BDA NGS Assays

Low-Depth NGS Sequencing to 0.01% VAF

NuProbe has used the Blocker Displacement Amplification (BDA) technology to create several proof of concept assays. These assays demonstrate the capabilities and benefits of this technology, including its ability for more efficient use of sequencing capacity. Similar assays can be developed to target your biomarker needs. For information on available technology solutions, contact us.  

Key Features

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Ultrasensitive

Detection of SNVs and indels down to 0.01% VAF

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Quantitative

Accurately quantitate mutations down to 0.01% VAF

Sample Flexibility

Compatible with cfDNA, FFPE, and other biospecimens

Sequencing Efficiency

Detection of mutations to 0.01% VAF using only 1 million reads

BDA NGS Assays Portfolio

Pan-Cancer NGS Panel

The only liquid biopsy panel to detect 0.1% VAF requiring only 1 million NGS reads

Overview

The Pan-Cancer NGS Panel enables highly sensitive variant detection and quantitation across hundreds of loci in 61 genes. Utilizing BDA technology and next-generation sequencing, the Pan-Cancer panel significantly improves the limit of detection (≥0.1% VAF) while reducing the number of reads required. The panel is compatible with several sample types, including cell-free DNA, tumor sections, and PBMC DNA.

Key Features

  • Detect SNVs and indels down to 0.1% VAF
  • Requires only 1 million NGS reads per sample
  • Compatible with tumor-derived or cell-free DNA
  • Simple and user-friendly workflow and bioinformatics

Gene List

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

AML MRD Panel

A robust quantitation of single-base substitutions and indels down to 0.01% VAF at a single locus for MRD analysis

Overview

20-gene assay for monitoring minimal residual disease in acute myeloid leukemia, through the sensitive detection (below 0.01% VAF) of SNVs and indels from liquid biopsy, while significantly reducing sequencing requirements.

Key Features

  • Detect SNVs and indels below 0.01% VAF
  • Requires only 4 million NGS reads per sample

Gene List

ABL1, ASXL1, BCOR, CBL, DNMT3A, EZH2, FLT3, GATA1, IDH1, IDH2, JAK2, KRAS, NPM1, NRAS, RUNX1, SF3B1, TET2, TP53, KIT, ETV6 

BDA qPCR Assays

Ultrasensitive Mutation Detection using qPCR

Using BDA with qPCR allows for ultrasensitive multiplexed detection of mutations in as little as two hours. NuProbe has created proof of concept assays for effective variant enrichment and simultaneous profiling of single nucleotide variants or indels without the need for post-qPCR melting curves or additional sequencing.

Key Features

Ultrasensitive

Detection of SNVs and indels down to 0.01% VAF

Rapid Workflow

DNA to results in as less than 2 hours

Flexibility

Compatible with most qPCR instruments

BDA qPCR Assays Portfolio

MSI Assay

Highly sensitive detection of microsatellite instability in five MSI loci using qPCR

Overview

NuProbe’s MSI Assay enables detection of MSI-high (MSI-H) status with a limit of detection down to 1% VAF in five mononucleotide markers (BAT-25, BAT-26, NR-21, NR-24, and MONO-27).

Five Mononucleotide Markers

BAT-25, BAT-26, NR-21, NR-24, and MONO-27

Key Features

  • Matched normal not required
  • Results in less than two hours
  • Compatible with tumor tissue or cell-free DNA
  • Limit of detection down to 1% VAF

As-BDA IDH2 qPCR Assay

Quantitative PCR for simultaneous enrichment and identification below 0.1% VAF

Overview

The As-BDA IDH2 qPCR Assay enables highly sensitive detection and quantification of 10 mutations in IDH2. The kits use BDA technology and are compatible with a variety of qPCR instruments.

Key Features

  • Detect targeted variants down to 0.1% VAF
  • Same-day results

Publication References:

Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction. Analytical Chemistry. (2021).

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Calibration-free NGS quantitation of mutations below 0.01% VAF. Nature Communications. (2021).

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Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nature Biomedical Engineering. (2021).

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Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nature Biomedical Engineering. (2017).

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