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results, Promethease adds new references as they become available, so your information from a couple years ago is out of date.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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