Rapid extraction of DNA suitable for NGS workflows from bacterial cultures using the PDQeX

BioTechniques
Jo-Ann L StantonDavid J Saul

Abstract

Background: PDQeX is a novel, single-step DNA extraction method that purifies nucleic acid from sample in under 30 min. Materials & Methods: Six bacterial suspensions from species with different cell morphologies and growth optima were made. DNA from half the suspension was purified using PDQeX and the other half using a conventional column purification method. Sequencing and analyses using Ion PGM were performed, blinded to extraction method and species. Results: Genomes extracted with either method sequenced successfully. No significant sequence distribution biases were evident between PDQeX and column purification. Surveyed community preference suggested comparable performance between the two extraction methods. Conclusion: DNA prepared using the PDQeX performs as well for whole-genome sequencing as DNA purified using a conventional method, albeit much more rapidly.

References

Mar 31, 2012·Forensic Science International. Genetics·Jenny A LounsburyJames P Landers
Jul 11, 2018·Forensic Science International. Genetics·Amy S HolmesSheree Hughes-Stamm

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Methods Mentioned

BETA
PCR
electrophoresis
Assay
DNA assay
chips

Software Mentioned

Ion Torrent
Ion PGM
MEGAN
in
Geneious
FastQC
BLAST
BLAST +
Stata

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