Overview
The process of designing a custom panel begins with target definition, including the gene(s) to be analyzed, regions of interest, and breadth of coverage. NuProbe’s assay design experts will work with you to define a panel that meets your project’s needs. During panel development, components are assembled followed by rigorous testing of sensitivity and reproducibility using reference materials. Panel verification is done to confirm assays are performing on applicable sample types and/or cell lines. Research sample testing is done in NuProbe’s Houston, TX facility.
The development of fully custom NGS panels can be done in as little as 10 weeks. Research sample testing is completed approximately 3 weeks after panel development is completed.
Development Process
Heme MRD Panels from NuProbe
- Uses BDA technology to selectively enrich targets of interest
- Custom panels from pre-designed and functionally tested components
- Flexible coverage options ranging from full coding sequence (CDS) to hotspots
- Optimized for measurable residual disease (MRD) research applications
Specifications
| Parameter | Specifications |
|---|---|
| Technology | BDA |
| Gene Targets | 1 – 5 custom-built from our heme gene list |
| Coverage | Full gene (80-100% coverage) and/or hotspots See gene list for coverage options |
| Alterations | SNVs, Indels (FLT3-ITD up to 50 bp) |
| Limit of Detection | 0.1 – 0.01% VAF |
| Sample Type | Genomic DNA from PBMCs |
| DNA Requirements | 2.5 – 6 μg** (recommended) |
| Sequencing Platform | Illumina NextSeq or higher |
| Custom Assay Development Time | Approximately 10 weeks |
| Research Sample Testing Turnaround | Up to 3 weeks from sample receipt* |
*sample testing is done after assay development is complete
**DNA input amount is based on assay size and configuration
Custom Solid Tumor ctDNA Panels from NuProbe
- Utilizes QASeq technology for ultrasensitive detection of CNVs
- Compatible with cfDNA or tumor tissue
- CNV detection, or comprehensive CNV and SNV detection
Specifications
| CNV Custom Panels | CNV+ Custom Panels | |
|---|---|---|
| Gene Targets | 1 – 5 genes | 1 – 5 genes |
| Coverage | Gene-level CNVs* | Full coding sequence for SNVs; gene-level for CNVs |
| Alterations | CNVs | CNVs, SNVs, Indels |
| Limit of Detection | Down to 2.05 ploidy | Down to 2.05 ploidy (CNVs), 0.2% VAF (SNVs and indels) |
| Sample Type | FFPE, fresh frozen tissue, plasma, cell lines, extracted DNA | FFPE, fresh frozen tissue, plasma, cell lines, extracted DNA |
| DNA Requirements | 10 μg (recommended) 5 μg (minimum) |
20 μg (recommended)10 μg (minimum) |
| Sequencing Platform | Illumina NextSeq or higher | Illumina NextSeq or higher |
| Custom Assay Development Time | 8 weeks | 12 weeks |
| Research Sample Testing Turnaround | Up to 3 weeks | Up to 3 weeks |
*smaller and larger CNVs may be detected in some cases, please contact us to discuss
Get Started
Our dedicated team of scientists will work with you to design and develop a custom assay to meet your specifications. The process includes the following steps:
Contact us to start discussing how NuProbe’s technologies can accelerate your research projects.
