Key Features

Checkmark

Ultrasensitive

Limit of detection down to 0.1% VAF

Checkmark

Quantitative

Quantify mutation VAF of samples down to 0.1% VAF

Checkmark

Affordable

Only 1 million reads per sample for liquid biopsy

Checkmark

Versatile

Compatible with several sample types

Checkmark

User-friendly

Easy workflow and data analysis

Benefits

  • Comprehensive Cancer Mutation Panel: Detects and quantitates over 6300 mutations in the COSMIC database in 61 genes
  • Fast workflow: from to DNA to library in 8 hours, including 3.5 hours of hands-on time
  • User-friendly data analysis software with 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

AKT1ALKAPCARATMBRAFCCND1
CDK4CDKN2ACHEK2CTNNB1DDR2EGFRERBB2
ERBB3ERBB4ESR1EZH2FBXW7FGFR1FGFR2
FGFR3FGFR4FLT3FOXL2GNA11GNAQGNAS
HRASIDH1IDH2JAK1JAK2JAK3KIT
KRASMAP2K1MAP2K2METMLH1MPLMTOR
MYCMYCNMYD88NPM1NRASPDGFRAPIK3CA
PTENPTPN11RAF1RB1RETROS1SF3B1
SMAD4SMARCB1SMOSTK11TP53

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

DNA Icon

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, GeneRead® DNA FFPE Kit.

Blocker Icon

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.

5 hrs (2 hrs hands-on)

Multiplex Icon

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)

7 hrs total time (STEP2+STEP3)

Device Icon

Step 4: Sequencing

Indexed samples undergo quality control, pooled, and sequenced on an Illumina sequencing instrument.

Computer Analysis Icon

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 mutation, number of molecules, VAF, and associated COSMIC ID (when applicable).
2-5 min per sample

Compatible Instruments

Illumina MiniSeq


Illumina MiSeq

Illumina MiSeq

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. Detecting these mutations simultaneously can provide profile on patients carried mutations and apply targeted therapies accordingly. In addition, this ultra-sensitive assay offers a much affordable way of monitoring post-treatment response.

The VarMap Pan-Cancer NGS Panel enables highly sensitive mutation detection and quantitation for cancer patients. 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 60-fold. Furthermore, the technology is compatible with a number of sample 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 monitoring and tumor heterogeneity characterization.

Request Quote / Demo

Pengying (Christina) Hao, Senior Scientist at NuProbe, Ph.D. in Molecular Biology, Cellular Biology and Biochemistry from Boston University.

Jinny Zhang, Research Scientist II at NuProbe, Ph.D. in Systems, Synthetic and Physical Biology from Rice University, Houston.

Fill in the form below to contact Christina and Jinny for questions about VarMap NGS products.



    Quantity (if requesting a quote)