From Sanger to Oxford Nanopore MinION Technology: The Impact of Third-Generation Sequencing on Genetic Hematological Diagnosis

TL;DR

This study compares Sanger sequencing with MinION technology for detecting genetic variants in blood cancers, finding that MinION is nearly as accurate but much faster.

Contribution

The study demonstrates that MinION technology can replace Sanger sequencing in hematological diagnostics with high accuracy and faster turnaround times.

Findings

MinION achieved 99.43% concordance with Sanger sequencing in variant detection.

MinION offers faster diagnostic results within 24 hours compared to traditional methods.

The technology is suitable for diagnosing myeloproliferative neoplasms and leukemias.

Abstract

With the aim of advancing and innovating improvements in genetic diagnosis, this work aims to compare traditional Sanger sequencing with MinION technology for detecting variants in short fragments. The routine use of this third-generation technology is expected to have a tremendous positive impact on improving the turnaround time (TAT), among other factors, directly contributing to improvements in patients’ health.

Background: Sanger sequencing remains the gold standard for characterizing genetic variants in short DNA fragments (<700 bp). However, the increasing demand for short TATs and high sensitivities in variant detection, particularly in oncohematology, is driving the need for more efficient methods. Next-generation sequencing (NGS) has improved sensitivity and allows for the simultaneous analysis of multiple genes, but it is still costly and time-consuming. Consequently, Sanger sequencing continues to be widely used. In this study, we have compared Sanger sequencing with Oxford Nanopore technology (ONT), which offers enhanced sensitivity and faster sequencing, delivering diagnostic results within 24 h. Methods: This study involves 164 samples (for a total of 174 analyzed regions of interest) previously characterized using either Sanger sequencing or a next-generation sequencing (NGS) panel, categorized by their genetic alterations. Validation was conducted on 15 genes crucial for the diagnosis, prognosis, or identification of drug resistance in myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). The primary objective was to assess whether MinION could identify the same variants previously detected in these patients. Results and Conclusions: With a 99.43% concordance observed in our comparison, our results support the implementation of MinION technology in routine variant detection in MPN, MDS, AML, and CML cases due to its significant advantages over Sanger sequencing.

Figures