Background

Our goal is to create an at-home genetic testing system which can be used by dairy farmers to perform genetic testing on their animals. This ability to conduct at-home genetic tests would allow farmers to make breeding decisions based on the genetic make-up of their animals, which would help them improve productivity, and therefore, profits. For this system to work, we have worked to develop procedures and equipment that are easy to use and cost effective.

Figure 1: Summary of the workflow for the SNflaPs genetic testing system. Genomic DNA samples from dairy cattle will be extracted using a cellulose paper dipstick. The isothermal amplification technique RPA will then be employed to amplify target gene fragments. We also created positive control DNAs and a heat block system for use with this system. Polymorphisms are then detected using the Flappase assay and fluorescently tagged oligos, cleavage of which is detected using a Raspberry Pi

Obtaining and extracting DNA samples

In our system, a farmer can obtain a DNA sample from the animal they wish to test and perform a simple cost-effective DNA extraction. We developed a protocol for isolating gDNA from hair samples taken from cows. Hair samples are easy to obtain even for those with minimal animal experience. As proof of concept, team members Jazmine and Louise visited the Tauzel family farm, and collected both hair and buccal swabs from cows to test our DNA extraction procedure. We then tested the simple, cellulose dipstick-based DNA extraction procedure on hair samples from two cows. We achieved excellent DNA concentration and purities from one of the samples, indicating that the procedure is effective.

For more information about this work, please see the sample extraction section of our wiki.

Creating simple, cost-effective devises for use with our system

Our genetic testing system will require a mechanism for incubating RPA and Flappase reactions at a stable and precise temperature. This device also must be simple to build and use, be reliable and be cost effective. To achieve this, we designed a simple heat block device. This device was made out of a significant number of recycled or commonly available parts, and is simple to construct. We performed testing on this device and demonstrated that the device consistently heats, holds temperature, and cools down, though several iterations of the design. While the device does not function perfectly, it does serve as a proof of concept that a device that meets our specifications can be achieved, and can be used with our system.

This heating device would also be used to maintain a constant temperature for conducting the Flappase-based detection of polymorphisms within the amplified DNA targets. More information about the heat block device can be found here.