Researchers Report on Use of Nanopore Technology to Detect AML Biomarkers
Nanopore technology has shown to be effective in helping to quickly detect acute myeloid leukemia (AML) predictive biomarkers for prognostic stratification, according to a new study published in Genes.
Currently, next-generation sequencing (NGS) is used for gene detection, however, according to study authors, that method is time consuming (up to 7 days) and costly. Timing is of the essence in AML predictive biomarker detection and researchers state that nanopore technology is a scalable, faster, and more cost-effective technology.
The study included 22 patients with AML. At diagnosis, molecular evaluations were performed for all patients. Researches selected 5 patients who had a complex karyotype to increase the chances of finding cases with the TP53 gene mutation. Nanopore-based assay was used for rapid (24 h) sequencing of 6 genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2).
“Through the NGS workflow optimization and innovative custom bioinformatics pipeline, the platform allows the analysis of selected genes useful for diagnosis and treatment decisions in hematologic malignancies within 48 [hours] of specimen collection," researchers wrote. “We propose a workflow that can potentially enable laboratories equipped with only basic molecular biology techniques to perform detailed targeted gene sequencing analysis in AML patients, shortening TAT and reducing costs (minimal IT infrastructure for sequencing and data analysis.”
Researchers say there are pros and cons to both NGS and nanopore technology. Although nanopore-based technology is still in its developmental phases, there have been great improvements in performance. NGS, while extremely powerful, generates short read, which may lead to misassembles and gaps. Large structural variations are also harder to detect using short reads.
Researchers say that the scalability of the technology is one of the strengths of nanopore testing, as well as being highly cost-effective. Processing the sample costs around $200.
Cumbo C, Francesco Minervini C, Orsini P, et al. Nanopore targeted sequencing for rapid gene mutations detection in acute myeloid leukemia [published online December 9, 2019]. Genes. doi:10.3390/genes10121026.