Promethease 2017

For those who aren’t acquainted with Promethease, they are a service that provides a comprehensive “health” report based on autosomal DNA results uploaded from the major testing companies.  You receive an informational report about your genetic health risks and some traits as reported in numerous academic studies that are archived and categorized relative to genetic information.

Quoting Promethease, they say:

Promethease is a literature retrieval system that builds a personal DNA report based on connecting a file of DNA genotypes to the scientific findings cited in SNPedia.

Please note that if you took the 23andMe test for health information, Promethease provides you with exponentially more information – and you can utilize your 23andMe file to obtain that information. If you tested at any of the other major vendors, you can utilize those reports as well, either separately or together.

I originally wrote about Promethease in December of 2013. At that time, I uploaded the files from various testing vendors to Promethease one by one and compared the results. Four years in this industry is forever, so I’m doing this again to share my results. There is a lot more information available from Promethease, and the testing vendors files have changed too.

This time, I’m uploading my Exome data, a very different DNA test than consumers receive at the typical genetic genealogy testing companies. You can read about this test in the article, Genos – A Medically Focused DNA Exome Test.

Keep in mind that even if you uploaded your autosomal file before and received results, Promethease adds new references as they become available, so your information from a couple years ago is out of date. The good news is that Promethease is very inexpensive, typically between $5 and $10.

What Does Promethease Do?

Promethease reports raw information, meaning that they do not massage or interpret this information for you. In other words, for a particular disease or trait, if there are 10 articles that report on that particular DNA location, based on your SNPs (one from Mom and one from Dad,) 2 information sources might indicate a possible increased risk, 5 might be neither good nor bad, and 3 might indicate a possible lower risk. Promethease shows you all 10, not distilling the 10 into a compilation or summary of your risk factors.

Promethease is NOT DIAGNOSTIC. Only a physician can diagnose complex illnesses correctly, incorporating genetic information.

I should note here that very few mutations are absolute, with a few notable exceptions like Huntington’s Chorea. In most cases, just because you have a specific mutation indicating an elevated risk, does NOT means you’ll ever get that disease. Other factors such as lifestyle, nutrition and environment are involved, as well as elements we don’t yet understand today.

Important

If you decide to submit your information to Promethease, it’s very important for you to understand and take the following points into consideration:

  • The DNA tests you are uploading are not medical tests. They do not test all possible locations. Furthermore, occasionally, tests run by different vendors produce different results at specific locations. Those differing results can and do produce conflicting information about traits or mutations associated with that location.
  • Testing errors occur.
  • Promethease results are not diagnostic, only informational.
  • If you are concerned about your health, either before or after testing, you should take the results and your concerns to your physician for interpretation in your particular situation. (I am not a doctor. This is common sense.)
  • The field of genetics, including medical genetics, is undergoing a steep learning curve. Very little is cast in concrete. Sometimes we learn that what we thought we knew previously was incorrect.
  • You cannot “unsee” what you will learn about your own genes and mutations. Be sure you really want to know before you participate in this type of learning.

Having said all of that, let me share some interesting information about my results with you.

My Results

I recently uploaded my Genos Exome test, which tests a LOT more locations than any of the typical genetic genealogy tests – 50 million as compared to less than 1 million in the typical genealogy autosomal tests. I utilized Genos results on purpose, after developing a DVT (deep vein thrombosis – a blood clot) in my leg after a fall and after a flight, both. I wanted to see if I carry any genetic propensity for developing DVTs, or if it had just been a combination of circumstantial factors other than genetics. I discovered that I don’t carry any known genetic predisposition to DVTs or other clotting issues. Neither did my parents, at least not that I know of.

Promethease returned a total of 45,595 locations with informational results of some type, meaning those locations had been found in medical or academic literature housed at SNPedia.

Of those locations, 41,766 were “good,” 104 were “bad,” and 3,725 were “not set” meaning neither good nor bad.

The great news is that you don’t need to read all of the results, but can search or see any results that are relevant for any particular word. So you can sort for “clot,” “thrombosis” or even something like “kidney” or “liver,” in addition to seeing and sorting information in various other ways.

Most everyone looks at their “bad” mutations first. Fortunately, most people don’t have many and often bad doesn’t really mean “bad,” simply a slight elevated risk.

The Process

When considering whether or not to utilize Promethease, you might want to take a look at the video provided on their main web page.

