Managing Complex Biomarker Data Archives - Page 2 of 5

AI/ML can be a powerful, error-reducing tool for managing clinical sample data as well as biomarker data.

AI/ML-based tools should not replace human judgment, particularly for insight generation, at least until AI/ML-based tools are extensively and rigorously validated (as any piece of critical software would be). Furthermore, regulatory compliance and data privacy are of utmost importance and must be considered when building and using solutions that leverage generative AI frameworks.

However, near-term applications of AI/ML can dramatically improve any tedious process involving a human inspecting data. We list some of these processes in the box below, along with steps we recommend taking to reduce risk in each case.

The 22nd Annual Bio-IT World Conference and Expo comes to Boston, MA, USA May 16-18, bringing 2,500 attendees together to discuss data management, -omics technologies, data ecosystems, analytics, computing, and other topics impacting life sciences research and development.

QuartzBio’s Adam S. Brown, PhD, Senior Director of Product Support, will join experts from Washington University and Dana Farber Cancer Institute in a panel discussion,

“Towards Precision Medicine: Oncological Applications of Data Integration” | May 18, 2:40 PM ET

The panelists will share ideas for how to bring oncologists together with data integration leaders to systematically assess factors contributing to disease.

QuartzBio works with sponsors to eliminate data bottlenecks by deploying source-agnostic, portfolio-level solutions for managing data from any technology — ‘omics, immunophenotyping, imaging, and many more.

Sound like a solution that could benefit your team? Use the button below to schedule a 15-minute slot with us at the conference.

Meet QuartzBio at Bio-IT World

QuartzBio’s team has deep experience in technology-enabled solutions for the life science industry. In this blog series, we invited you to get to know a member of the QuartzBio team.

This month, we are delighted to talk with Mike Waters, QuartzBio Vice President of Sales. After learning about Mike here, please feel free to connect with him on LinkedIn.

In your own words, what do you do?
My team and I provide solutions to help pharmaceutical and biotechnology companies accelerate the development of new treatments for the patients that need them. We encourage our customers to think differently about the way they currently approach sample and biomarker data management.
What is your fondest memory of working at QuartzBio?
It is not a single memory, but rather the culture of the organization that inspires me to do the best work I possibly can for our customers, my colleagues, and the patients that we serve. We do our best work as a team. There is mutual respect for all who contribute whatever it takes to deliver a world class customer experience.
Complete this sentence: QuartzBio is _________ because _________.
QuartzBio is best solution in the market because we say what we are going to do and then we do it. You can count on us.
Complete this sentence: QuartzBio customers are _________ because _________.
QuartzBio customers are innovators because they seek new solutions to address existing challenges.
What piece of art – book, movie, music, artwork, etc. – inspired you the most and why?
I get great pleasure from all forms of art, especially music. The Beatles are my favorite band. Not only because they composed some of the greatest pieces of pop music of the late 20th century but because their music and perspectives evolved and matured over their amazing 10-year career. Curiosity and growth inspire me in all endeavors.
What’s the best piece of advice you have ever been given?
You can’t make more time. It is the most precious resource we have. Use it wisely.

Connect with Mike Waters on LinkedIn

Duration: 30 minutes

Register to Watch Webinar On Demand:

Biomarker data can be time-consuming to clean and prepare for analysis, because assay results data files are often disconnected and have inconsistent formats.

This “data chaos” prevents translational, clinical, and bioinformatics teams from extracting insights to advance therapeutic development.

Join the webinar led by Adam Brown and Mike Waters, who will show how using a unified biomarker data management solution to acquire and process biomarker data, connected to clinical and sample data, empowers teams to break down data silos, creating an integrated data asset across the enterprise.

You’ll learn how the QuartzBio^® enterprise Biomarker Data Management solution enables teams to:

Systematically verify data quality, consistency, and availability with automated checks
Navigate and explore cleaned, annotated data at scale across your entire portfolio—whether a single program or hundreds of studies, at all phases of development
Link assay and clinical data across file types from any assay technology–transcriptomics, genomics, proteomics, flow cytometry, imaging, and more
Explore and visualize biomarker trends across cohorts, subjects, and timepoints and perform exploratory analyses to surface signals of interest
Integrate non-clinical/pre-clinical data to further enhance your data asset

During the presentation, the team will highlight how QuartzBio’s scalable data standardization and integration technology helps scientists shorten time from data acquisition to data insight and exploration of historically siloed data.

Register Now >>

Who should attend:
Translational Research teams, Biomarker Strategy teams, Clinical/Biomarker Data Science teams, Clinical Development teams, Bioinformatics and Computational Biology teams, Office of the CIO/CTO, Data Management teams

December 10, 2020 — Biomarker-guided trials frequently have an international footprint of sites to reach targeted patient populations and involve a complex network of specialty labs. Join us for our upcoming webinar, where QuartzBio’s Tobi Guennel will discuss how his team is breaking down data siloes to create actionable insights into availability and quality of samples and data. These insights allow clinical and translational teams to streamline trial operations and enable early course correction.

