Effective DNA Extraction for Sequencing in Extremely Remote Settings: Pairing PDQeX with MinI ON and MinIT to Diagnose Cassava Mosaic Virus on East African Farms

摘要

We have successfully paired the PDQeX DNA purification technology, developed in New Zealand, with the Oxford Nanosystems MinION and MinIT mobile sequencing platform to produce an effective point-of-need diagnostic. The PDQeX system extracts DNA using a cocktail of thermophilic proteinases and cell wall degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This single-step closed system delivers purified DNA without sample cross contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output locally in real time obviating the need for high specification computer equipment and large datafile transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and set up.To evaluate this approach, we worked with subsistence cassava growers in three countries: Tanzania, Uganda and Kenya.