Key Features

Sensitive
Limit of detection down to 0.1% VAF

Quantitative
Able to quantify mutation VAF in original sample

Versatile
Applicable to a variety of sample types

Comprehensive
Wide range of mutations covered

User-friendly
Easy workflow
For research use only. Not for use in diagnostic procedures.
The VarTrace™ products enable highly sensitive detection and quantification of mutations for NSCLC, AML, melanoma patients. The kits use NuProbe’s PCR-based Blocker Displacement Amplification (BDA) technology to enable the selective amplification of low abundant sequence variants (SNV and indels) in a background of wildtype DNA. Following PCR enrichment, Sanger sequencing is applied to reveal the identity of the variants.
Product Offerings
EGFR | Mutation position | Mutation type | Detectable mutations |
---|---|---|---|
Hotspot mutations in Exon 18-21* | SNV, Indel | 272 |
BRAF | Mutation position | Mutation type | Detectable mutations |
---|---|---|---|
Any mutations in codons 596–601 | SNV, Indel | 67 |
AML | Mutation position (AA) | Mutation type | Detectable mutations |
---|---|---|---|
FLT3 (TKD) | 835-836 | SNV | 45 |
DNMT3A | 882 | SNV | 17 |
IDH1 | 132 | SNV | 17 |
IDH2 | 140, 172 | SNV | 31 |
KIT | 816 | SNV | 36 |
NPM1 | 288 | Indel | 105 |
Product Specifications
Kit size | EGFR, AML: 24 reactions / kit |
BRAF: 33 reactions / kit | |
Turnaround time | Same day results |
Sample type | Plasma samples, tumor biopsies, paraffin-embedded sections (FFPE), and fresh frozen tumors (only blood samples for AML panels) |
Sample input | 10-100 ng cfDNA from blood plasma, or 10-1000 ng DNA from tissue biopsy or blood plasma |
Workflow

Step 1: DNA Extraction
DNA is extracted from clinical samples with commercial extraction kits such as cobas® cfDNA Sample Preparation Kit (not applicable to AML panel), QIAamp® DNA Blood Mini Kit, GeneRead® DNA FFPE Kit(not applicable to AML panel).
40 min (40 min hands-on)

Step 2: qPCR BDA Reaction
NuProbe’s qPCR/Sanger kit reagents and clinical samples are prepared for qPCR reactions. After running the reaction, Ct results and BDA products are obtained.
1.5 hrs (30 min hands-on)
2.5 hrs total time for qPCR reactions (STEP1 + STEP2)

Step 3: Sanger Sequencing (Optional)
BDA products are prepared for Sanger sequencing, including PCR product purification, cycle sequencing and sequencing clean-up. Purified Sanger products are analyzed by capillary electrophoresis.
5.5 hrs (1.5 hrs hands-on)
8 hrs total time including Sanger Sequencing (STEP1+STEP2+STEP3)
Compatible Instruments
qPCR

