Key Features
Ultrasensitive
Limit of detection down to 0.1% VAF
Quantitative
Quantify mutation VAF of samples down to 0.1% VAF
Affordable
Only 1 million reads per sample for liquid biopsy
Versatile
Compatible with several sample types
User-friendly
Easy workflow and data analysis
For research use only. Not for use in diagnostic procedures.
The VarMap Pan-Cancer NGS Panel is the only liquid biopsy panel to detect 0.1% VAF on the MiniSeq and MiSeq requiring only 1M reads. It covers 337 hotspots in 61 genes with clinical high-significance in many cancer types and includes detection of over 6300 COSMIC mutations including JAK2 V617F, BRAF V600E, KRAS G12D/G12V/G12C, EGFR exon 19 deletions and insertions, EGFR T790M, EGFR L858R, and TP53 R248Q.
The VarMap Pan-Cancer NGS Panel enables highly sensitive mutation detection and quantitation for cancer research. The kit uses NuProbe’s PCR-based quantitative Blocker Displacement Amplification (qBDA) technology to enable the selective amplification of low abundant (≥0.1% VAF) sequence variants (SNV and indels) in a background of wildtype DNA. Next-generation sequencing of the PCR enriched samples enables accurate variant identification and variant allele frequency (VAF) quantitation. NuProbe’s technology significantly decreases the limit of detection (≥0.1% VAF) for NGS while decreasing the number of reads per sample by 60-fold. Furthermore, the technology is compatible with a number of specimen types including cell-free DNA, tumor sections, and PMBC DNA. The kit’s sample versatility and increased sensitivity allow for a number of applications such as cell-free DNA profiling, minimal residual disease (MRD) monitoring, and tumor heterogeneity characterization.
Benefits
- Comprehensive Cancer Mutation Panel: Detects and quantitates over 6300 mutations in the COSMIC database in 61 genes
- Fast workflow: from DNA to library in 8 hours, including 3.5 hours of hands-on time
- User-friendly data analysis software with a graphical user interface, enabling FASTQ-to-variant reports in minutes
- Compatible with 20 ng cfDNA, gDNA (10ng/tube) and 40 ng FFPE DNA (20ng/tube)
- Number of reads required per sample reduced to only 1 million reads, 60X less than standard deep sequencing
List of Genes and Mutations
| AKT1 | ALK | APC | AR | ATM | BRAF | CCND1 |
| CDK4 | CDKN2A | CHEK2 | CTNNB1 | DDR2 | EGFR | ERBB2 |
| ERBB3 | ERBB4 | ESR1 | EZH2 | FBXW7 | FGFR1 | FGFR2 |
| FGFR3 | FGFR4 | FLT3 | FOXL2 | GNA11 | GNAQ | GNAS |
| HRAS | IDH1 | IDH2 | JAK1 | JAK2 | JAK3 | KIT |
| KRAS | MAP2K1 | MAP2K2 | MET | MLH1 | MPL | MTOR |
| MYC | MYCN | MYD88 | NPM1 | NRAS | PDGFRA | PIK3CA |
| PTEN | PTPN11 | RAF1 | RB1 | RET | ROS1 | SF3B1 |
| SMAD4 | SMARCB1 | SMO | STK11 | TP53 |
Sample Data
- Sample Report
- Fast variant reporting within minutes using our designated GUI based data analysis pipeline. This automated bioinformatics pipeline can be run locally or on the cloud to comply with custom data security requirements.
- Performance demonstration
- Detect low VAF hotspot mutations down to 0.1% VAF with only 1M reads, using total input as low as 10ng cfDNA or 50ng gDNA from FFPE/Fresh Frozen(FF) samples. By implementing unique molecular identification (UMI) technology to label each DNA, VarMap is able to differentiate real variants from PCR and sequencing error to achieve a much lower detection limit.
- Enrichment performance
- Detect variants with only 1M reads giving 60-fold reduction to traditional deep sequencing. By implementing blocker displacement amplification (BDA) technology to selectively amplify variants, VarMap™ Pan-Cancer Panel uses 1M reads versus 50-60M reads required for deep sequencing.
- Quantitation accuracy
- Quantitate variants with high accuracy despite low sequencing depth. Quantitative BDA technology (qBDA) can accurately quantify variant allele frequency (VAF) with more than 94% variants showing concordance with traditional deep sequencing results.
Workflow
Step 1: DNA Extraction
DNA is extracted from clinical samples with commercial extraction kits such as cobas® cfDNA Sample Preparation Kit, QIAamp® DNA Blood Mini Kit, or GeneRead® DNA FFPE Kit.
Step 2: qBDA Variant Enrichment
NuProbe’s VarMap kit reagents and clinical samples are prepared for two sequential reactions to add unique molecular identifiers to each original input molecule and to preferentially amplify variant molecules.
6 hrs (2 hrs hands-on)
Step 3: Adapter Addition and Library Indexing
qBDA enriched samples are prepared for Illumina sequencing with the addition of sequencing adapters and indices.
2 hrs (1.5 hrs hands-on)
8 hrs total time (STEP2+STEP3)
Step 4: Sequencing
Indexed samples undergo quality control, pooling, and sequencing on an Illumina sequencing instrument.
Step 5: Data Analysis
NuProbe’s user-friendly analysis software analyzes demultiplexed FASTQ files to generate a comprehensive Variant Analysis Report outlining all detected variants’ genomic location, CDS and AA change, number of molecules, VAF, and associated COSMIC ID (when applicable).
2-5 min per sample
Compatible Instruments
Catalog number
2R-0501-S
24 reactions;
2R-0501-M
8 reactions
| Illumina Instrument and Kit | Samples per Run |
|---|---|
| iSeq System (i1) | 4 |
| MiniSeq System (mid-output) | 8 |
| MiniSeq System (high-output) | 24 |
| MiSeq System (v2 chemistry Micro) | 4 |
| MiSeq System (v2 chemistry) | 14 |
| MiSeq System (v3 chemistry) | 24 |
| NextSeq System (mid-output) | 130 |
Request More Info
Pengying (Christina) Hao, Associate Director of Assay Development at NuProbe, Ph.D. in Molecular Biology, Cellular Biology and Biochemistry from Boston University.
Fill out the form to contact Christina for questions about VarMap NGS products.
