review on 13 April 2018
by Rebecca Fishwick
At a Glance
Gencove provided a fun and interesting platform to reuse my genetic data and gather more information from it. The range of web apps offered was not very extensive, but those that were available were free and for the purposes of research, so I hope to see them continue to grow in accuracy and comprehensiveness.
Gencove allowed me to upload my data from a range of sources, and also gave the option to purchase one of their DNA testing kits, for a competitively low price. One of the downsides to this was that not all of the web apps and features were available to me, since I chose to upload my data. Still, for a free service, Gencove’s marketplace provides several interesting options for anyone looking to reuse their data.
Gencove was founded in 2017, by three scientists at the New York Genome Center: Joe Pickrell, Kaja Wasik and Tomaz Berisa. The company aims to make genome sequencing accessible and interpretable. They plan to do this by building inexpensive and enjoyable genomic applications, using the data generated to find the genetic variants that really matter, and build the next generation of genetic tests based on these findings, while continuously growing their knowledge and improving.
The Gencove site was bright, dynamic, and interesting. There was a demo of the interactive map included in their ‘Explore Your Ancestry’ web app, showing which regions they covered (which was most of the globe!). Clicking on each area showed me which reference populations were included for that region. For instance, when I clicked on “East Asia”, it zoomed in on China, Mongolia, the Koreas, and the west coast of Japan. The reference populations for this area were Han, Miao, Naxi, She, Tujia, and Yi.
Scrolling down the page, I was given a preview of which web apps and research projects I would be able to access after signing up. Most of these were developed by Gencove, but the ‘How Happy Are You?’ web app (for exploring the genetics of happiness) was developed by the USC Behavioral and Health Genomics Center. I also found out that I could download the Gencove marketplace app on my phone, or log into it via an internet browser. I chose the latter option.
The ‘How does it work?’ section gave me a breakdown of the three stages of using Gencove: inputting DNA data (either by uploading my genetic information, or ordering a kit), connecting with the free Gencove web apps or external web apps and research projects, tracking my activity and securely storing my DNA files.
At the bottom of the page, I found an FAQs section. Here, I discovered that a DNA upload would typically be processed within around 30 minutes, while results from a DNA collection kit would take six to ten weeks from when the sample was returned to Gencove. They described the type of sequencing they used as “genotype imputation” which “fills in” blanks where genetic variants hadn’t “been directly measured”. I’d never heard of this and it sounded a bit like they would guess some of my data, but a quick scan of the linked Wikipedia article reassured me that this was a legitimate method.
I also learnt that I would be able to access my raw data online. They didn’t ship DNA collection kits outside the United States, so my only option was to upload my genetic data.
As previously mentioned, the site gave me a choice of uploading my genetic data for free from another source or purchasing a DNA testing kit from them, which was very inexpensive compared to other providers (though not available in the UK). Since I’d already had my DNA analysed by 23andMe, I chose to upload this data, but was informed that Gencove accepted data “from all major genomics providers”.
Once I had created my free account, I saw I had access to eleven different web apps, including a ‘Relative Radar’ for finding genetic relatives, ‘My Genome’ for exploring my genomic data, and an ‘Open Humans’ web app where I could contribute my genetic data to research and citizen science. I was most interested in the ‘How Happy Are You?’ web app, which would predict my predisposition to happiness based on my genetics.
After creating my account, I was sent an email asking me to verify it, which I did before uploading my data.
Clicking on ‘Upload Data’, I was taken to a page about Gencove research. This was optional, and I could skip to the bottom if I wasn’t interested in taking part.
Looking through the ‘Gencove Consent Document’, I found that the study was run by Gencove, Inc., and aimed to identify genetic variants that may influence personal characteristics and disease risk. In order to participate in the study, I would have to use and return one of Gencove’s saliva collection kits. As I couldn’t order the kit from the UK, I wasn’t able to do this. Had I participated in the study, then my genomic data would be stored indefinitely, as it would be used for any new studies that may arise. However, I would be able to withdraw at any time. I also read that any genetic data would be identified by a barcode (rather than by name), and any personal identifiers or contact information would not be shared with third parties, except if required by law. Anyone consenting to the study would have to be older than 18.
The next page allowed me to upload my genetic data directly from my computer. There was a ‘Need help?’ section below, with screenshots showing me how I could download my information from several different providers.
I uploaded the .zip file of my genetic information from 23andMe, which took about fifteen minutes to process. I clicked a button to go back to the homepage, where I could view a progress bar to see long the upload was taking (shown below).
I was sent an email once my data had finished processing, and was immediately able to access the web apps offered by Gencove and their associates. I chose ‘How Happy Are You?’ by USC Behavioral and Health Genomics Center.
Results Section: ‘How Happy Are You?’ – Preliminaries to Happiness
Clicking on ‘How Happy Are You?’ took me to a page saying I was authorising USC Behavioral and Health Genomics Center to access the genetic data stored in my Gencove account. There was also a message from Gencove telling me that they had filled in gaps in my genome using ‘imputation’, with a link to find out more. It was made clear that the data in my Gencove account could not be used for medical purposes, as it may not be entirely accurate. Soon after clicking ‘Continue’, an email from Gencove popped up, telling me I had successfully joined ‘How Happy are You?’ – a useful security feature.
The next page broke down the steps of finding out just how genetically happy I am. It wanted me to answer a few questions for research purposes, after which I could see how my answers compared to the general population (which I thought would be quite interesting!), and lastly I would learn what my genetics predicted about my happiness.
In order to use the web app, had to consent to participate in their research study, the details of which were outlined in a Consent form. The purpose of this study was to help the USC Behavioral and Health Genomics Center learn about genetic influences on behavioural traits, such as subjective well-being, and to learn through user responses how people respond to their genetic information. There was a promise that my information would be confidential, and that I could opt out of the study at any time.
Results Section: ‘How Happy Are You?’ Web App
Next, I answered a series of thirteen questions about my personal happiness, and a few general ones about myself (age, marital status, etc.).
After submitting my answers, I was taken to my results. According to the answers I gave, I was ‘moderately happy’, falling into the same range as about 50% of the population, according to their graph (shown below).
Interestingly, according to my genetic score, I fell into the lowest third for happiness, with low confidence. I found this rather surprising, though of course – as had already been stated – environmental and lifestyle factors also play significant roles in overall happiness. Looking at another graph, I saw that while I had been placed in the lowest third, I was in its upper echelons.
I decided to explore the other web apps and features offered by Gencove and their partners. Clicking on ‘Explore Your Ancestry’ took me to an interactive map, which I could open in full screen on another tab. This map was shaded to show where my ancestors came from (shown below).
My ancestral mix was broken down into percentages. It was unsurprising to see that my ancestors came predominantly from Northern and Central Europe, accounting for 87% of my DNA. I could click on the highlighted areas to zoom in and see which populations came from there.
Though visually impressive, the information the map provided was rather vague. ‘Northern and Central Europe’ covered Belgium, the Netherlands, Switzerland, the Czech Republic (labelled “Czechia”) and half of France, among others.
There was also a ‘Friends’ section, showing whom I’d connected with on Gencove. To make me feel less lonely, I had been given two default friends: Genbot, and “Chuck” Darwin.
Exploring the Gencove marketplace again, I clicked on ‘Microbiome’, which would tell me about the bacteria and viruses living in my mouth. However, this was unavailable to me as I had not sent in a saliva kit to Gencove. There were also the Gencove ‘Sleep’ web app (which was in a similar format to ‘How Happy Are You?’) and web apps for finding relatives or connecting with friends.
I also found a link to download my raw genetic data (under ‘My Genome’). Curiously, there was a link to ‘GenePlaza’, which was another marketplace, and would require me to create another account and upload my genetic data from 23andMe. There were also links that allowed me to share my genetic data with ‘Open Humans’ and ‘YouGenomics India’. It seemed to me that all these features were rather diverse to be included under the broad banner of ‘Apps’.
Looking at ‘My Genome’, I found I could also see which web apps had access to my data, and could choose to disconnect them if I wished (shown below).
Gencove provided a fun and interesting platform to reuse my genetic data and gather more information from it. As yet, the range of web apps offered was not very extensive, but they were free and for the purposes of research, and so I hope to see them continue to grow in accuracy and comprehensiveness.
Gencove allowed me to upload my data from a range of sources, and also gave the option to purchase one of their DNA testing kits, for a competitively low price. One of the downsides to this was that not all of the web apps and features were available to me, since I chose to upload my data. Still, for a free service, Gencove’s marketplace made an interesting option for anyone looking to reuse their data.