Of course, to proceed, you’ll need to actually READ the legal verbiage and click that you accept to proceed.

Please click on any image to enlarge.

Promethease said this, and I said this, but I want to say it again.

You may discover things that will worry you. You may find conflicting information about a trait or mutation. You cannot “unsee” this once you’ve seen it.

Vendor Upload Files

You can upload your results from any of the vendors, noted above, as well as see example reports. Occasionally when a vendor changes something in their file, or changes testing chips, there will be a delay while Promethease makes adaptations. As I write this today, Promethease is working to handle the 23andMe V5 chip which is the new Illumina GSA chip.

One VERY interesting feature is that you can upload your results from multiple vendors and Promethease will combine them to provide you with one report. This costs a little more – mine was $17.  If I didn’t taken the Exome test, I would have uploaded all of my other files for combination.

Actually, after I uploaded my Exome file and ran the results, I did upload the rest. I’ll be publishing an article shortly with the results of that comparison titled “Imputation Analysis Utilizing Promethease.”

I would NOT utilize files from vendors that impute DNA data and include imputed information in your download data file. Of the vendors listed, I know that today MyHeritage makes use of imputed data on their site, but only downloads your actual tested locations, so their file would be fine to use.

DNA.Land facilitates uploads from other vendors, then imputes additional results, allowing you to download the imputed data file. I would not suggest using this file.

At this link, Promethease discusses imputation and says that some results from imputed information will be unreliable. I would recommend AGAINST using the imputed data. You will have no idea which results are from your real test and from the imputed data, that isn’t actually yours.

If you choose to use an imputed file, I would suggest that you also separately run the same file that you uploaded to DNA.Land in order to see which of your report locations are real and which are imputed by comparing the results of the two separate runs.

Promethease provides information, shown below, about the various vendors and vendor files. Note that some are not accepted, and some are less reliable.

It’s interesting that the Family Tree DNA Big Y test is accepted in addition to their Family Finder autosomal test.

The Results

Processing takes about 20 minutes and you will receive an e-mail when processing is complete with a link to both view and download your report. Click “download” which provides a zip file. Results are only held on the Promethease website for 45 days unless you make a selection to retain your results on the website to enable future processing.

Promethease provides a nice tutorial, both via their video and onscreen as well.

Click the link in the e-mail to see your results.

Promethease results are color coded with red being a probable pathogenic result (meaning potentially concerning, or bad), green being a good or protective result and grey meaning not assigned as bad or good – just information.

In total, I had the following categories of results utilizing my Genos file:

  • Probably Pathogenic, red – 104
  • Not Set, grey – 3725
  • Protective, green – 41,766

Please note that while red equals bad, that’s a relative thing. For example, having a “bad” mutation that MAY elevate your risk to 1.2% from 1% isn’t really terribly concerning. Most of my “bad” mutations fall into this category, and may have good offsetting mutations for the same condition. So, no jumping to conclusions allowed and no panicking, please.

Here’s my first result. It’s grey.

Whew, I’m a female!

You can see that I have 45,595 results returned, 10 being shown on the screen and the rest of the 45,595 being held in reserve and visible by sorting any number of ways, including by key word in the search box shown top right above. Below, lots of other sort options.

Here’s an example of a “grey” result when I searched for “eye color.”

You can see that this genotype, or result, as described, influences eye color.  I carry the nucleotides G and G, noted beside the rs id, where an A is required for the propensity to blue or grey eyes.

From this information, we know that my children received a G from me, because that’s all I have to give them, but if they received an A from their father, their eyes could be blue or grey.

Caution

If you don’t want to know, and I mean really know about your medically connected mutations, don’t utilize Promethease.

If you are prone to anxiety or worry, this might not be for you. If you are a hypochondriac, for Heaven’s sake, don’t use Promethease.

If you do want to know, run Promethease occasionally, because new SNPs are being added to the data base regularly.

Be cautious about introducing this entire report into your medical record, especially given that the state of health care and pre-existing condition coverage is uncertain in the future in the US. However, be vigilant and inform your physician of anything that might be relevant to your conditions or treatment, or especially any variants that might help them diagnose a condition or tailor medications.

While I am providing an informational article about this product, I am not specifically recommending or suggesting that anyone utilize Promethease.  That is an individual decision that everyone needs to make personally after weighing all the factors listed above, plus any not mentioned.

