Guiding Clinical Trial Decision-making with Reliable Clinical Insights: How BluMaiden Biosciences Brings its Pharma Service to Global Clients through AWS

By Lakshmanan Lakshmanan, Head of Information Technology – BluMaiden Biosciences
By Oleg Moskvin, Ph.D., Head of Computational Sciences – BluMaiden Biosciences
By Damien Keogh, Ph.D., Founder, Chief Executive Officer, Director – BluMaiden Biosciences
By Toh Yun Yun, Assc. Specialist SA, Analytics – AWS
By Terence Tan, BDM, HCLS VC BD – AWS

BluMaiden

Successful therapeutic development relies on Pharma-led clinical trials, which require robust, high-quality end-points data to guide trial decision-making. Effective patient enrichment, stratification, and clinical end-point optimization. Along with these, drug responder vs. non-responder analysis, are pivotal decision points that determine the outcome of a clinical trial. Through advanced analytics and predictive modelling, insights gleaned from clinical trial data can support targeted drug development strategies and identify promising candidates earlier in the process, saving significant time and money. Furthermore, optimizing the design and execution of clinical trials based on data-driven insights can lead to greater efficiency and cost-effectiveness using the BluMaiden Pharma Services platform.

Challenges: Navigating the Complexities of Clinical Trial Insights Generation

Navigating the complexities of generating insights from clinical trials involves numerous challenges, starting with the imperative to process data safely and securely. Given the sensitivity and confidentiality of patient information, robust data management systems are essential, ensuring compliance with stringent regulatory requirements while safeguarding privacy. The task extends beyond mere storage; it encompasses implementation of encryption, access controls, and data anonymization protocols to mitigate risks effectively.

Another critical challenge is the sheer volume and complexity of clinical trial datasets which include metadata and raw sequence data. Moreover, serving the needs of organizations and clinical study sites spread across diverse locations adds an additional layer of complexity to the process.

In this blog, we discuss the challenges of clinical data processing and generating insights at scale. We also explore how BluMaiden Bioscience’s platform and clinical analytics solution, built on AWS, is delivering valuable clinically useful insights to its global clients and collaborators.

Solution Overview

In response to these pressing challenges, BluMaiden Biosciences, in partnership with AWS, created a global solution designed to empower clinical researchers with actionable insights and guide decision-making through integration with existing clinical trial processes. This solution upholds pharmaceutical industry security and quality standards such as HIPAA, GDPR, MTCS-T3, and PHIA.

A key point of differentiation for this platform is its ability to deliver new clinical insights to the clinical trial sponsor, supporting decision-making. These insights include, but are not limited to, End-Point Optimization, Drug Responder vs. Non-responder analysis, and Patient Enrichment and Stratification. Acting as a single point of contact, BluMaiden Biosciences offers an end-to-end Pharma Service, providing logistics and standardized protocols for sample collection and processing, as well as data analysis and reporting through proprietary AI and machine learning algorithms, ensuring pharma clients have ease of implementation.

Architecture Design

The fundamental design principle of the Pharma Services platform centers around precise data annotation and curation. These critical processes are essential for extracting meaningful insights from clinical studies. As raw data volumes continue to grow, scalable architectures become crucial. The platform achieves scalability both vertically and horizontally by adhering to predefined rules and metrics.

High-level data flow:

1. Raw sequenced data from the clinical trial site is uploaded to an encrypted Amazon S3 bucket.
2. De-identified metadata relating to the samples shared by site is uploaded to the same Amazon S3 bucket.
3. Data shaping and processing is done using pre-defined Amazon Elastic Container Registry (ECR) images and AWS batch which uses Amazon EC2 spot instances to spin up required containers for processing.
4. Intermediate and processed data is stored back in separate folders with the study specific Amazon S3 bucket.
5. Data volume increases multiple folds as we start the processing and DNA is sequenced, some of this data is archived for compliance using the Amazon S3 Glacier.
6. Processed data in study specific Amazon S3 bucket and folder is used by the BluMaiden computational team for data analysis using Amazon SageMaker.

