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Beyond NGS: Recovering Results from Challenging FFPE Samples

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In the world of molecular testing, every sample represents a crucial opportunity for insight. Yet laboratories face a persistent challenge: up to 25% of samples submitted for next-generation sequencing (NGS) fail to yield results due to quality and quantity issues. This significant failure rate not only impacts research timelines and costs but also represents lost opportunities for advancing our understanding of disease.

The Challenge of FFPE Samples

Formalin-fixed, paraffin-embedded (FFPE) samples are the standard in molecular testing of tumors, but they present unique challenges. DNA extracted from these samples is often degraded into small fragments , making them particularly challenging for NGS workflows, which require relatively intact DNA for library preparation.

Common issues include:

• Insufficient DNA quantity (QNS)
• Low tumor fraction (<10%)
• High levels of DNA degradation
• Presence of PCR inhibitors

A Breakthrough Solution

Recent research has demonstrated that the MassARRAY^® System can overcome these limitations. A groundbreaking study conducted by Precision for Medicine examined 196 lung FFPE samples that had previously failed NGS testing.

The results were significant:

• 100% of samples passed quality control
• Results were validated with 100% positive predictive value using ddPCR
• The system required only ≤20 ng DNA input

This success is attributed to the system’s unique characteristics:

• Short amplicon PCR (80-120 base pairs)
• Single global PCR reaction
• Variant-enriched single-base extension chemistry
• Sensitivity down to 1% variant allele frequency
• Implications for Research

The ability to recover results from failed NGS samples has significant implications for molecular research. It means:

• More efficient use of precious samples
• Reduced costs from failed runs
• Faster time to results
• More complete data sets

The Future of Molecular Profiling

While NGS remains a powerful platform for comprehensive genomic analysis, the addition of complementary technologies like the MassARRAY System can help laboratories maximize their success rates and ensure no sample is left behind.

Download our detailed white paper to learn more about how mass spectrometry is revolutionizing the handling of challenging FFPE samples.