THE CHALLENGE: OVERWHELMING COMPLEXITY

The client: large biotechnology company.

Clinical samples traverse a complex path. Whether the samples originate from sites halfway across the planet or across the street, clinical research teams are faced with the challenge of monitoring the status of biospecimens across multiple sites, labs, and repositories at multiple phases of development. Complex sample operations, disparate vendors, and inconsistent metadata across labs are common challenges sponsors face when keeping track of samples across clinical programs. ​

Complexity was the challenge one large biotechnology company faced as its clinical operations and translational science teams sought to track clinical samples across dozens of studies, dozens of specialty labs, and multiple central labs. The client previously used a custom-built, internally developed solution that enforced a rigid deployment approach and was unable to accommodate a variety of data types and data structures.

THE SOLUTION: QUARTZBIO® vSIM SOLUTION

When the client began to search for a new platform to replace its homegrown solution, QuartzBio’s virtual Sample Inventory Management solution (vSIM)​ presented itself as a more capable alternative solution. The client partnered with QuartzBio experts to ramp up quickly and provide immediate results.

  • The vSIM solution enabled the client’s teams to evaluate the status of samples on study and easily track consent, collection, and processing of samples. This made it easier to manage queries and identify discrepancies or patterns of non-compliance.
  • The client was able to start studies with new levels of speed and efficiency. Because the vSIM solution was “source-agnostic” in its approach to data collection, the client now had the flexibility to accommodate a variety of data types, formats, and structures. Ultimately, this range of seamless data consumption and integration enabled the client’s teams to identify sample availability by patient, assay, and other parameters. The client no longer had to devote time and resources to anticipate and set up a multitude of data pipelines. Instead, teams were able to utilize a library of configuration-ready application programming interfaces (APIs) as well as connectors and data processing pipelines. This enabled teams to visualize and review key pre-analytical data, detect patterns of site-based noncompliance, and identify data discrepancies early.
  • The client was able to build versatile portfolio-level dashboards and provide unprecedented visibility into key performance indicators (KPIs) such as missing samples, samples with expiring/expired stability or consent dates, lab turnaround times, sample testing status, and other operational metrics to drive on-study decision making.
  • Because the vSIM solution alerted the client to samples with imminently expiring consent and stability windows, the client was able to use over 500 samples before expiration to support current and planned studies.

Where sponsor teams previously lacked centralized visibility, they now possessed insight into the collection, processing, and storage status across multiple siloed source systems.

This powerful centralized visibility also had bottom-line ramifications on the client’s overall growth. Senior executives, including the CEO and CFO, were conducting serious discussions with another company that had identified it as a potential acquisition target and began auditing their inventory of valuable clinical biospecimens. Where requests for sample collection data had previously required extensive lead-time and resource allocation to perform, senior executive users now had real-time metrics at their fingertips to drive decision-making.

THE RESULTS: THE vSIM SOLUTION BECOMES THE “SINGLE SOURCE OF TRUTH”

QuartzBio’s vSIM solution quickly became a true game-changer for the client. By ingesting lab sample inventories, relevant electronic data capture (EDC extracts), sample manifests, electronic sample requisition forms (SRFs), and informed consent forms (ICFs), the client was ultimately able to create a virtual master sample inventory to track samples across every site, lab, and repository over their entire lifecycle. New growth opportunities emerged because vSIM powered a new level of flexibility and scalability to support everything from a single clinical program up to an entire portfolio of hundreds of studies across all phases of development – a single source of truth for all sample-related data.​

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QuartzBio eBDM solution deployed across five clinical studies
QuartzBio eBDM solution deployed across five clinical studies

The client: Clinical development and translational research teams executing phase I and II studies for precision oncology 

A clinical-stage biotechnology company developing precision oncology therapeutics recently worked with QuartzBio to tackle challenges facing execution of three phase I and two phase II biomarker-informed studies.

Challenges facing clinical development included:

  • Limited pool of potential patients to recruit for studies
  • Challenges facing patient screening and stratification – ideal biomarker profile not well-defined

Specific challenge: integrating siloed data

The clinical development team was challenged to solve the problems of patient qualification and stratification by integrating data from multiple streams, across multiple clinical programs:

  • Electronic medical records
  • Lab data
  • Biomarker profiling with indication data for patients
  • Immune profiling data
  • Publicly available data
  • Preclinical data: cell data and animal (cytokine and biomarker) data

The data sets being generated as a result of the clients’ clinical programs were scattered across multiple, disconnected cloud storage solutions. The team needed data to be integrated in a unified, query-friendly database that complied with regulatory requirements.

