Review of Genos – Whole Exome Sequencing

Screen Shot 2017-03-13 at 3.40.18 PM

UPDA/TE:  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.

Screen Shot 2017-03-13 at 3.40.00 PM
Genos Website –

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.

Screen Shot 2017-03-13 at 3.39.42 PM
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!

Screen Shot 2017-03-13 at 3.39.32 PM
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.


Wishing that you had an easy way to know which Genetic Lifehacks articles apply to you? Get a Genetic Lifehacks Ultimate Cheat Sheet that matches your data to all of the articles available.

Genetic Lifehacks Weekly Update

* indicates required

18 Comments on “Review of Genos – Whole Exome Sequencing

  1. 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?

    • 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.

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

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

    • 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). 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. is another site you might want to look at. It takes your 23andMe data and compares it to everything in 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!

  4. Hi Debbie,

    Yes I have used 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 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, 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.

  5. 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 as well as the 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

    • 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 ( 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 –
      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.

    • has a vcf data viewer and tools to convert from any file type to any other file type. Since having my bam and vcf file from Dante Labs I have been using it quite often. They are reasonably priced in my opinion.

        • Thanks for posting that – but if anyone is planning to use, I suggest double-checking with them on the Genos file format before uploading data. The VCF and BAM files from Genos (at least when I did the test) does not contain the rs id numbers and seem to be in a slightly different format than most providers.

          I have chosen not to use online genome storage platforms and generally don’t recommend using them. My main reason for caution about uploading genome files to (and elsewhere) is the privacy issues and security issues related to online storage places for genetic data. As the recent Promethease and buyout shows, there is a lot of money in genetic data. I can’t help but think that the main goal of a lot of genome storage companies is to build up a large amount of user data, including genetic data, with the goal of eventually being bought out.

 does state in their terms that your data (user data, personal information, and genome) will be included if they sell the business (as is usually done). “In the event that Company goes through a business transition such as a merger, acquisition by another company, or sale of all or a portion of its assets, your Personal Information will likely be among the assets transferred.”

          My other concern is that when using the third-party apps, including the free ones, the third-party app creators may be storing and using your genome data as well.

  6. “The Genos genotype file (Promethease file) had about 43,000 rsIDs in it, and I compared those to the 600,000+ rsIDs from 23andMe.”

    So are you saying the raw data provided by 23andMe is more thorough? Or at least, more of it is testable with other programs? My friend is trying to decide between the two to see where his depression might be coming from. I used 23andMe and quite like it, but he’s uncertain that it provides thorough data

    • Hi Kay –

      Keep in mind that I used Genos a couple of years ago, so things may have changed! The Genos test is a whole exome scan — so it actually looks at the coding regions for all the genes. It is a huge amount of data, but… the data file that includes the rs id’s was just the data that matches up with the rs id’s in I was also able to download the full exome file, but that file doesn’t contain rs ids. It is a .vcf file with only chromosome number and position included.

      For most people, I think that the 23andMe data is more usable with other programs. It may be a good starting point for your friend, and at $69 right now it is affordable. But depression can have multiple genes involved (along with environmental factors), so 23andMe may not give him all the answers. If he is working with a psychiatrist, there are genetic testing companies that offer specific tests for depression genes and depression related medications. Genomind is one, and I think there are several others available now as well. Most of these you need to order through a doctor.

      One more thing to think about with Genos is that while it covers the whole exome (coding part of DNA), there are important genetic variants in the promoter regions of the genes that won’t show up in the test. Whole genome scans are coming down in price as well, so your friend may want to check that out as well.

    • Kay,
      I would recommend Genos over 23andme (I use both). Frankly 23andme covers the more common variants in the genome (because it’s cheaper), but that’s not where the game is. I believe that the rare and very rare variants are where the most important data is. So to find a gene causing serious depression, I would get the Genos test and then look at the variants that have a frequency of about 2% or less (the rarer the better to find your culprit). Look at the Pathogenic gene variations, the Likely Pathogenic gene variations and the ones of Uncertain Significance. The rarest ones I think is probably where you will find your depression gene. But it won’t be waving a red flag so you will need to do detailed research on all those rarest of gene variants to find the one you are looking for. Also Genos doesn’t seem to list the insertion/deletion/frameshift variants with their viewer, so you might want to download the VCF file from Genos and use another analysis website to find those frameshift variations (I’m using Ensembl but I am unsure of their security – no https at the moment it looks like). I have had very good luck in finding culprit gene variations by using Genos. A very rare variation in the HMGCS2 gene is a prime suspect in my search for a depression gene in one person, ATP1A2 as a prime suspect in causing migraine headaches in the family, and a CTNNB1 gene variation which is almost a sure cause of the retinal problems in one close family that I know of. From what I am seeing, I think the future of genetics is going to be the study of the rare variations (which everyone has by the way) explaining similar symptoms running through a family. Science is just getting to this point now and I think it will result in a new genetics revolution where everyone will be rushing to analyze their rare variants. Unfortunately, common variations don’t explain that much, but figuring out one’s very rare variations is still quite expensive (which is why the science is still fairly immature when it comes to connecting the very rare variants (and all people have some very rare variants I’m finding) to their symptoms.

    • Hello Kay,

      Please read my longecity post on why not to bother with
      Dante Labs is an additional WGS service to consider; they often have promotions (black Friday for example) that reduce the cost to a couple of hundred dollars. You might wait for a few months to get the results but it is worth it. Make sure to email them and ask them to send a hard drive with the bam files (much larger than the vcf files).

    • There are so many genes and SNPs that could be involved in triggering depression.
      You can find a list published by Malacards at
      (click on show top 50 for a more comprehensive list)
      The ones with a star are elite genes, so they might have a bigger influence in triggering depression. Unfortunately there is no one single gene, or SNP, that can explain depression and epigenetic causes could also come into play. I found Rhodiola (from a quality and reputable brand) to help a lot with anxiety and depression triggered by chronic stress in my case. If you google “Mechanism of action of Rhodiola” it will appear a study from Panossian showing the multitude of mechanisms of action and genes affected by rhodiola. It is at the top of my list in supplements I take to reduce stress/cortisol. However, everyone is different and I guess there are many forms of depression and anxiety and related causes. We tend to simplify and put everything under an “umbrella” name but in my opinion there so many different forms of depression and anxiety. Similarly, especially in the past when we did not know much about it, we used to consider cancer like one single illness triggered by the same mechanism and cause. These days we know that there are so many types of cancer and so many different ways to treat it.

    • Hi – Thanks for reading the article… but there is no way that I’m publishing my genos file publicly :-) It is a VCF format. You could contact Genos for a sample file.

Leave a Reply

Your email address will not be published. Required fields are marked *