Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome.
BACKGROUND:
Demonstrating the presence of myelodysplastic syndrome (MDS)-specific molecular abnormalities can aid in diagnosis and patient management. We explored the potential of using peripheral blood (PB) cell-free DNA (cf-DNA) and next-generation sequencing (NGS).
MATERIALS AND METHODS:
We performed NGS on a panel of 14 target genes using total nucleic acid extracted from the plasma of 16 patients, all of whom had confirmed diagnoses for early MDS with blasts <5%. PB cellular DNA from the same patients was sequenced using conventional Sanger sequencing and NGS.
RESULTS:
Deep sequencing of the cf-DNA identified one or more mutated gene(s), confirming the diagnosis of MDS in all cases. Five samples (31%) showed abnormalities in cf-DNA by NGS that were not detected by Sanger sequencing on cellular PB DNA. NGS of PB cell DNA showed the same findings as those of cf-DNA in four of five patients but failed to show a mutation in the RUNX1 gene that was detected in one patient’s cf-DNA. Mutant allele frequency was significantly higher in cf-DNA compared with cellular DNA (p = 0.008).
CONCLUSION:
These data suggest that cf-DNA, when analyzed using NGS, is a reliable approach for detecting molecular abnormalities in MDS and should be used to determine if bone marrow aspiration and biopsy are necessary.
Published Online:14 Jul 2016 https://doi.org/10.1089/gtmb.2015.0278
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