Platform Benefits

The Pharma Service platform has features to ensure the success of day-to-day operations in clinical trial data processing. Here are the main features of the platform:

1. BluMaiden Pharma Services’ platform facilitates data ingestion, including initial, incremental, and re-processing approaches, customized for specific use cases. Leveraging Amazon S3 for data storage and retrieval, BluMaiden and its partners have achieved a 36% reduction in secure data sharing time using Amazon S3 pre-signed URL feature.
2. Utilizing Amazon S3, BluMaiden Pharma Services has achieved a 42% reduction in data costs through lifecycle management policies. By strategically transitioning data to lower and archival tiers, they ensure cost-effective data management. Additionally, the platform integrates built-in capabilities and leverages Amazon S3 features like Content-MD5 and ETag for verifying uploaded objects, thereby maintaining data quality from raw sequenced data to processed information.
3. To optimize costs, BluMaiden leverages the AWS Batch service in conjunction with Amazon EC2 Spot Instances, resulting in a 30-50% reduction in expenses. Additionally, the platform seamlessly integrates with the BioContainers community, which is accessible through the Amazon ECR Public Gallery.
4. At scale, Amazon EC2 Spot Instances across availability zones and provides partners with clinically insightful data analysis up to 2.5x times faster.

By decoupling storage and compute components through a serverless approach using services like Amazon S3, BluMaiden benefits from resilient systems that remain operational even in the face of component failures. These modular structures allow flexible adaptation of storage and consumption methods without disrupting overall data flow. Additionally, BluMaiden’s data repositories in Amazon S3 facilitate seamless global data sharing and re-analysis. Leveraging knowledge graphs on Neo4j enhances the ability to derive actionable conclusions from data on complex microbial communities, benefiting clinical trial decision-making. The BluMaiden Amazon S3 Data Lake and Amazon Aurora database serve as central repositories, accommodating diverse data types and providing seamless access for processing and analysis. This architectural approach enables swift extraction of valuable insights from business operations.

Building on a solid AWS foundation, BluMaiden Biosciences’ innovative solution offers meaningful value propositions. By unlocking deep clinical insights from vast repositories of data, BluMaiden empowers Pharma stakeholders with the knowledge needed to drive informed decision-making and optimize trial outcomes. This Pharma Service sets itself apart from others in many aspects.

Clinical Utility and Outcomes

BluMaiden’s Pharma Service offers an end-to-end solution that provides new clinical insights, guiding better decision-making in clinical trials. These are applicable across entire trial cohorts, spanning Phase 1, 2, and 3 trials, and can inform early pilot analysis, while also being applicable in subsequent pivotal Phase 2 and 3 clinical trials. Additionally, the Pharma Services can be applied retrospectively, leveraging raw sequence data and metadata for re-analysis.

Moreover, through customizable analysis tailored to individual clinical trials, an enhanced functional understanding can be readily achieved. BluMaiden prioritizes regulatory compliance and data security through rigorous quality control and assurance ensuring reliable insights generation. Their Pharma service adheres to industry standards, safeguarding sensitive patient information.

Conclusion: Shaping the Future of Clinical Research with BluMaiden Biosciences and AWS

BluMaiden Biosciences Pharma Services is a powerful new resource to guide decision-making in clinical trials. Onboarding the Pharma Service as an approved vendor for Pharma clinical research teams will provide data analysis conclusions with clear clinical utility. In partnership with AWS, the service is provided through a secure and compliant platform with pharma industry grade quality standards.

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BluMaiden – AWS Partner Spotlight

BluMaiden is an AWS Advanced Technology Partner and AWS Competency Partner that provides Pharma Service with a global presence by being a data-driven innovator producing actionable clinical insights to enhance clinical trial decision-making.

Contact BluMaiden | Partner Overview