The solution: QuartzBio® enterprise Biomarker Data Management (eBDM) Software-as-a-Service (SaaS) Application

The client’s clinical development team worked with QuartzBio’s informatics subject matter experts and data engineers to deploy the eBDM platform within 6 weeks.

QuartzBio® eBDM, an enterprise SaaS solution, enabled scalable, user-driven data management of the client’s entire ecosystem of biological data (Figure 1).

QuartzBio eBDM solution deployed across five clinical studies
Figure 1. Overview of the QuartzBio® enterprise Biomarker Data Management solution as deployed across 5 clinical studies. Multiple data types were automatically loaded into the data platform. After indexing, quality control (QC), and mapping in the landing, ingestion, and configuration layers of the platform, client teams could interrogate the data ecosystem using both the web interface and API access.

Because the QuartzBio® data platform is data type-, data source-, and vendor-agnostic, every one of the clients’ data streams could be acquired, ingested, quality-controlled, and harmonized within the platform.

  • Data type-specific templates were used to automatically harmonize and annotate data from different vendors at the time of or after data import
  • QuartzBio’s library of configuration-ready workflows spanned all assay technologies used by the client: genomics, high-content imaging, flow cytometry, immunohistochemistry

The outcome: freedom to explore and transform data via web-based UI

Once data was set up within the platform, users had the freedom to explore and transform data via a web-based user interface (UI) with data access controls, version history and audit trails.

The enterprise Biomarker Data Management application enabled collaboration among a diverse user base across the client’s organization. Not only did the clinical development team uncover insights to inform trial execution, but the clients’ bioinformatics, translational biology, and biomarker operations teams also used QuartzBio’s visualization, data analysis, and top-line reporting capabilities as follows:

Functional TeamHow the team used enterprise Biomarker Data Management
Biomarker OperationsOn-study reporting of data quality, data conformity, data availability, vendor performance, and turnaround times.
Data Integration and Validation
Bioinformatics / Computational BiologyGenerated visualizations (e.g., line plots, clustering, dimensionality reduction) and were able to connect data to existing tools (e.g., SpotFire, Prism)
Connect to Raw Data and Download Data
Translational ResearchObtained early insights into the ideal genomic profile of patients that showed response to the therapeutic candidate.
High dimensional  heat maps

Watch our webinar on demand to learn more about the QuartzBio® enterprise Biomarker Data Management solution:

sample-collection-status-clinical-KPIs
sample-collection-status-clinical-KPIs

The challenge: Maintaining clinical trial timelines dependent on vendor performance

A global biotechnology company with seven clinical-phase programs approached QuartzBio with a challenge shared by many organizations in the industry — overall assessment of clinical trial vendors and sites was time-consuming and unreliable, given global site footprints, complex sample lifecycles, and inconsistent naming across sites and vendors.

Tasked with preparing regular executive summaries, the company’s clinical and biomarker operations teams were spending significant time deriving trial-wide key performance indicators (KPIs), lacking visibility into vendor performance – and challenged to translate current experience into future study planning.

This lack of visibility was exacerbated by the absence of standard nomenclature and inconsistent data entry across vendors. Clinical operations teams were spending time manually mapping and reconciling data and metadata from multiple independent sources.

The QuartzBio approach: Continuously updated visibility through consolidated dashboards

The client implemented the virtual Sample Inventory Management solution, powered by the QuartzBio® Data Platform.

Using the platform’s built-in dynamic dashboards (examples shown in Figure 1), augmented by some bespoke reports custom-built by QuartzBio for the client, the clinical operations team was able to easily monitor and report on multiple vendor performance parameters:

  • Turnaround times from sample collection to sample processing to test result generation
  • Completion rate of samples tested within stability window
  • Sample processing quality KPIs by site and vendor
  • Rate of missed/incomplete baseline and on treatment collections
  • Data discrepancies by site and vendor
  • Protocol violations by site and vendor
  • Consent violations by site and vendor

Core to QuartzBio’s approach is rigorous sample data integration. The virtual Sample Inventory Management solution automatically harmonizes sample information from multiple sites, vendors, and other sources, regardless of format or nomenclature. QuartzBio applies an adaptive data dictionary that learns and updates common nomenclatures over time, creating a flexible model. Using this model, it harmonizes the non-standard nomenclature across vendors and studies, enabling clear visibility and eliminating manual processes.

