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.
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 (down to 0.01% VAF) of SNVs and indels from liquid biopsy, while significantly reducing sequencing requirements.
Key Features
- Detect SNVs and indels as low as 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
KMT2A-rearranged Heme NGS Panel
Detection of low-frequency KMT2A gene fusions without prior knowledge of exact fusion partners and breakpoints.
Overview
The KMT2A-rearranged (KMT2Ar) Heme NGS panel enables highly sensitive detection of known and novel KMT2A rearrangements down to 0.05% tumor fraction. Using FusionBDA NGS technology to selectively enrich KMT2A fusion transcripts, the KMT2Ar panel enables identification of low-frequency gene fusions while minimizing sequencing requirements.
Key Features
- Ultrasensitive detection of known and novel fusion partner genes
- Agnostic detection of KMT2Ar with various fusion partnersRNA input
Target Fusions
KMT2Ar
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.
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).
Calibration-free NGS quantitation of mutations below 0.01% VAF. Nature Communications. (2021).
Download PDF | Go to publication
Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nature Biomedical Engineering. (2021).
Download PDF | Go to publication
Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification. Nature Biomedical Engineering. (2017).
