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UPDATE:  Genos was bought out by another company…  Good reminder to read through privacy policies!  The company that bought them now owns customer’s data but said they would abide by the Genos privacy policy.  I did ask for my data to be deleted and account to be removed out of an abundance of caution.

————

Genos is a fairly new company in the direct-to-consumer genetic sequencing market.  They offer sequencing of the whole exome, instead of just the specific locations that are covered by services such as 23andMe or AncestryDNA. Moreover, they are bringing in research study partners that then will pay their clients for participating in the studies.  It is definitely an interesting business model and one that may end up being a game changer for the genetic sequencing market.

I was intrigued enough to go ahead and try it out and will share what I have learned from the experience. (Yep – this was my birthday present this year!)

First off, sending off the saliva sample was similar to the way 23andMe does it — spit in a tube, register online, and send it off.  Nice and simple process.  The Genos website was easy to use as far as ordering and registering the sample.  The wait time was a little over two months to get the results back, which is a bit longer than 23andMe, but Genos is brand new and was still in beta when I ordered.

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Genos Website – www.genos.co

When my data finally came in, I was eager to dig in and geek out with it. The Genos website offers a variant viewer that compares my results with ClinVar, which is an NIH-funded database of genetic variants that have been submitted by various sources.  The database marks the variants as pathogenic, benign, or somewhere in between, and it is a good source of information about rare genetic diseases.

While the Genos variant viewer was interesting, there seems to be a lot of information submitted to ClinVar showing a variant to be both benign and pathogenic. And for me, personally, it didn’t show me a lot that I didn’t already know from 23andMe testing. I would imagine that it may be useful for some people in terms of carrying rare genetic diseases.  Keep in mind, though, that Genos is only sequencing the exome.

So what is an exome?  Of the 3 billion plus nucleotide base pairs in our DNA (the A, C, G, and T’s), only a small portion actually make up the coding part of genes.  On each of our 23 pairs of chromosomes, there are sequences that code for genes and then sections that are called non-coding, which have to do RNAs, telomeres, regulatory elements, etc.  Basically, in DNA, genes code for proteins which are made up of amino acids. Most genes have portions of the DNA sequences that code for amino acids (the exons) and then portions that don’t code for part of the protein (introns).  The whole exome is then the sum of all the coding parts of the gene.  While a lot of the serious, rare genetic diseases are a result of variations in the exome, the non-coding parts of our DNA not sequenced by Genos also play a big role in our health as well.

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Genos Website

Genos offers a download of your data as a VCF file.  This is where it got complicated for me.  I was under the impression from their website copy that I would be getting 50 million rows of data, and I thought I would need to figure out how to dig through that big of a file with lots of rsIDs and my genotype.  What I downloaded was about 300,000 rows of data with just the HGSV nomenclature and no rsID’s included. Hmmm….  After several emails back and forth with their customer support and bioinformatics department, I finally got a bit of a grasp on what was contained in the VCF file.  Basically, it is everything in my exome that is different from the reference data.  This doesn’t mean that it is everything that is heterozygous or homozygous for the minor allele (a bad assumption on my part), but it is just everything that is different from a reference file.  So I’m going to have to spend some time this summer learning more about bioinformatics and VCF file types in order to get anything out of my whole exome file.  Definitely not an easy way to unlock my curiosity.

The other file that Genos offers for download is a Promethease formatted file.  This allows you to use Promethease (for $5) to compare all of your data against the SNPedia database.  The file is formatted similarly to the raw data file you can download from 23andMe.  Again, I personally learned a lot more from my 23andMe results than I did from my Genos results in Promethease, but your mileage may vary on this as well.

Since I have all my 23andMe data imported into an Excel spreadsheet, I imported in my Genos “Promethease” file to compare the two.  This is where it got interesting for me!

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Genos website

The Genos genotype file (Promethease file) had about 43,000 rsIDs in it, and I compared those to the 600,000+ rsIDs from 23andMe. A few formatting tweaks, merging of the data and I was on my way to seeing how closely the data matched.  Out of the 600,000 data points from 23andMe and 43,000 data points from Genos, only 4,433 were common to both.  (Granted, 23andMe uses “i” numbers instead of rsID’s sometimes, so there could be more in common between the two files than what I could easily count.)  Of those 4433 rsID’s in common, 25 were different between

Of those 4433 rsID’s in common, 25 were different between Genos and 23andMe which is about a 0.5% error/difference rate.  I have my parents’, my husband’s, and my children’s 23andMe data (in a nice spreadsheet, of course), and looking at the inheritance pattern there were 2 spots where 23andMe is probably wrong on my variants (and Genos is probably right).  There were several more spots where Genos was probably wrong and some heterozygous calls that I couldn’t determine which was correct.

I emailed Genos customer support about the differences between the files, and the head of the bioinformatics department pointed me towards a study showing the accuracy of the sequencing.  A 0.5% error rate was actually about average…  This was eye-opening to me.  Even though I knew that there was a possibility for errors, realizing that 1 out of every 200 could be wrong drives home the point that no one should make major health decisions based on this data.

