People are beginning to ask about how they can obtain some of the health information that they were previously receiving from 23andMe. For $5, at Promethease, you can upload any of the autosomal files from either Family Tree DNA, 23andMe or Ancestry.com. They will process your raw data and provide you with a report that is available to download from their server for 45 days. They also e-mail you a copy.
At Promethease, your raw data file is deleted within 24 hours of completion of your report, and your report file will be deleted after 45 days, so be sure to download your report for future reference. Currently they process about 20,000 genotypes, or SNPs. They do note that they update their data base regularly from SNPedia, fed from PubMed publications. Therefore your report in the future will include SNPs that won’t be in your report today and what we’ve learned about those SNPs may differ as well.
They have also noted that you receive different items in your report based on which vendor’s full data file you submit. That’s true. I uploaded all 3 of my raw data files, from Ancestry, 23andMe and Family Tree DNA and ran Promethease against each of them. While 23andMe optimized their chip for medical and health results, Family Tree DNA intentionally removed some medically relevant data in order to avoid any FDA type of issues. It’s unknown how Ancestry treats medically significant SNPs, but I’m running all 3 vendor’s files to view differences.
- The Promethease report utilizing the 23andMe raw data file reported on 20,080 genotypes.
- The Promethease report utilizing the Family Tree DNA raw data file reported on 8179 genotypes.
- The Promethease report utilizing the Ancestry raw data file reported on 10,498 genotypes.
To start the process of uploading your file and running your report, visit:
https://promethease.com/ondemand
Of course, you’ll need to take care of housekeeping, sign up and pay.
You will then be asked to select an ethnicity. I always hate this question, because I’m more than one and the categories never fit. If you don’t fit any category well, select the closest. Promethease says it only affects the sort order. That was a relief to me, as I always wonder what I’m missing by making one selection over another.
While the report actually runs, which takes about 15-20 minutes, amuse yourself by watching the video about how to download, read and understand your results. Or you could write a blog, like me!
You can review this video at any time by visiting the original link. It does make more sense after you have your report in hand.
My report only took 8 minutes to run, and according to the front page of my report, they analyzed over 20,000 SNPs or known mutation locations. I’m excited to see what my report holds.
One of the reasons I’ve been interested in this type of DNA reporting is that my mother was “diagnosed” with Parkinson’s Disease. I put diagnosed in quotes, because Parkinson’s is a diagnosis of exclusion, for which there is no specific diagnostic test, meaning the diagnosis is one made after other alternative diseases for which there are tests, are excluded. However, she never had some of the traditional symptoms, like the specific walking gait typical in Parkinson’s patients, nor some of the other symptoms, nor were the Parkinson’s medications effective in controlling her hand tremors. Her father also had the same tremors, which I’ve always suspected was Familial Tremor, not Parkinson’s. I wanted to see if Mom or I carried elevated risk for Parkinson’s. Mom’s DNA was archived at Family Tree DNA, so I could run the Family Finder test even though she had passed away by the time autosomal testing was available. So I uploaded and ran her file at Promethease too, and compared with my own.
So, let’s look at my report based on the 23andMe raw data file.
At this point, you have to choose to click on “Bad News” or “Good News” first. Someone should do a study about whether you select bad or good is genetically influenced.
In my case, I was interested to see if my “bad news” was the same “bad news” that 23andMe provided. My top “bad news” item is indeed the same item that is reported at 23andMe. Having said that, there are a lot more and different items here that were not reported at 23andMe. After looking at the varied results from Promethease, I suspect that 23andMe was trying to distill data on my behalf.
However, Promethease does not attempt to analyze your results. Some mutations are known to be connected to multiple conditions, so they simply tell you that. In some cases, you will have some negative and some positive mutations for the same disease. Again, they simply inform you, complete with a reference. It’s worth noting that for one disease I’m particularly interested in, Parkinson’s, I have a lot of conflicting data, pages worth. This just goes to show how complex interpreting this information really is, and shows that genetic predisposition, positive or negative, with only a few exceptions, is not genetic predetermination.
