Key Features

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Rapid

Ultrafast turnaround enabling 10 hours DNA to results

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Ultrasensitive

Limit of detection down to 0.1% VAF

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Affordable

Low sequencing cost

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Versatile

Compatible with several sample types

Benefits

  • Detects 254 AML hotspot mutations in 6 genes: FLT3, DNMT3A, IDH1, IDH2, KIT, and NPM1
  • Fast workflow: from DNA to results in 10 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 10-500 ng DNA from whole blood or bone marrow lysate (AML Panel), 1 tube of reaction
  • Compatible with MinION and Flongle flow cells
  • Requires only 30 minutes of sequencing time on MinION for up to 24 samples per run

Sample Data

Minimum Residual Disease
  • Horizon Myeloid reference sample (HD829) – 15,000 haploid copies ~ 50 ng was tested using the VarMap AML panel.
  • 100% concordance in variant calling.
AML Mutation Detection
  • Summary of VarMap nanopore results for 25 clinical cancer samples (7 fresh/frozen, 18 FFPE).
  • Relative to the NGS results, VarMap had a sensitivity of 100 % and a specificity of 99%.
  • The numbers in quadrant display the number of loci in each group. Purple dots represent variants that passed the variant call filter. 22/23 variant calls below NGS sensitivity were confirmed by ddPCR.

Workflow

Workflow Step 1

Step 1: DNA Extraction

DNA is extracted from clinical samples with commercial extraction kits such as QIAamp® DNA Blood Mini Kit.
40 min (40 min hands-on)

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Step 2: BDA Reaction

NuProbe’s kit reagents and clinical samples are prepared for BDA reactions.

2.5 hrs ( 30 min hands-on)

AML Steps

STEP 3: Adapter attachment PCR

BDA products are amplified and adapters are attached.

1.5 hrs (30 min hands-on)

AML Steps

STEP 4: Amplicon Assembly

Amplicons are assembled to generate high-quality long DNA for nanopore sequencing

3 hrs (30 min hands-on)

AML Steps

STEP 5: Nanopore Sequencing

Oxford Nanopore’s Ligation sequencing kit (SQK-LSK109) is used for library preparation for nanopore sequencing on MinION

3 hrs (2 hrs hands-on)

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STEP 6: Data Analysis

NuProbe’s user-friendly analysis software analyzes demultiplexed FASTQ files to generate a Variant Analysis Report that reports all detected variants, the quality scores for the detected variants, and genomic locations.

(10 – 15 min per sample)

Compatible Instruments

Nanopore Instruments

Oxford Nanopore Flongle

Oxford Nanopore Flongle


Oxford Nanopore MinION

Oxford Nanopore MinION


Oxford Nanopore GridION

Oxford Nanopore GridION

Background

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

In patients with Acute Myeloid Leukemia (AML), several genes are frequently mutated, including FLT3, IDH1, IDH2, DNMT3A, KIT, and NPM1. The presence of these specific mutations can guide treatment with targeted therapies such as RYDAPT® (midostaurin), XOSPATA® (gilteritinib), TIBSOVO® (ivosidenib), and IDHIFA® (enasidenib).

The VarMap™ AML Nanopore Panel enables highly sensitive detection and quantification of mutations for AML patients. The kit uses 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, Nanopore sequencing is applied to reveal the identity of the variants.

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