The client: Clinical operations team at a mid-sized oncology biotechnology company. 

The clinical operations teams at a mid-sized oncology biotechnology company approached QuartzBio as they sought ways to close sample information gaps that would appear during reconciliation. 

Gaps in this process typically included the inability to report in a timely manner on: 

  • Missed collections 
  • Unexpected samples 
  • The status of samples and derivatives as they move onto third-party testing labs 

The challenge: The sponsor team lacked global visibility into their expected sample schedule across all collection sites. Too much time was spent on manual reconciliation, with delays of three months costing the client significant time and resources. 

In their existing reconciliation process, clinical operations leaders were often frustrated in their attempts to maintain robust global visibility. Generating reports was a time-consuming process that involved complex spreadsheets manually linking key information from the EDC, central labs, testing labs, and biorepositories to illuminate critical information like discrepancies or missed collections. 

Without global visibility, the client had trouble generating reports continuously throughout the life of a study. New data was often unavailable, vendor-specific nomenclature was frequently inconsistent, and data structures were sometimes incompatible. Consolidated insight across sample collection and processing status, consent status, and sample and derivative quality information was difficult to obtain. 

The solution: The sponsor team used the QuartzBio® virtual Sample Inventory Management (vSIM) Enterprise Software-as-a-Service (SaaS) solution to systematically monitor and identify:  

  • Gaps in sample data  
  • Issues with sample shipments 
  • Data discrepancies 
  • Consent violations 
  • Subject exclusions 

The client’s clinical operations team worked with QuartzBio’s biospecimen operations experts and data engineers to deploy the vSIM solution and create a centralized, reliable source of sample information. This single solution closed the gaps that were hampering the reconciliation process. 

QuartzBio’s data ingestion and harmonization pipeline continuously integrated sample information from multiple sources. As this sample information was generated over the course of the study, the vSIM solution automatically performed edit checks and highlighted any data inconsistencies. For instance, teams could now see any direct reconciliation issues between the EDC and inventories at central labs, specialty labs, and biorepositories (Figure 1).

Figure 1. Samples with Discrepant Sample Collection Entries (EDC vs. Inventory) 

The outcome: Eliminating manual reconciliation processes with sponsor-centric visibility across the sample lifecycle 

Reconciliation efforts typically have large gaps in sample information that is critical for sponsor teams to maintain robust global visibility across all collection sites. Clinical data management traditionally reconciles the EDC from other points of view (e.g., adverse events, concomitant medications, patient history, RECIST response evaluation, investigational product guideline (IP) compliance, and many others). The QuartzBio vSIM solution functioned as an additional tool pulling information together from the EDC, each lab, and each biorepository. The solution also incorporated the sample schedule from the protocol, including changes to the protocol as new patients were enrolled and the protocol was amended.

With reconciliation gaps reduced and closed, clinical operations teams now had sponsor-centric visibility into sample status across the lifecycle of collections, processing, testing, and storage. With a single day of delay in getting a new product to market costing $1-$8 million in sales (source), the benefits of more effective sample and biomarker operations providing a holistic view of samples on-study cannot be understated.  

Learn more about implementing QuartzBio® solutions for your organization.


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.


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.


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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The client: Biologics company developing cell therapies for blood cancers, generating large amounts of genomics data across four clinical programs and preclinical research teams

The client’s bioinformatics teams approached QuartzBio seeking a better workflow for sharing insights obtained from their genomics data.

They were using complex, manual workflows to ingest and process next-generation sequencing (NGS) data. These workflows comprised multiple steps, including alignment processing, variant processing, annotation, and clinical interpretation in the context of clinical data and publicly available data.

The challenge: Complex data management workflows hindered decision-making and created bottlenecks

The company had made a large financial investment in their data-rich therapeutic development programs – approximately $150M across the portfolio to date.

However, the complexity of their bioinformatics workflows made it difficult to share reports, analyses, and other visualizations with these stakeholders to get necessary signoffs and approvals.

Other specific concerns included

  • Data integrity
  • Data security and regulatory compliance
  • User access management – not possible with existing workflows

The solution: Centralized visibility across a wide user base with QuartzBio® enterprise Biomarker Data Management (SaaS) solution

The client’s bioinformatics and translational medicine teams worked with QuartzBio’s genomics experts and data engineers to deploy the enterprise Biomarker Data Management (eBDM) solution.

QuartzBio® eBDM, an enterprise SaaS solution, provided intuitive data query and topline reporting on data availability, enabling seamless data consumption across a wide user base. Bioinformatics teams were able to give stakeholders access to a centralized data vault where they could search, navigate, and explore all raw and processed data related to their genomics workflows (Figure 1).

Genomics file viewer QuartzBio eBDM solution
Figure 1. Genomics file preview capabilities within QuartzBio® enterprise Biomarker Data Management solution provided stakeholders with centralized visibility across all source files, harmonized datasets, and various configuration files associated with a bioinformatics project. Vaults were access-controlled, with permissions controllable by the client’s administrative users. Shown here is an example of the .bam file preview tool within the eBDM solution.

To address the client’s concerns around data integrity, the eBDM solution included automated checks for data integrity and conformity with data transfer agreements (DTAs), providing transparent quality control of incoming data. All data workflow processes were set up in the eBDM solution with secure, 21 CFR part 11-compliant audit trails.

The outcome: Streamlined stakeholder approvals + integration with internal workflows = faster decisions

Deploying the QuartzBio® eBDM solution automated processes for cleaning and harmonizing the client’s genomics data and centralized it within a single solution.

The solution was further integrated with internal client workflows via API capabilities and native R/Python support, shortening the time from data acquisition to insight generation.

Most importantly, the bioinformatics teams could streamline stakeholder approvals by using a solution with both data security and fine-grained user access management.

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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

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


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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clinical sample KPIs trials
clinical sample KPIs trials

The clinical operations team at a mid-sized oncology biotech client depends on QuartzBio’s virtual Sample Inventory Management solution to gain global visibility into their expected sample schedule, across all collection sites.

They can identify gaps in sample data and sample shipments. Full oversight enables the team to identify data discrepancies, consent violations, and subject exclusions.

Explore virtual Sample Inventory Management