NuProbe Technology Enables Low-Frequency DNA Variant Detection using Low-depth Sequencing
HOUSTON, May 3, 2021 /PRNewswire/ -- NuProbe, a genomics and molecular diagnostics company specialized in ultrasensitive sequencing assays, announced research demonstrating the ability to detect single nucleotide variants (SNVs) in DNA with a variant allele frequency (VAF) of ≤0.02% using a sequencing depth of only 250x. The findings, published today in Nature Biomedical Engineering, are the latest research involving the blocker displacement amplification (BDA) technology, a novel PCR-based enrichment method that enables the selective amplification of low abundant sequence variants (SNVs and indels) in a background of wildtype DNA.
While next-generation sequencing (NGS) is one of the most powerful methods available for highly multiplexed characterization of DNA, detecting SNVs with 0.1% VAF is expensive because the DNA needs to be sequenced to 60,000x depth. This can cause the sequencing cost per-sample to be more than $1000. Data from the study shows that multiplex blocker displacement amplification (mBDA), a library preparation method exclusively licensed and developed by NuProbe, allows for NGS-based detection and quantitation of DNA variants at <0.1% VAF using only 250x sequencing depth. This approach represents a potential sequencing cost saving of up to 99.5%.
"Although NGS methods for low VAF mutation sequencing have been extensively researched, to my knowledge, this is the first instance of a scalable allele enrichment approach to allow low-depth NGS analysis of low VAF mutations in a greater than 10-plex format," said Dr. Abhijit Patel, Associate Professor of Radiation Oncology at Yale, co-author of the study, and a member of the Scientific Advisory Board at NuProbe.
In addition to decreasing the time and cost per sample, mBDA technology uniquely allows liquid biopsies to be performed on benchtop sequencing instruments including Illumina MiSeq and MiniSeq. The reduced sequencing reads required by mBDA also significantly reduces the bioinformatics analysis time and data storage.
"These findings support the use of mBDA for decentralized NGS testing of clinical samples, particularly for low-VAF somatic mutations. Using the mBDA technology, we can monitor the DNA profile in cancer patients to not only watch for changes in existing mutations, but also identify new resistance variants in real time," said Dr. Ping Song, lead author of the study, Senior Research Scientist at Rice University, and a Senior Scientific Consultant at NuProbe. "By accelerating the adoption of precision medicine, we hope to produce improvements in cancer patient outcomes."
"NuProbe's recently released VarMap Pan-Cancer NGS panel builds on the mBDA technology to provide affordable, accessible, and accurate reagents for performing liquid biopsy NGS analysis," said Dr. David Zhang, senior author on the study, Associate Professor of Bioengineering at Rice University, and co-founder of NuProbe. "Since the submission of our initial mBDA research for publication, we have further scaled up the technology in both breadth and depth. Additionally, our NGS panels have now been validated on clinical samples using a variety of sequencing platforms including those from Illumina, Ion Torrent, and Oxford Nanopore."
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