Extracting the Necessary Data From Specimens for Research, Part 2—Webinar Summary

PRECISION FOR MEDICINE | WEBINAR SERIES: THE RIGHT BIOSPECIMEN PLAN FOR YOUR RESEARCH PROGRAM

Before conducting an experiment with a biospecimen, researchers must consider many factors regarding the type of data to be generated, including the platform technology, the specific assay, and the level of validation required.

On February 10, 2021, Precision for Medicine® hosted Extracting the Necessary Data From Specimens for Research, the second of a 3-part webinar series called The Right Biospecimen Plan for Your Research Program. Precision for Medicine is a global leader in supplying biospecimens, lab services, and CRO services to the life sciences.

Darren Davis, PhD, Senior Vice President, Lab Services, shared valuable insight on the challenges and best practices of extracting quality data from biospecimens.

Precision for Medicine’s in-house specialty lab capabilities span the spectrum from DNA and RNA assays to protein-, cell-, and tissue-based assays. Dr. Davis highlighted distinguishing capabilities and best practices for technologies such as RNAseq, NanoString, T-cell activation assays, single-cell quantitative image analysis, and ApoStream®, Precision for Medicine’s proprietary cell separation technology for circulating tumor cells (CTCs) and cell-free DNA (cfDNA).

The Right Specimen for the Right Assay

Dr. Davis began by highlighting the obvious importance of starting with the right specimen. Whole blood, plasma, and serum are the typical sample types for protein assays. For cell-based assays, whole blood can be used but the process for obtaining cells varies depending on sample type. CTCs, for instance, will need to be isolated from whole blood with ApoStream for use in downstream applications. Notably, Precision for Medicine is the first CRO to analyze CTCs on the Vectra® Polaris™ system.

Fresh or frozen tissue can also be used for protein-based assays. There are, however, challenges in working with these tissues. For example, automated staining platforms use microfluidics that can hinder whole cell-based slides or frozen sections, especially for repetitive staining.

Davis explained, “FFPE may be a better solution as the tissue adheres more robustly to the slide, creating a more stable matrix and allowing the use of archival biopsies for clinical trials. Using FFPE is also simpler and more economical when it comes to collection and logistics.”

For genomic applications, fresh or frozen tissue has traditionally been the sample of choice. However, there are now multiple kits and technologies that enable the use of more stable sample types such as FFPE. NanoString, for example, has been optimized for DNA fragments, while digital droplet PCR (ddPCR) is ideal when working with extremely low amounts of genomic material. The Thermo Fisher QS 12K PCR has OpenArray capabilities that enable it to run large numbers of samples simultaneously.

Davis emphasized, “To generate high quality data, it is important to consider both the platform and the biospecimen type, as well as the throughput required.”

Specimen Stability and Handling

The most important component of generating quality data from various biospecimen types is the collection and stability of the samples en route to the testing laboratory. To maintain full control of the specimen’s condition, Precision for Medicine provides comprehensive support for the sample collection and logistics, while a dedicated logistics team also manufactures custom kits, including temperature validated kits that ensure temperature stability during transit from the collection site to one of its seven global laboratories. These kits can be shipped directly to the clinical trial sites where samples are being collected.

“Precision for Medicine has optimized complex specimen and experimental workflows to help our clients maximize data generation from tissue and liquid biopsies,” said Davis. “We understand the importance of upstream sample preparation for maintaining the ability to generate reliable processing and quality data in downstream applications.”

Running Multiple Assays on a Single Specimen

Biospecimens are often a limited resource. Consequently, there is significant value in being able to optimize the data extracted from a single sample. Davis shared a case study on a client seeking to perform multiple assays on a skin punch biopsy. Precision for Medicine’s scientific team developed a solution that allowed the client to optimize the sample for downstream analysis with multiple assays and data end points (see Figure 1).

Figure 1. Case Study: Optimization of Specimen Procurement for Multiple Assays

A key component of this solution was initial preservation of the biopsy in RNAlater, a storage reagent that stabilizes and protects cellular RNA in unfrozen specimens. Storage and shipment in RNAlater did not impact H&E staining or multiplex immunofluorescence. Moreover, the RNA yield and quality allowed for successful next generation sequencing (NGS) library construction.

Assay Validation and QC

The above case study demonstrated another important component of generating high-quality, accurate data: ensuring that assays are validated and quality control (QC) metrics are applied. Davis used the Illumina TSO500 NGS Panel to illustrate the need for QC at various steps of the workflow (see Figure 2).

Figure 2. Example of the Need for QC Metrics: Illumina TSO500 NGS Panel

Davis cautioned, “QC metrics may vary depending on sample type and should be tested in a pilot experiment before being implemented in a large-scale clinical trial.”

TSO500 is a powerful application that can be used on human FFPE and circulating tumor DNA (ctDNA). Running the TSO500 panel is more efficient and cost-effective than whole genome sequencing. In addition, the data are more manageable and it allows for a better depth of coverage to detection of mutations that require greater sensitivity.

Davis concluded the webinar with a brief discussion on QuartzBioSM, Precision for Medicine’s proprietary bioinformatics solutions, which can integrate and perform secondary analyses on diverse biological data from virtually any platform to generate actionable insights.

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Darren Davis, PhD
Senior Vice President,
Biospecimens Solutions