To sum it all up…

  • I like the goals of Genos and that they recognize that customers should be compensated for participating in research studies.  This is a big contrast to 23andMe asking customers to give away information for free.
  • I personally didn’t find the information received from Genos, though, to be worth the price.   The variant viewer on the Genos website was somewhat interesting, but the information out of ClinVar is too narrow in its scope.  It would be great to have something like the gene lookup function that 23andMe has to really be able to know what your genotype is for a specific rsID without the need to conquer the VCF file format.
  • Keeping in mind that Genos is new to the game, things may change on their website and with what they offer to their customers.  Do check with them if you have questions.  Their customer support response sometimes took a day or two, but they were good at patiently answering my many questions.

 

Categories: Genetics

8 Comments

Elaine · June 8, 2017 at 7:53 pm

Interesting article describing your experience with Genos. Did you know that they have recently been acquired by another company and are no longer providing sequencing services?

    genelife · June 9, 2017 at 1:32 pm

    Yes, I knew that Genos had been bought out — I need to update this post!
    It is a good reminder as to the issues surrounding genetic data privacy as well. I contacted Genos at the time they were bought out and had them remove my account and data, even though their emails did say that the new company would honor their privacy policy.

jlib · September 20, 2017 at 4:32 am

Genos is offering their consumer sequencing services again but the price is $50 more than the previous beta price.

fabio · January 14, 2018 at 1:41 pm

Have you tried SelfDecode.com or livewello.com to interpret your raw data?
If so, what are your thoughts on those services?

    Debbie Moon · January 14, 2018 at 6:02 pm

    Hi,
    I’ve checked out both but am not a current user of either of them. Selfdecode seems like a neat concept, but most of it is information I already have here. I also came across a couple of errors in the information there — not trying to disparage that site since it is a lot of information and errors are totally understandable (I’ve caught errors on my own site as well).
    Livewello.com has a way for you to upload your genome and then see what other people have written about different snps. The community aspect is interesting, but I tend to go with research studies on topics rather than notes from people that I don’t know. It is a good place, though, to find a naturopath or health coach, if you are looking for someone like that.
    Promethease.com is another site you might want to look at. It takes your 23andMe data and compares it to everything in Snpedia.com. I like the promethease privacy policy and how it spells out exactly what they do with your data, when it is deleted from their server, etc. The drawback to promethease is that it can be a little confusing tyring to figure out what is important and what is now.
    Thanks for reading and commenting!
    Debbie

fabio · January 15, 2018 at 10:05 am

Hi Debbie,

Yes I have used Promethease.com. Recently they revamped their online website and you can browse everything online. Pretty cool. They offered a free upgrade to old customers recently. I really like selfdecode.com because it provides a comprehensive list of supplements to try (and to avoid) for most popular SNP mutations based on research papers. What I do not like is the subscription model which could be quite expensive in the long run. Livewello provides you the opportunity to create your own SNPs templates and many links to the major sources for each SNP. I do not bother to check what other people write because you do not know who is behind the research. I prefer to do the research myself. Usually my approach is to start with malacards.org, search the illness I have (in my case Generalized Anxiety Disorder and chronic stress) and search for the genes and SNPs that have the highest association with the ilness. Nutrahacker gave me also some good hints. The problem with Nutrahacker is that it does not provide any reference to peer-reviewed publications for their claims and recommendations.
My next step is to try genos which should be much more comprehensive than 23andme.

Linda · May 17, 2018 at 10:22 am

So glad to find your discussion. Like you I ignore most anything I can’t back up with published research. I will usually start with pubmed and then choose “all databases” as a jumping off point. Malacards, genecards, OMIM all useful. Have had some insights tinkering with both http://www.ctdbase.org as well as the https://www.proteinatlas.org/ for tissue expression and another favorite nextprot for verifying enzyme co-factors when trying to optimize enzyme-substrate when the “connection” is less than optimal [think MTHFR C677T that tends to drop the cofactor Riboflavin 5 Phosphate so I supply more of this B2 which helps-when it’s dropped there’s more hanging around to “pick up”]

Would love some advice on the following: I have the option of receiving a VCF file from my child’s exome sequencing done at a major university. I’m trying to choose a method or suite of tools that would allow me to go from this data to individual SNPs. Sounds like you are several months ahead of me. Would you be willing to share what you’ve found?The university has offered to supply the data in one of 3 formats. We have tried 3 times to submit my child’s sample to 23andme but each time it’s been rejected for not having enough DNA in the sample. Hence my attempts to translate the exome sequencing in a way that gives me the information I need on individual SNPs. Most pressing is the need to see TCN1 rs526934, TCN2 rs1801198. I am a motivated tinkerer but unsure of whether this is possible without software other than excel.

Very gratefully your,
Dedicated Parent

    Debbie Moon · May 17, 2018 at 12:34 pm

    Hi Linda,
    The VCF file is going to be a large, text-based file. It should be too large to import into Excel.
    If the VCF file has the rs numbers already in it, finding the two TCN snps may be as easy as just searching the file for the rs id. Atom (www.atom.io) is an open source text editor that should be able to open the vcf file.
    For a more a more powerful (and confusing) vcf tool, check out the Broad Institute’s Integrative Genomics Viewer – https://software.broadinstitute.org/software/igv/viewing_vcf_files.
    Good luck on getting all of this figured out! No greater motivation than helping out your kids :-) Once you get the vitamins and minerals (cofactors) dialed in, I suggest also looking into the role that our circadian rhythm plays in so many issues.
    Debbie

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