexport/). More information about cloud computing, detailed cost analysis, and security can be found in references.

Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.

BACKGROUND: Comparative genomics resources, such as ortholog detection tools and repositories are rapidly increasing in scale and complexity. Cloud computing is an emerging technological paradigm that enables researchers to dynamically build a dedicated virtual cluster and may represent a valuable alternative for large computational tools in bioinformatics. In the present manuscript, we optimize the computation of a large-scale comparative genomics resource-Roundup-using cloud computing, describe the proper operating principles required to achieve computational efficiency on the cloud, and detail important procedures for improving cost-effectiveness to ensure maximal computation at minimal costs. METHODS: Utilizing the comparative genomics tool, Roundup, as a case study, we computed orthologs among 902 fully sequenced genomes on Amazon's Elastic Compute Cloud. For managing the ortholog processes, we designed a strategy to deploy the web service, Elastic MapReduce, and maximize the use of the cloud while simultaneously minimizing costs. Specifically, we created a model to estimate cloud runtime based on the size and complexity of the genomes being compared that determines in advance the optimal order of the jobs to be submitted. RESULTS: We computed orthologous relationships for 245,323 genome-to-genome comparisons on Amazon's computing cloud, a computation that required just over 200 hours and cost $8,000 USD, at least 40% less than expected under a strategy in which genome comparisons were submitted to the cloud randomly with respect to runtime. Our cost savings projections were based on a model that not only demonstrates the optimal strategy for deploying RSD to the cloud, but also finds the optimal cluster size to minimize waste and maximize usage. Our cost-reduction model is readily adaptable for other comparative genomics tools and potentially of significant benefit to labs seeking to take advantage of the cloud as an alternative to local computing infrastructure.