Maximizing biomarker insights from minimal samples

A critical but constrained tool

Biomarker testing is central to oncology research and clinical care, driving targeted therapy development and personalized treatment. Next-generation sequencing (NGS) based approaches can detect diverse genomic alterations in a single assay, however, their broad adoption is hindered by the quality and quantity of available tumor samples.

The sample quality gap

A persistent challenge in biomarker testing is the reliance on formalin-fixed paraffin-embedded (FFPE) tissue samples. FFPE is the standard for specimen preservation, but extracting high-quality DNA and RNA for NGS is difficult.^1-3 Many clinical samples—especially core needle biopsies—may yield only a few nanograms of usable material.

Dr. Erin Newburn, PhD, Director of Field Applications at Labcorp, highlights the widespread nature of this issue: “Clinical trial samples from FFPE blocks often have low nucleic acid yields and degradation. This impacts extraction, library preparation and post-sequencing data processing.”

Unlocking value with optimized workflows and scalable technologies

To address these limitations, labs are adopting standardized workflows that maximize data output from challenging samples. Labcorp has developed automated dual extraction protocols to improve nucleic acid yield and quality from FFPE tissues, reducing the number of quantity not sufficient (QNS) samples.⁴

“Automated, standardized workflows significantly improve nucleic acid yield and quality,” says Dr. Newburn. “This enables more successful genomic profiling and ultimately better patient outcomes.”

Beyond extraction, quality control (QC) metrics help ensure high-confidence variant calls.⁵ QC tools filter low-confidence data and minimize false results, providing reliable data to drive informed decisions.

Broad genomic solutions for maximum insight

Technologies including whole-exome sequencing (WES), whole-transcriptome sequencing (WTS) and large targeted panels are a key strategy for maximizing variant detection from minimal input.

Adds Dr. Newburn, “Comprehensive platforms help biopharma teams maximize data outputs for current and future biomarkers of interest from limited material.”

Best practices for success

To optimize comprehensive genomic profiling (CGP) in sample-constrained settings, early alignment with experienced genomics providers is key. Best practices include:

• Standardized extraction for reproducibility and scalability
• QC-informed library preparation to improve data quality and reduce rework
• Advanced sequencing platforms that deliver insights from low-input samples

These approaches improve outcomes, accelerate timelines and reduce costs—critical in clinical and research environments.

Case studies: Enabling high-confidence variant detection for your biomarker-driven trial
 

Reliable variant detection with minimal sample input

OmniSeq® INSIGHT whole exome sequencing assay provides robust detection of small variants from tissue specimen.⁶ All samples were processed in our CAP/CLIA Laboratory in Buffalo, NY.

• DNA input amounts of 20 ng, 50 ng, and 200 ng, surrounding the 100ng optimal input, demonstrate tolerance to potential DNA input variability with minimal effect on variant detection.
• The analysis demonstrated a mean APA of 96% (range 82%-98%) and mean ANA of 98% (range 82%-100%).

Dependable performance with both resected and core needle biopsies 

PGDx elio tissue complete, available as the Labcorp Tissue Complete service in Labcorp’s Baltimore, Geneva and Shanghai labs, is a 505-gene comprehensive genomic profiling (CGP) solution for global clinical trials. The optimized Tissue Complete workflow provides robust performance using both resected and core needle biopsy (CNB) FFPE tumor materials. All samples were processed in our CAP/CLIA Laboratory in Baltimore, MD.

• High DNA yield success rate across sample formats; 100% for resections and 92.5% for CNBs 

• Additionally, excellent post analytical success rate; 95.5% overall

  	Samples Enrolled	Overall Success Rate	Tumor Purity Success Rate	DNA Yeild Success Rate	Post-Analytical Sucess Rate
  CNB	373	83.4%	94.1%	92.5%	96.8%
  Resection	145	90.4%	100%	100%	93.6%
  Total	529	85.5%	94.9%	94.6%	95.8%

As CGP becomes integral to oncology development, generating reliable data from limited samples is essential. Through innovations in extraction, sequencing and analysis, Labcorp is helping unlock the full potential of precision oncology, one sample at a time.