Ever curious what happens to your sample once it arrives back at Darwin’s dogs?
There are many steps to the process before we are able to give you your data back. Right now some of the steps we are working towards will hopefully make for a more efficient and quicker process.
The first thing that happens is the return of your saliva kits. Every afternoon Brittney receives a bin of your returned kits from the mail room and scans the barcode on the box to bring up your dog’s record. We are currently working on generating an email that will alert you that we have received your kit and adds it to your member profile page. Then each kit is opened to make sure all the barcodes match on the paperwork and the swabs. The swabs are then transferred to a tube rack for storage until DNA extraction. This process can usually be done in about a day depending on the number of kits we receive back that day.
Our current process entails matching your dog’s sample up with an ongoing, funded project. This is the part that is most time consuming and out of our control. We are working hard to find funding from both public and private organizations to cover genetic analysis of all the dogs enrolled in Darwin’s Dogs, but this project grew much faster then we expected! In applying for funding it can take anywhere from one to two years from conception to being awarded the money. Once we have matched your dog up with a funded project, that is when the fun begins!
Another option, we are just starting to looking into is setting up an additional non-profit to allow people to pay the cost of DNA sequencing. This will allow owners the opportunity to bypass the time it takes to apply for and receive funding to sequence the samples. Once we iron out all the wrinkles we hope to have your data back to you within 2 or 3 months - if you choose to pay to have your sample sequenced instead of getting it sequenced for free. However, this is something we are just now starting to explore and aren’t sure of the time line or feasibility yet. We will definitely let everyone enrolled know if we are successful in setting up this option.
Once we have matched your sample to a funded project the next step is DNA extraction. Michele currently does all of the extractions by hand and is making her way through the 3220 samples we have received in so far (We are planning a separate post on the DNA extraction process later). This process takes anywhere from 3-4 hours to extract the DNA plus an overnight incubation step. This is just to extract 10 samples. So imagine all the time it takes to extract the thousands of samples we have received in!
We are hoping in the future to send these samples off to a company whose primary job is DNA extractions. This will automate the process a bit more. Since we are getting such an overwhelming response it is hard for one person to keep up with all those extractions! This will also mean that we will be able to send the saliva samples off for extraction immediately after Brittney has had a chance to process them. This will make the next step more efficient because instead of waiting for all of the samples to be matched then extracted we can move right into sequencing them once we have matched them to the appropriate project.
Currently, the existing sequencing technology we have for running the saliva samples covers 170,000 different places in your dog’s genome. While this works well for studying many physical traits such as eye color and ear shape studying behavior is far more complex. We are currently testing new technology from a company called Affymetrix that will cover over 650,000 spots in the genome, which should help give us enough data points to look at patterns of variation in DNA that might be associated with certain behaviors. So far we have genotyped 100 dogs using this new tool to make sure everything looks as it is intended to. We are also testing new DNA sequencing technology, from a company called Illumina, that looks at all 3 billion letters of DNA, and trying to figure out ways we can bring the cost down enough to make it a good option. The next step is to run 500 dogs spanning the continuum from calm to anxious and from greatest to least self-control. This type of analysis can take many months to ensure we are getting enough data from the new technology to be able to study something so complex like behavior.
To read more about the data analysis and how it is done Jesse McClure a post-doc in our lab has written a great article, which you can find here: How Do You Spell Behavior?
All this leads up to the question what will my dog's data look like?
We do plan on giving you all the information we have about your dog’s breed makeup and ancestry. We’ll even give you the raw genetic data itself if you are interested! And we also plan to keep you in the loop as we make new discoveries.
However, this is a true research project. As you can see from the process that we have explained above, science takes time, funding and testing of new technology. So please hang in there with us while we take this journey together and keep asking all those great science questions on the Forums!