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

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Benefits

  • Detects and quantitates 1150 mutations in the COSMIC database across 31 hotspots in 14 genes
  • Fast workflow: from to DNA to library in 7 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 10 – 100 ng of cell free DNA, tumor sections (FFPE and fresh frozen), and PBMC DNA
  • Number of reads required per sample reduced to only 1 million reads, 60X less than standard deep sequencing

Sample Data

  • VarMap enrichment performance
  • Utilizing blocker displacement amplification (BDA), VarMap NGS Panels preferentially amplify variant molecules over wildtype, resulting in a reduction of sequencing reads by 60-fold. Deep sequencing approaches would require approximately 60 million reads to achieve the same variant read coverage as our VarMap technology with 1 million reads.
  • Quantitation accuracy of VarMap
  • Quantitative BDA (qBDA) technology of VarMap enables molecular counting of input variant molecules and the accurate calculation of variant allele frequency (VAF). Molecular counting with qBDA enables a high quantitation accuracy with >95% of variants in concordance (2-fold) with traditional deep sequencing results.
  • VarMap sensitivity
  • Quantitative BDA (qBDA) technology of VarMap enables molecular counting of input variant molecules down to 0.1% variant allele frequency (VAF). Molecular counting with qBDA increases the sensitivity of NGS, with over 95% of variants detected at 0.1% VAF.

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, 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 identifies to each original input molecule, and to preferentially amplify variant molecules.

5 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)

7 hrs total time (STEP2+STEP3)

Step 4: Sequencing

Indexed samples undergo quality control, pooled, and sequenced 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 mutation, number of molecules, VAF, and associated COSMIC ID (when applicable).
2-5 min per sample

Compatible Instruments

Illumina MiniSeq


Illumina MiSeq

Background

For research use only. Not for use in diagnostic procedures.

The VarMapTM NSCLC Panel covers 31 hotspots in 14 genes frequently mutated in NSCLC patients. NuProbe’s NSCLC panel detects over 1100 COSMIC mutations including BRAF V600E, EGFR exon 19 deletions and insertions, EGFR T790M, EGFR L858R, KRAS G12C, and TP53 R248Q. The presence of these mutations can indicate the presence of NSCLC during disease monitoring, and/or guide treatment with a number of targeted therapies such as TAFINLAR® (dabrafenib), MEKINIST® (trametinib), GILOTRIF® (afatinib), VIZIMPRO® (dacomitinib), TARCEVA® (erlotinib), IRESSA® (gefitinib), and TAGRISSO® (osimertinib).

The VarMapTM NSCLC Panel enables highly sensitive detection and quantitation of mutations for NSCLC 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) quantification. 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 allows for a number of applications such as cell-free DNA profiling, minimal residual disease monitoring and tumor heterogeneity characterization.

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