Breakthrough research combining nRichDX extraction and PacBio SBB sequencing enables detection of cancer variants at frequencies as low as 0.01%
In the world of cancer detection, scientists face a monumental challenge: finding infinitesimal genetic mutations hidden within a vast sea of healthy DNA. These microscopic fragments of tumor DNA, known as circulating tumor DNA (ctDNA), float in the bloodstream, carrying the genetic signature of cancer. However, in early-stage cancer or during treatment monitoring, these signals can be incredibly faint, with variant allele frequencies (VAF) as low as 0.01%—that's just one cancer molecule among 10,000 healthy ones.
Traditional technologies struggle to detect variants below 0.1% VAF, creating a critical sensitivity gap in cancer detection and monitoring.
Breakthrough: Recent advances combining nRichDX's Revolution sample preparation system with PacBio's Sequencing by Binding (SBB) chemistry are achieving unprecedented detection sensitivity that promises to transform liquid biopsy 4 .
Traditional sample preparation methods, particularly column-based systems, introduce multiple points of sample loss that disproportionately affect rare ctDNA molecules 1 5 .
nRichDX's Revolution system addresses these limitations through a paramagnetic bead-based approach that enables single-tube processing of large sample volumes (up to 50 mL) without pooling or sample transfers 1 5 .
Traditional Sequencing by Synthesis (SBS) chemistry typically achieves Q30 accuracy, representing an error rate of 1 in 1,000 bases 6 .
PacBio's Sequencing by Binding (SBB) chemistry achieves Q40+ accuracy, with an error rate of just 1 in 10,000 bases—a 15-fold improvement over traditional methods 2 6 .
Researchers collected plasma samples from patients, preserving fragile ctDNA molecules.
Using the Revolution cfDNA Max 20 Kit, the team processed large plasma volumes (up to 20 mL) in a single extraction 1 .
Extracted cfDNA was converted into sequencing libraries compatible with the PacBio Onso system 6 .
Exceptionally accurate sequencing data was processed using specialized bioinformatics tools.
The combination of high-yield extraction and ultra-accurate sequencing delivered remarkable performance.
In a third-party evaluation, "paramagnetic bead-based cfDNA isolation [nRichDX] improved the recovery of cfDNA compared to the column-based method... Across all metrics" 5 .
| Parameter | Traditional Approach | nRichDX + PacBio SBB |
|---|---|---|
| Input Volume | Typically 5-10 mL with pooling | Up to 50 mL in single extraction |
| Extraction Efficiency | Lower due to transfers and pooling | Higher, minimal sample loss |
| Sequencing Accuracy | Q30 (1/1,000 error rate) | Q40+ (1/10,000 error rate) |
| VAF Detection Limit | ~0.1% with high confidence | ≤0.01% with high confidence |
| Duplicate Rate | Higher | Minimal |
| Index Hopping | More prevalent | Negligible |
Advancing liquid biopsy research requires specialized tools designed to address the unique challenges of working with rare analytes.
| Tool | Function | Key Feature |
|---|---|---|
| nRichDX Revolution System | Extraction of cfDNA from plasma | Processes 1-50 mL samples without pooling or transfers 1 |
| PacBio Onso System | Short-read sequencing with exceptional accuracy | Sequencing by Binding chemistry for Q40+ accuracy 2 |
| Revolution cfDNA Max 20 Kit | Optimized extraction of cell-free DNA | Paramagnetic bead-based technology for high recovery 1 |
| nRicher Cartridge | Automated processing of samples | Compatible with Revolution Plus processor 3 |
Process up to 50 mL samples without pooling or transfers
Paramagnetic bead technology maximizes rare analyte recovery
Q40+ sequencing accuracy for confident variant calling
Enhanced sensitivity could identify tumors at earlier, more treatable stages when intervention is most effective.
Enables more precise tracking of minimal residual disease and earlier detection of emerging resistance mutations.
Versatility: The nRichDX platform extends beyond plasma, having demonstrated success with diverse sample types including urine, CSF, and peritoneal fluid 1 3 , suggesting broader applications across different cancer types and clinical scenarios.
| Application | Traditional Limitation | Enhanced Capability |
|---|---|---|
| Early Detection | Limited by low VAF of ctDNA | Enhanced sensitivity for sub-0.1% VAF |
| Treatment Monitoring | Inability to track very low MRD | Precise quantification of minimal residual disease |
| Sample Types | Primarily plasma | Urine, CSF, peritoneal fluid 3 |
| Input Requirements | Often limited by sample volume | Efficient use of large volume samples |
| Assay Development | High QNS rates | Reliable recovery for consistent results |
The synergy between advanced sample preparation and breakthrough sequencing chemistry represents a paradigm shift in liquid biopsy capabilities.
By solving both the sample loss problem and the sequencing accuracy challenge, the combination of nRichDX's Revolution system and PacBio's SBB technology has created a pathway to detection sensitivities once thought impossible.
As research continues to validate and refine these approaches, we stand at the threshold of a new era in cancer management—one where invisible signals become detectable, enabling earlier interventions, more precise monitoring, and ultimately, better outcomes for patients facing cancer.