______________________________________________________________________

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17 thoughts on “Promethease 2017

  1. Great article! We all did Promethease a few years ago, for fun, and to find the blood types of our two younger adopted daughters. We not only got their blood types (for $5 apiece), we also found out they are lactose intolerant, which we suspected.

  2. Thank you for this thorough discussion. I have a relative who promotes it to our family FB page without really understanding it . You have covered a lot of important points. I’ll be sharing this. 🙂

  3. Anyone get this before the report. Has me puzzled:
    Data Quality Warning Some of your data claims that you have 2 Y chromosomes. In particular it is claiming heterozygosity for a Y chromosomal SNP. Originally this was an issue with data from Ancestry.com and the reason is explained at the bottom of that page. We’ve begun to see this for some 23andMe data and there is some discussion of this at https://www.23andme.com/you/community/thread/40845/. You are actually quite unlikely to have 2 Y chromosomes, even if you are the (rare) XYY male. This is because our understanding is that the two Y chromosomes in an XYY individual should be duplicates of each other, since they come about from a nondisjunction event in meiosis (II). As duplicates, they shouldn’t show heterozygosity. In other words, even in an XYY individual, the Y chromosome SNPs should not show heterozyg…

    • See the full text at
      https://www.snpedia.com/index.php/Gs266

      Promethease has always been reflecting what is in the raw data. The data has been that the various companies are letting too many low quality calls into their raw data. Ancestry.com was particularly egregious in this regard. As of about a month ago promethease now does some additional aggressive filtering of the X and Y chromosome for Ancestry.com, and as a result these gs266 reports are now extremely rare.

  4. I uploaded my data from FTDNA about 3 years ago. My cardiologist and neurologist were fascinated by the information, as was I. It’s pretty spot on for me, and has helped my doctors in prescribing medications. In particular, I cannot take the normal dose of warfarin. I am also overly sensitive to certain antidepressants, and it shows that. I have thought for years that I had RA, but tests were not showing it. However, Promethease showed I was at a higher risk. And in August, I was diagnosed with RA.

  5. I did upload my Ancestry data, and noticed early on that there were SNPs both increasing and decreasing the odds for certain conditions. Makes sense. I think that this site aggregates research studies that associate particular SNPs associated with particular diseases?
    But another thing I found was that they sometimes put warnings on particular SNPs that, if from Ancestry, it may be over-reported.
    Not necessarily true…. The dominant autosomal SMP that shows that warning is me right now.
    But the line it came from all have 15 kids who have 15 kids, etc, and a number of them also got the “you must get your DNA tested” gene…. 😉

    • Promethease only reports information from SNPedia and from academic or medical studies. The frequency information comes from the Thousand Genomes and HapMap projects, not from their customer data. So there is no over-reporting associated with how many clients upload information with that gene.

  6. My doctor said, “Don’t bite yet” when I told him about Genos – sent him your post. He suggested I look at New Amsterdam Genomics – which, incidentally, gives ancestry info as well. Have to go thru a doctor to get it.

    Thot you might be interested.

    b

  7. I’d like to clarify two very minor points.

    #1. “You can upload your results from any of the vendors, noted above, as well as see example reports.”. Actually we support many vendors which are not shown. Some have come and gone (like ‘Decode’), others remain obscure enough that we haven’t gotten many questions about them, others just happen to provide files so similar to the formats of other companies that there isn’t much need for the software to do anything new. If you have raw data, and it includes dbSNP identifiers like rs12345 we probably support it. Just upload and promethease will quickly tell you whether or not the format is supported.

    #2. “You will have no idea which results are from your real test and from the imputed data, that isn’t actually yours.” While I agree that we discourage imputed data, we sometimes are able to distinguish imputed from real, and we do have a way to show that. However the whole UI still makes it difficult to make a useful distinction when searching and sorting. See https://www.reddit.com/r/promethease/comments/6x0j8s/submitting_info_from_genes_for_good_is_it_best_to/dmd0qqa/

      • I think they are pretty similar, except that codegen.eu does not give you a downloadable report (but you could print the online one). Both use information already available through SNPedia if you want to go gene-by-gene or SNP-by-SNP, and if you tested at 23andMe, which allows you to view your genotype by entering the rs or GS number in the “view raw data” window.

  8. Pingback: Imputation Analysis Utilizing Promethease | DNAeXplained – Genetic Genealogy

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