NuProbe QASeq Technology Enables Simultaneous Ultrasensitive Detection of CNVs and Mutations from FFPE Tissue and cfDNA

April 5, 2022

Houston, April 5th / NuProbe, a global genomics and molecular diagnostics company, announced new published data in Nature Communications describing the use of Quantitative Amplicon Sequencing (QASeq) to simultaneously detect copy number variations (CNVs) and mutations from the same sample.  The results show detection of CNVs down to 5% heterozygous single copy gain or loss, and mutations down to 0.1% variant allele frequency (VAF), from both formalin-fixed, paraffin-embedded (FFPE) tissue samples and from cell-free DNA (cfDNA) samples1.

Watch a video about the mechanism and learn more about QASeq.

CNVs are an important class of DNA biomarkers for cancer.  Depending on the exact type of cancer, CNVs can be present in up to 98% of patients2 and can influence therapy selection and prognosis prediction.  CNVs are currently detected using fluorescence in situ hybridization (FISH) or digital droplet PCR (ddPCR).  However, these methods are limited in their multiplexing, and typically no more than about 4 genes can be profiled for CNVs with these methods.  Furthermore, these methods cannot be used for profiling DNA mutations from the same samples.  Consequently, comprehensive DNA profiling of many genes would require larger input quantities of patient DNA, which are often not available.

“By achieving higher analytical sensitivity for multi-gene CNV panels, QASeq has the potential to improve the clinical sensitivity in CNV assessment,” says Peng Dai, co-first author of the study. “Our collaborations with Drs. Ueno, Reuben, and Barcenas at MD Anderson applying QASeq to breast cancer samples have demonstrated the unique capabilities of QASeq.” QASeq provides better sensitivity to CNVs than other NGS solutions3. The publication featured collaborative research including clinical sample testing on cfDNA samples from breast cancer patients.  CNVs and/or mutations were detected in all patients that had tumor progression.

“CNVs are more difficult to accurately and sensitively detect than other cancer DNA biomarkers, such as single-base mutations or gene fusions, due to the lack of sequence differences,”  says David Zhang, co-Founder and General Manager of NuProbe USA, and the corresponding author of the research. “The simultaneous CNV and mutation profiling capabilities of QASeq allows NuProbe to provide our biopharma partners with powerful patient stratification tools.  Further down the line, these panels could become companion diagnostics for new drugs.”


About NuProbe

NuProbe is a cutting-edge genomics and molecular diagnostics company with revolutionary molecular diagnostic technologies to improve the sensitivity of sequencing mutations and copy number variations by over 10-fold. NuProbe has sites in Houston, USA, Shanghai, China and Suzhou, China. NuProbe’s vision is to offer affordable, timely, and accurate disease state information to enable precision medicine and improve patient outcomes.

NuProbe’s products and services are for Research Use Only and are not intended for In Vitro Diagnostic use.

NuProbe currently offers customized QASeq panels covering up to 50 genes for translational research partners and collaborators. Contact NuProbe’s scientists to see how QASeq can help advance your product development and services.


  1. Wu, L. R. et al. Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling.  Comms.  (2022).
  2. Ciriello, G. et al. Emerging landscape of oncogenic signatures across human cancers. Genet. 45, 1127–1133 (2013).
  3. Frampton, G., Fichtenholtz, A., Otto, G. et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol 31, 1023–1031 (2013).


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