The outcome: Fast, accurate reports, timely decisions, course correction on-study

Empowered by 24/7 access to vendor performance, visibility into expected sample schedules, and full reconciliation oversight, the client’s clinical operations teams started using the QuartzBio Data Platform for generating visualizations to guide executives and inform investors.

These visualizations enabled the client to take action at specific sites and vendors that were underperforming. Armed with more reliable trends in sample schedules and turnaround times, the biomarker operations team could more accurately project data delivery timelines and anticipate when key decisions could be made.

Watch our webinar, “Biomarker Operations KPIs,” to see these dashboards in action, as well as the latest reporting capabilities available to users of QuartzBio’s vSIM solution.

flow cytometry data management QuartzBio
flow cytometry data management QuartzBio

Our client’s translational research team needed to be able to monitor clinical outcomes with respect to patients and biomarker-defined subgroups. Within weeks, QuartzBio deployed virtual Sample Inventory Management and Biomarker Data Management solutions for the clinical trial in progress, enabling the team to:

  • Gain centralized visibility into status of samples as they move from sites to central and specialty labs
  • Reveal insights on actual samples collected versus expected samples collected
  • Generate hypotheses based on biomarker assay results linked to patient clinical data and dosage information
  • Eliminate time-consuming and manual data cleaning and cross-referencing processes

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sample data multiple trials QuartzBio
sample data multiple trials QuartzBio

One of the core challenges faced by clients in biomarker-informed clinical trials is the integration of key sample and subject metadata derived from multiple independent sources. One case involved multiple immuno-oncology studies, with data coming from multiple sources, in multiple formats.

The QuartzBio® platform was deployed to create a Master Sample Inventory view, yielding answers to key on-study questions, such as:

  • How does the number of available plasma samples compare to the number of available FFPE samples for Study X?
  • What proportion of samples have data available? What’s the breakdown of data availability by sample type?

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data management KPIs clinical trials
data management KPIs clinical trials

The translational research teams at a clinical-stage biopharma client rely on QuartzBio to report to stakeholders on how their clinical programs are progressing. Together with the clinical data management team, they can monitor vendors, turnaround times, and gaps in contracts – across the entire program.

Using dashboards on the QuartzBio Data Platform, the team can deliver executive summaries and presentations to investors, guiding key decisions and projected timelines.

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QuartzBio Helps Keep Oncology Trial on Track at a Clinical-Stage Biotech 

A clinical-stage biopharmaceutical company has been developing novel therapeutics that selectively modulate gene expression to address unmet medical needs in cancer patients.  

To keep their phase I study of an epigenetic modulator on track, the program’s translational research team needed to be able to monitor clinical outcomes with respect to patients and with respect to biomarker-defined subgroups. 

To achieve this goal, the team needed to manage multiple data streams: 

  • Central lab sample inventory 
  • EDC/Clinical data 
  • Assay results data from multiple specialty labs, including IHC, flow cytometry, PK, and gene expression 

Biomarker Data Management (BDM) & virtual Sample Inventory Management (vSIM) 

In weeks, QuartzBio deployed its vSIM and BDM solutions to the clinical trial in progress, enabling the translational research team to: 

  • Gain centralized visibility into status of samples as they move from sites to central and specialty labs 
  • Revealed insights on actual samples collected vs. expected samples collected 
  • Generate hypotheses based on biomarker assay results linked to patient clinical data and dosage information 
  • Eliminate time-consuming and manual data cleaning and cross-referencing processes
Figure 1 gene expression v response status heatmap
Figure 1 gene expression v response status heatmap
Biomarker Data Management in phase 2-3
Biomarker Data Management in phase 2-3

QuartzBio’s approach to biomarker data management can be seen in the context of a phase 2/3 dose evaluation and expansion oncology study with 5 assays run at 4 different labs. Using QuartzBio’s technology-driven solution, the sponsor could:

  • Pull together and visualize PK, cytokine, and flow cytometry data to inform optimal dosing
  • Integrate mutation, IHC, and cytokine data to develop a multimarker signature to stratify patients

The cross-functional QuartzBio team—including data scientists, biomarker data management programmers, and data managers—delivered a centralized data hub for biomarker data transfer, integration, and collaboration, as well as interactive reports and support for ongoing trial activities.

The client found that our approach transformed their ability to reach key clinical trial objectives.

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