NuProbe Published Method for Designing Highly Multiplex PCR Primer Sets

April 19, 2022

Houston, April 19th / NuProbe, a global genomics and molecular diagnostics company, announces its recent publication in Nature Communications describing a massively multiplexed PCR primer design algorithm, named Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE). The SADDLE algorithm is applicable to both real-time quantitation PCR (qPCR) assays and to next generation sequencing (NGS) panels. Unlike other highly multiplexed PCR approaches, NuProbe’s SADDLE approach uses computational primer design to minimize primer-dimer formation, and thus does not require enzymatic primers and primer-dimer removal. The publication demonstrated proof-of-concept experimental results in oncology, but the same approach could in principle be applied to a wide variety of clinical genomics applications including in infectious diseases and hereditary diseases.

“Primer dimer formation can reduce the mapping rates of NGS panels, increasing their cost and reducing their sensitivity,” says Nina G. Xie, first author of the study. “By computationally designing highly multiplexed PCR primer sets unlikely to form primer dimers, SADDLE solves one of the major bottlenecks of PCR-based enrichment as an NGS library preparation method, and enables simplified workflows for targeted sequencing panels.”

Targeted sequencing and qPCR are alternative approaches widely used for detecting disease-related DNA mutations. Targeted sequencing provides a higher breadth of information, but requires higher costs and longer turnaround times, while qPCR is rapid and easy to implement but provides information only on a limited number of DNA markers (typically ≤6). SADDLE significantly improves both technology platforms.

“With SADDLE, we were able to design and validate a targeted NGS panel with dramatically reduced primer dimer fractions”, says Harry Shengxiang Ren, co-corresponding author of the study and Professor of Medical Oncology at Shanghai Pulmonary Hospital and Tongji University School of Medicine. “Furthermore, we were able to design and clinically validate a single-tube qPCR assay that detects 56 distinct gene fusions, something not previously possible.”

“We view qPCR and targeted NGS panels as equally important tools for precision medicine,” says David Zhang, Co-Founder and General Manager of NuProbe USA, and co-corresponding author of the research. “The former allows affordable and rapid testing, while the latter offers comprehensive genomic information that can be used to inform therapy. NuProbe is committed to developing and translating technologies to advance the gamut of molecular diagnostic approaches to improve human health.”

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.


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