Nanopore sequencing makes the analysis of copy number variations (CNVs) faster, cheaper, and simpler, according to a preprint paper from researchers at Dartmouth-Hitchcock Medical Center (DHMC).
CNVs activate oncogenes and inactivate tumor suppressor genes. These actions drive the development and progression of cancers, making copy number analysis an important part of tumor grading and diagnosis. However, the current reliance on nucleotide hybridization and next-generation sequencing means CNV analysis is limited to high-complexity centralized laboratories and takes at least several days.
A faster, cheaper, and simpler approach to CNV analysis could enhance clinical decision-making, optimize surgical planning, and enable identification of potential molecular therapies within surgical time frames. Researchers at DHMC identified nanopore sequencing as a way to improve CNV analysis.
In the preprint paper, the researchers describe the use of Oxford Nanopore Technologies’ MinION device in CNV analysis. The device provides real-time interpretation of long-read nucleotide sequences. To apply the technology to CNV detection, the researchers randomly analyzed linked DNA fragments. The approach enabled the identification of multiple mappable DNA fragments in one sequencing read.
“The low cost per sample, a mere $125 USD, and the ease of setting up the infrastructure with a budget of $6,000-8,000 USD for MinION and $14,000-16,000 USD for PromethION make it an economical option for clinical applications,” the team wrote. “The unmatched turnaround time of 120-140 minutes further positions our method as a robust and invaluable tool for widespread implementation in clinical settings.”
DHMC’s team studied 26 malignant brain tumors. Nanopore analysis detected the same alterations and amplifications as clinically validated next generation sequencing and chromosomal microarray results. The method enables concurrent tumor methylation classification without additional tissue preparation. Promoter hypomethylation was seen in all detected amplified oncogenes.
A patent application for the approach to CNV analysis, named irreversible Sticking Compatible Overhang to Reconstruct DNA (iSCORED), is pending. The researchers see accelerated CNV analysis as a way to cut the time it takes to identify patients who are suitable for treatment with molecular targeted drugs.