QuartzBio Connecting Raw Processed and Ancillary Data

Translational and clinical teams spend more than 70% of their time managing, cleaning, and harmonizing data generated in biomarker-rich clinical programs.

In a webinar now available on demand, we demonstrated how the QuartzBio® enterprise Biomarker Data Management (eBDM) solution addresses one set of frequently intractable challenges: connecting raw, processed, and ancillary data across multiple clinical studies.

We invite you to sign up for on-demand access to the recorded webinar.

Multiple Assay Modalities, File Types, Data Storage Locations

As we have previously described, research teams are generating biomarker data from a wide variety of assay modalities, and this data can be housed in multiple, disconnected storage locations. In the example use case described in the webinar, data was being generated from targeted assays like flow cytometry and immunohistochemistry to high-throughput omics assays.

The QuartzBio eBDM solution is specifically engineered to ingest, standardize, visualize, and analyze this data. The unified data platform connects raw and processed data to ancillary files, such as the images used for immunohistochemistry quantification or PDF omics reports. All of the raw files are available for download individually or in bulk. They can also be previewed directly within the user interface.

As shown in Video 1, the QuartzBio enterprise data platform can centralize and harmonize data from multiple file types across clinical programs, including:

Image files
Tabular files
Omics files, e.g., BAM or VCF files
Sequencing reports for particular mutations or genomic regions of interest

**Video 1** (Click image to view video): The QuartzBio enterprise data platform can centralize and harmonize data from multiple file types across clinical programs. Video demonstrates access to images, PDF files, and genomics data.

As shown in Video 2, the QuartzBio eBDM solution can combine processed files with harmonized clinical annotations, with both subject and sample level data, as well as the relevant quantified reportables for a specific assay modality. These reportables are very configurable and can be changed according to the needs of a sponsor, a program, or even a specific study.

**Video 2** (Click image to view video): Processed files combine harmonized clinical annotations with both subject- and sample-level data.

The QuartzBio team can also further preprocess raw assay data directly and apply quality control metrics as well as normalization techniques. We can also extract relevant data and metadata from PDFs, such as omics reports and informed consent forms.

In summary, the webinar demonstrated how the biomarker data modules of the QuartzBio platform can enable easy access to both key raw and processed data assets through the user interface, in addition to robust visualization and data exploration capabilities.

Flexible Biomarker Data Management Means Faster Deployment

QuartzBio’s enterprise-grade Biomarker Data Management application provides a flexible, scalable solution for transforming biomarker data into consumable information across a sponsor’s entire study portfolio.

This resilient approach is enabled by a robust enterprise data platform with a library of pre-built, configuration-ready pipelines for data ingestion.

Contact us to learn more about data management SaaS solutions and let us know which additional features and capabilities you’d like featured in our next webinar.

Contact Us to Continue the Conversation

Duration: 30 minutes

Register for the Webinar:

Translational and clinical research teams spend more than 70% of their time wrangling information from disconnected clinical trial data sets.

Data ends up in silos, making it hard to compile information and surface insights.

Watch this short webinar, where Adam Brown and Mike Waters will demonstrate how integrating exploratory biomarker, PK, and clinical data in a unified data platform enables teams to interrogate trends and identify insights as data is generated on-study.

Register for the Webinar:

Translational and clinical research teams spend more than 70% of their time wrangling information from disconnected clinical trial data sets.

Data ends up in silos, making it hard to compile information and surface insights.

Watch this short webinar, where Adam Brown and Mike Waters will demonstrate how integrating exploratory biomarker, PK, and clinical data in a unified data platform enables teams to interrogate trends and identify insights as data is generated on-study.

Join QuartzBio at the 8th Annual Bioinformatics Strategy Meeting East Coast USA for the “Omics-Driven Approaches” track on 23 May 2022.

ROUNDTABLE DISCUSSION: “Turning Multi-omic Data Chaos into Translational Insights”

Mike Waters of QuartzBio will facilitate a discussion among 10-15 industry leaders around critical topics relevant to biomarker-rich clinical trials:

January 10, 2022 — With immuno-oncology assets progressing in the clinic, a growing biotechnology company we work with faces an increasingly common challenge:

Their trials are generating large datasets across a wide range of assay modalities (Figure 1), but the data remains siloed.

In addition to clinical data coming from the clinical research organization (CRO), the velocity of data coming from an assay services laboratory continuously delivering biomarker data from flow cytometry, immunohistochemistry, and genomics platforms quickly becomes overwhelming. Still another, separate data stream comes from a specialty laboratory delivering T-cell receptor (TCR) profiling data.

August 31, 2021 — Clinical samples are moving across an increasing number of physical/virtual locations and data is delivered in an expanding array of file formats as clinical trials become increasingly more complex and data rich (report).

Biospecimens are analyzed using a variety of assay technologies, each generating its own set of reportables, quality control metrics and data/file formats. Data is delivered through multiple, disconnected pipelines (Figure 1).

This complexity creates obstacles for many functional groups within sponsor organizations: