Wednesday, January 17, 2018

Gencove Review

Some of the apps Gencove offer
UPDATE: Gencove no longer accept uploads from other companies.

Gencove sells DNA tests for $59.99, but they also offer a free upload of your raw DNA data if you tested elsewhere. With the free upload, you get all the same options you do if you tested with them, namely an ethnicity report and matching with DNA relatives.

They also offer "apps", some from third parties. There is even a Promethease app for $10, though it would be cheaper and probably easier to just upload directly to Promethease (see a full review of Promethease here). There's also an app for GenePlaza, which was also previously reviewed here. Though the app is free, GenePlaza's reports each cost a small fee. Clicking on the GenePlaza app in Gencove merely takes you to GenePlaza's website. The other apps are free too, but they aren't particularly useful. They include:
  • Discover your microbiome - Bacteria and viruses that live in your mouth
  • My Genome - Info about your genomic data
  • Sleep - Are you a morning or evening person?
  • iobio.io - Compare your genome to ClinVar
  • YouGenomics India - Help improve genomics for South Asia
  • Gencove Mobile App - Compare results with friends on iOS or Android
  • Open Humans - Contribute to research and citizen science

When I tried Microbiome it simply said "Microbiome not available" with no explanation as to why, so that was totally useless.

My Genome is just that - it's where you find your raw DNA data. You can download your raw data, you can view which apps on Gencove you've given permission to access your data, and you can view and manage your consent to participate in research.

The Sleep app is interesting but the results claimed I'm a morning person, which I have never been. The app asks you a few questions about your sleep habits before showing your results and it did note "It seems that the genetic score and questionnaire results don’t match - an interesting outlier! That's probably because the genetics of sleep is not very well understood yet."

iobio
The iobio app loads your DNA to gene.iobio.io which is a little bit of a technical app that will tell you if you have any variants of certain medically related genes. For example, it includes a report on BRCA1 and BRCA2, which are genes associated with breast and ovarian cancer. Despite the technical looking nature of the site, it will tell you, in plain English, if you carry any variants of the genes included in the report or not. Hovering over each gene will pop up a brief summary of what it is associated it. Most of them are likely somewhat rare, since I had no variants for any of them. There are 40 in total: PTEN, BRCA1, BRCA2, TP53, STK11, MLH1, MSH2, MSH6, PMS2, APC, MUTYH, VHL, MEN1, RET, RB1, SDHD, SDHAF2, SDHC, SDHB, TSC1, TSC2, WT1, NF2, COL3A1, FBN1, TGFBR1, TGFBR2, SMAD3, ACTA2, MYH11, MYBPC3, MYH7, TNNT2, TNNI3, TPM1, MYL3, ACTC1, PRKAG2, GLA, MYL2, LMNA, RYR2, PKP2, DSP, DSC2, TMEM43, DSG2, KCNQ1, KCNH2, SCN5A, LDLR, APOB, PCSK9, RYR1, CACNA1S, ATP7B, BMPR1A, SMAD4, OTC. If you have reason to check on any of these and want a quick, free way to do this, this is a good option, but it can also be easily accessed independently of Gencove, just go to http://iobio.io, however, it's not very user friendly and I couldn't find a way to upload my data, so going through Gencove may actually be the better option.

YouGenomics India, recently renamed "Genavli Biotech", is a research project for South Asia, attempting to improve ethnicity reports for people with South Asian ancestry. Naturally, it wouldn't be useful for anyone who is not South Asian but if you are, you should look into this. As far as I can tell, Gencove's app simply links to the YouGenomics India website.

The Gencove Mobile App doesn't really offer anything that the website doesn't apart from some surveys which I presume are for research purposes. It allows your to see your ethnicity report and the unavailable microbiome report, and connect with or invite your friends. That's about it. 

The Open Humans app merely takes you to openhumans.org, which is an open research project. Gencove does not load your data there, so there's really no need to go through Gencove if you wish to participate in this project.

Gencove's populations for their ethnicity report
Most people will likely be most interested in the ethnicity report. There are 26 populations available, some of them are broad, large regions, while others only cover a small region. They include: Northern and Central Europe, Northern Italy, Northern British Isles, Southwestern Europe, Middle East, Eastern Mediterranean, Bengal, Central Africa, Eastern Africa, Northern Africa, Central Indian subcontinent, Southern Indian subcontinent, Oceania, Southeast Asia, Northeast Asia, Anatolia-Caucasus-Iranian Plateau, Central Asia, East Asia, North-central Asia, Northeast Europe, Scandinavia, Finland, Southern Africa, Western Africa, Ashkenazi Jewish, Americas. A map showing what these populations cover is shown left/above.

My personal results were not particular accurate, although I did note that if I added together all my results in populations probably associated with my Italian ancestry versus those from my Northwest European ancestry, the numbers were consistent with what most other companies say. Here are my Gencove results:

My Gencove ethnicity report
48% Northern and Central Europe
21% Northern Italy
15% Northern British Isles
7% Southwestern Europe
6% Middle East
3% Eastern Mediterranean

My Italian ancestry is southern, not northern, but if you add up the results for Northern Italy, Southwestern Europe, Middle East, and Eastern Mediterranean, you get 37%, which is very similar to the 36% from AncestryDNA and 38% from FTDNA. While my results in more specific regions may be all over the place across different companies, the divide between northern Europe and southern seems very distinct with me so when an ethnicity report is consistent with that, I know there's at least some reliability to it. 

Lastly, Gencove offer the "Relative Radar" which finds people you share DNA with. Unfortunately, there must not be very many testers/uploaders in their database because it found none for me so all I can say about it is that it seems to use a visual display, plotting relatives who share more DNA with you closer to your profile icon.

Conclusion: Since it's free, there's really no harm in checking out Gencove (unless you have concerns about research participation). Because some of their "apps" simply link to other sites, it looks like they offer more than they really do. The ethnicity report, sleep app, and iobio data were the only really interesting or useful options, but even with those, don't expect too much. I definitely wouldn't pay $59.99 to test with them, although the low price point in comparison with other testing companies may be appealing, you would get more out of your money by testing with AncestryDNA or 23andMe and then uploading to Gencove for free.

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