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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Master-Sample-Inventory-Sample-Tracking-QuartzBio-2
Master-Sample-Inventory-Sample-Tracking-QuartzBio-2

The client: Biopharmaceutical company conducting phase I/II clinical studies 

The biomarker operations and clinical operations teams at a biopharmaceutical company approached QuartzBio as they sought ways to streamline biomarker sample operations in order to find synergies across their portfolio.

The biomarker operations team was responsible for tracking samples across a complex ecosystem of physical sample locations and sample data streams:

  • 19 clinical trials across 5 therapeutic areas
  • 60 different vendors handling samples over the course of the biospecimen lifecycles
  • 6-8 vendors per study

The challenge: Time and resources spent chasing sample status information for ad hoc requests  

Spending over $1M annually across the portfolio for biospecimen shipping and logistics, the client nevertheless faced challenges in understanding where their samples were at any given time.

Whenever there were discrepancies, such as missing samples, samples not collected, or missing data, it was the biomarker and clinical operations teams’ task to find the samples, or at least, the reason for the discrepancies.

The team voiced multiple frustrations, such as:

  • “When we realize too late that there’s an issue with the sample inventory, reconciliation can be a rushed, manual process.”
  • “We’re unable to see sample data all in one place, vendors collect and report data differently, and it’s hard for them to change.”
  • “Our teams spend so much time on manual tracking and ad hoc reports, we don’t have bandwidth to analyze the big picture or to make important, patient-centric improvements that would have a real impact on the getting therapies to patients faster.”

The solution: Tracking samples with QuartzBio® virtual Sample Inventory Management Software-as-a-Service (SaaS) solution

The client’s biomarker operations team worked with QuartzBio’s biospecimen experts and data engineers to deploy the virtual Sample Inventory Management (vSIM) solution, which began delivering value just 4 weeks after kickoff.

QuartzBio® vSIM, an enterprise SaaS solution, provided a master sample inventory that enabled the client to track all parent samples and derivatives — a single interactive hub for browsing, visualizing, and downloading harmonized sample data (Figure 1). All data, whether extracted from the electronic data capture (EDC) system or from other inventories, was systematically mapped to a common data dictionary using QuartzBio’s robust, scalable data ingestion pipelines.

Figure 1. QuartzBio® vSIM master sample inventory provides a roadmap of where a sample has been in its journey from collection to testing to storage. Each row of the master sample inventory represents a sample or a derivative aliquot of that sample. Columns contain all information associated with a particular sample, such as collection dates, time points, subject identifiers, testing status, accession information, and more.

The outcome: Eliminated manual tracking, reduced time spent generating status reports

Since deploying the QuartzBio® vSIM solution, the client’s biomarker operations and clinical operations teams have been able to eliminate all manual sample tracking processes from their workflow. Because the teams now spend 75% less time generating sample status reports than they spent before, they have been freed to focus on higher value tasks and pursue strategic initiatives, such as optimizing data generation plans and site training.

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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

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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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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.

Explore virtual Sample Inventory Management