Jo-Ann L Stanton1, Abishek Muralidhar2, Christy J Rand1, David J Saul2. 1. Department of Anatomy, University of Otago, PO Box 56, Dunedin 9054, New Zealand. 2. ZyGEM NZ Ltd, Waikato Innovation Park, Ruakura Road, Hamilton 3216, New Zealand.
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.
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.
Entities:
Keywords:
DNA extraction; Ion PGM; PDQeX; QIAGEN DNeasy; ZyGEM; bacterial DNA preparation; genome sequencing; whole-genome sequencing
Authors: Laura M Boykin; Peter Sseruwagi; Titus Alicai; Elijah Ateka; Ibrahim Umar Mohammed; Jo-Ann L Stanton; Charles Kayuki; Deogratius Mark; Tarcisius Fute; Joel Erasto; Hilda Bachwenkizi; Brenda Muga; Naomi Mumo; Jenniffer Mwangi; Phillip Abidrabo; Geoffrey Okao-Okuja; Geresemu Omuut; Jacinta Akol; Hellen B Apio; Francis Osingada; Monica A Kehoe; David Eccles; Anders Savill; Stephen Lamb; Tonny Kinene; Christopher B Rawle; Abishek Muralidhar; Kirsty Mayall; Fred Tairo; Joseph Ndunguru Journal: Genes (Basel) Date: 2019-08-21 Impact factor: 4.096