BioRad CFX96

ABI 7500

Cobas z480
Sanger sequencing

ABI 3500 Dx Genetic Analyzer
Vartrace AML Panel
Benefits
- Comprehensive hematological panel: Detects 254 AML hotspot mutations in 6 genes: FLT3, DNMT3A, IDH1, IDH2, KIT, and NPM1
- Requires 80 ng – 1.5 μg of DNA from whole blood sample
- Rapid mutation testing: Delivers results in 8 hours, with 2.5 hours of hands-on time
List of Mutations
Gene | AA mutation | CDS mutation |
---|---|---|
FLT3 | p.D835H | c.2503G>C |
p.D835N | c.2503G>A | |
p.D835Y | c.2503G>T | |
p.D835A | c.2504A>C | |
p.D835V | c.2504A>T | |
p.D835E | c.2505T>A | |
p.D835E | c.2505T>G | |
p.I836F | c.2506A>T | |
p.I836L | c.2506A>C | |
p.I836V | c.2506A>G | |
p.I836D | c.2506_2507delATinsGA | |
p.I836H | c.2506_2507delATinsCA | |
p.I836M | c.2508C>G | |
DNMT3A | p.R882C | c.2644C>T |
p.R882G | c.2644C>G | |
p.R882S | c.2644C>A | |
p.R882H | c.2645G>A | |
p.R882L | c.2645G>T | |
p.R882P | c.2645G>C | |
IDH1 | p.R132C | c.394C>T |
p.R132G | c.394C>G | |
p.R132S | c.394C>A | |
p.R132H | c.395G>A | |
p.R132L | c.395G>T | |
p.R132P | c.395G>C | |
IDH2 | p.R140G | c.418C>G |
p.R140W | c.418C>T | |
p.R140L | c.419G>T | |
p.R140Q | c.419G>A | |
p.R172K | c.515G>A | |
p.R172M | c.515G>T | |
p.R172S | c.515G>C | |
KIT | p.D816H | c.2446G>C |
p.D816Y | c.2446G>T | |
p.D816I | c.2446_2447delGAinsAT | |
p.D816V | c.2447A>T | |
NPM1 | p.W288fs*12 | c.863_864insTCTG |
p.W288fs*12 | c.863_864insCATG | |
p.W288fs*12 | c.863_864insCCTG |
Sample Data
Variant verification by Sanger sequencing
Because NuProbe’s BDA technology enriches the variant allele frequency (VAF) of mutations by over 200-fold, our AML sequencing research panel effectively improves Sanger’s limit of detection of 20% VAF to 0.1% VAF. Sanger sequencing can be applied to confirm the identity of quantities detected and quantitated by qPCR using standard sequencing protocols.
Download Product User Manual
Vartrace BRAF Assay
Benefits
- Detects any mutations in codons 596–601 (c. 1786-1802)
- Compatible with plasma samples, tumor biopsies, paraffin-embedded sections (FFPE), and fresh frozen tumors
- Requires 10-100 ng cfDNA from blood plasma, or 10-1,000 ng DNA from tissue biopsy
- Delivers results in 8 hours, with 2.5 hours of hands-on time
List of Mutations
AA mutation | CDS mutation |
---|---|
p.G596Vfs*2 | c.1787del |
p.G596D | c.1787G>A |
p.L597S | c.1789_1790delinsTC |
p.L597V | c.1789C>G |
p.L597Q | c.1790T>A |
p.L597R | c.1790T>G |
p.L597P | c.1790T>C |
p.A598T | c.1792G>A |
p.A598V | c.1793C>T |
p.T599dup | c.1794_1796dup |
p.T599del | c.1794_1796del |
p.A598_T599insV | c.1794_1795insGTT |
p.T599dup | c.1795_1797dup |
p.A598_T599insI | c.1795_1796insTAA |
p.A598_T599insKKIGDFGLA | c.1795_1796insAAAAAATAGGTGATTTTGGTCTAGCTA |
p.T599_V600delinsIK | c.1796_1799delinsTAAA |
p.T599I | c.1796C>T |
p.T599R | c.1796C>G |
p.T599_V600insTT | c.1797_1798ins? |
p.T599_V600insTT | c.1797delinsTACTACG |
p.V600R | c.1797_1799delinsGAG |
p.V600_K601delinsEN | c.1797_1803delinsTGAGAAT |
p.T599_V600ins2 | c.1798_1799ins6 |
p.V600L | c.1798G>T |
p.V600M | c.1798G>A |
p.V600K | c.1798_1799delinsAA |
p.V600dup | c.1798_1800dup |
p.T599_V600insEAT | c.1798_1799insAGGCTACAG |
p.V600R | c.1798_1799delinsCG |
p.T599_V600insETT | c.1798_1799insAGACTACAG |
p.V600T | c.1798_1799inv |
p.V600R | c.1798_1799delinsAG |
p.V600Q | c.1798_1799delinsCA |
p.V600L | c.1798G>C |
p.V600A | c.1799T>C |
p.V600E | c.1799_1800delinsAA |
p.V600E | c.1799T>A |
p.V600D | c.1799_1800delinsAT |
p.V600Efs*11 | c.1799_1800del |
p.V600G | c.1799T>G |
p.V600D | c.1799_1800delinsAC |
p.V600_K601delinsE | c.1799_1801del |
p.K601L | c.1801_1802inv |
p.K601E | c.1801A>G |
p.K601del | c.1801_1803del |
p.K601Gfs*44 | c.1801_1816del |
Sample Data
Variant verification by Sanger sequencing
Because NuProbe’s BDA technology enriches the variant allele frequency (VAF) of mutations by over 200-fold, Sanger’s limit of detection of 20% VAF is effectively improved to 0.1% VAF. Sanger sequencing can be applied to confirm the identity of quantities detected and quantitated by qPCR using standard sequencing protocols.
Download Product User Manual
Vartrace EGFR Assay
Benefits
- Detects 272 EGFR mutations and quantitates 43 mutations
- Enables distinction of cis/trans mutations in C797S/T790M
- Compatible with plasma samples, tumor biopsies, paraffin-embedded sections (FFPE), and fresh frozen tumors
- Accepts 10-100 ng cfDNA from blood plasma, or 10-1000 ng DNA from tissue biopsy
- Accepts 2-10 ml of blood, 1-5ml of blood plasma, as little as 1mm*1mm (5 μm) tissue sections (fresh frozen or FFPE)
- Delivers results in 8 hours, with 2.5 hours of hands-on time
List of Detected and Quantitated Mutations
Exon | AA mutation | CDS mutation |
---|---|---|
18 | p.G719S | c.2155G>A |
p.G719C | c.2155G>T | |
p.G719A | c.2156G>C | |
19 | >20 Exon 19 del mutations | |
20 | p.T790M | c.2369C>T |
p.C797S | c.2389T>A | |
p.C797G | c.2389T>G | |
p.C797Y | c.2390G>A | |
p.C797S | c.2390G>C | |
p.S768I | c.2303G>T | |
>5 Exon 20 insertion mutations | ||
21 | p.L858R | c.2573T>G |
p.L861Q | c.2582T>A |
Sample Data
- Variant verification by Sanger sequencing
- Because NuProbe’s BDA technology enriches the variant allele frequency (VAF) of mutations by over 200-fold, Sanger’s limit of detection of 20% VAF is effectively improved to 0.1% VAF. Sanger sequencing can be applied to confirm the identity of quantities detected and quantitated by qPCR using standard sequencing protocols.
- Variant verification by Sanger sequencing
- Because NuProbe’s BDA technology enriches the variant allele frequency (VAF) of mutations by over 200-fold, Sanger’s limit of detection of 20% VAF is effectively improved to 0.1% VAF. Sanger sequencing can be applied to confirm the identity of quantities detected and quantitated by qPCR using standard sequencing protocols.
Download Product User Manual
Request Quote / Demo
Alessandro Pinto, Ph.D., Senior Development Scientist at NuProbe.
Fill in the form to contact Ale for questions about the VarTrace products.
