Log in
My story with 23andmeMy story with diagnosed diseasesLatest DiscussionOpen CurationCuration Log

Frequently Asked Questions

Updated on 6/26/14

Why are we doing this project?

It started as curiosity when we got 23andme results. One GeneKnot member had a lot of questions about the results, but felt very limited to handle 23andme results. Although 23andme is a great resource for DTC services, we need more community efforts to understand genetic results with lifestyles and physical information.

Our goal is to build the community website where an individual can have more data ownership and transparent curation steps. We started this self-funded project in our spare time after work. We plan to maintain and improve this site for community resources.

Is there any example suggesting that GeneKnot is useful?

(As of 10/30/15) Promising cases for separation between diagnosed and undiagnosed users include Atrial fibrillation, Type 2 diabetes and Crohn's disease. More descriptions for Atrial fibrillation are available here: My 23andMe trio data: My family's risk? and 23andMe vs. GeneKnot: Atrial fibrillation. These are very preliminary observations and we need more data from users with diagnosed diseases. For other diseases, there are not enough phenotypes we can compare. If GeneKnot has more reported diseases, we will provide more examples.

How are the results for Disease Risk generated?

Disease risk is from simple search results from GWASCATALOG of National Genome Research Institute. Many of these results are from taxpayer-funded studies for a few decades. The community deserves using these resources in a transparent manner. All we did was to select representative diseases from GWASCATALOG and show odds ratios with less than 10E-5 in p-values (We found this threshold is reasonable to include most of GWASCATALOG while excluding non-informative records. This may change in future and will be listed in Curation log). GWASCATALOG is already curated to some extent. No curation is perfect. We hope that we can further curate the details based on community suggestions.

How are the results for GeneKnot generated?

To calculate genetic distances in a particular disease, we use the numbers of (high or low) risk alleles that are known to be associated with a disease. For example if you have two Ts in rs2294008 which is known to be related to bladder cancer, 2 will be assigned. The rationale behind this approach is that the users with more similar subsets will have more similar genetic risk or disease progression. Risk alleles are also from GWASCATALOG. Based on best separation between diagnosed and undiagnosed users, or among races, these SNPs are further optimized. In the backend process we use python and rpy2 to use multidimensional scaling. "Multidimensional scaling (MDS) is a means of visualizing the level of similarity of individual cases of a dataset "-cited from wiki. Currently the minimal number of SNPs for MDS is five. We'd like to explore other computational techniques in future.

What about data privacy?

Due to the nature of data sharing, you need to agree that your data will be visible to other users. As of 2/1/2015, your relative genetic distances are visible to other users, but your SNPs are not visible for data privacy. In addition, you don't need to reveal who you are by using user id that is not related to your personal information. This is what we recommend. Your disease risk (odds ratios) will not be visible to other users (Disease Risk Menu). The analyzed genetic distances will be visible to other users (GeneKnot Menu). The uploaded user information (e.g. ages, diagnosed diseases and so on) will be visible by other users to find similar people (in Profile). GeneKnot.com does not hold the responsibility for loss of the uploaded genome file. Please make sure that you keep a copy of your data. This policy is listed in terms and conditions when you register. The uploaded raw file will be used only when it needs to be updated in this website. You can delete your raw data anytime by sending us an email. We don't keep any copy of your data file if you don't want to keep it in GeneKnot.

Why do you emphasize ages?

Why do you do DTC tests regarding disease risk? From now, you want to know when you would develop any diseases. It sounds too ideal but at least that's what we're aiming for. If we have enough for similar genetic risk, physical information and lifestyles, it may be possible to predict disease progression. Please understand that current population studies do not cover all races, physical information, and lifestyles. Please use this site at your own risk and talk with professionals for further action.

How can you download DTC data?

For 23andme, you can download from here.

Why unlogged users can see the data?

The demo data for disease risk is accessible without login. As of 9/22/13, login is required to see the results in a GeneKnot menu for data privacy.

Why do I get an error during registration?

The current plugin seems to have a bug. We're told that if you switch the browser (e.g. Chrome to Firefox), it'd be fine. If you still have a problem, please contact us by email. We'll make a new account.

If you have any questions, please let us know (contact (at) geneknot (dot) com)

Copyright (C) 2013-2015 by GeneKnot