My good news made me feel really good. I’m at decreased risk of frontotemporal dementia or Alzheimer’s and Parkinson’s. I’m optimistic and empathetic. I wonder if this has anything to do with selecting the bad news option first – I knew I had the good news to look forward to. Get the bad stuff over with and get on with it…
Ironically, some of my good news items are in direct conflict with some of my bad news items. And yes, some are Parkinson’s, which has apparently been more heavily studied that some other diseases. Hopefully, the decreased and elevated risks will cancel each other out and I’ll just be average.
However, when running my Ancestry data file at Promethease, one of my elevated risks was Parkinson’s, based on the SNPs discovered in the 23andMe research, which conflicts directly with the information provided based on the 23andMe raw data file. Searching further, different SNPs have been reported to either be associated with increased or decreased incidence of the disease – and I carry some of each – but none are extremely elevated.
So where does this leave me in terms of whether Mom had Parkinson’s, or not? There is nothing to indicate an extremely high risk of Parkinson’s. Some indicators are for elevated risk, some for reduced risk. Compared to the one condition I know she had, which has a very highly elevated risk in all 3 reports, the Parkinson’s risk is simply unremarkable and doesn’t stand out. Bottom line – I still don’t know for sure, but I still don’t think she had Parkinson’s. Had I found highly elevated risk factors, I would have rethought my opinion.
Many diseases have multiple genetic components along with other external factors. Of course, not all studies report the same findings, and this report is based on academic medical studies.
Rarely are genetic predispositions more than just that, a slightly increased or decreased probability. Few are fatal and some are more of a life sentence than a death sentence. Having said this, there are notable exceptions, and if you really don’t want to know a worst case scenario, or aren’t prepared to deal with the results, don’t participate in DNA testing or reporting for medical or health information. If you have reason to suspect your family may carry one of the genetic terminal illnesses, visit your doctor for advice.
And speaking of physicians, much of this information, such as the information about how certain medications are metabolized could be critically important. In my case, I’m actually taking one of the mediations that is referenced where I have a decreased sensitivity. Yep, I knew that, but now I can provide this information to my physician.
For those who tend to worry and borrow trouble they don’t yet have, running this type of report might not be a good idea. It’s certainly not for hypochondriacs – IMHO. It’s a personal choice, and a very inexpensive one at that, so financially available to everyone. If what it contains is going to worry you, don’t do it. I noticed that there are several anxiety categories in these reports – but then you have to run the report to see if you carry them – kind of a catch 22 if you tend to be anxious and worry.
My personal perspective is that there may be information here that is valuable to me, or to my physicians, or to my children. The worst “bad news” item I already knew about through 23andMe, but I also anticipated that condition, without genetic testing, because my mother had this same disease in old age. I’m not referring now to the Parkinson’s, but a vision related condition that she definitely did have. This item was also consistently reported at a high degree of risk utilizing the data files of 23andMe, Family Tree DNA and Ancestry. Thankfully, it is an old age problem and one that can be treated, if not cured today. The Promethease reports, along with 23andMe’s report, have simply reinforced that I need to be proactive and vigilant and to eat lots of veggies. The good news is that many items include preventative measures in the verbiage or associated studies that your Promethease report links to at SNPedia.
How does this report compare to the 23andMe experience, assuming 23andMe was still an option or might be again in the future for health information? The 23andMe customer interface is much smoother and more user friendly. It seems to be focused on more “fun” and less “worry.” The Promethease report is that, a report, although they do a great job making it interactive. There is no sugar coating – just the facts Ma’am. And I think it’s actually much easier to use. You can easily search by disease, by category, and the searches actually work.
Promethease differs in another way too. Personally I like the idea that my data is mine, I’m in complete control of it, and it’s not being sold by Promethease out the back door for studies or purposes I might not be too thrilled about. I don’t want my DNA to be used to patent genes that cause the tests for the condition to be restricted to the patentee at dramatically inflated prices. While the Supreme Court determined that genes can’t be patented in the case of the BRCA breast cancer genes, the fight continues with lawsuits being filed, and 23andMe holds a Parkinson’s patent that was obtained by utilizing customer data. Nor do I want my data to be used to patent the technology for “designer babies.” If my DNA is going to be utilized for research, I want the ability to authorize that use, specifically.
Therefore, I feel much better about uploading a raw data file from an autosomal test at a firm like Family Tree DNA, who NEVER sells or otherwise divulges my data without first requesting permission. I thereby maintain complete control over my genetic results, rather than utilizing companies who either sell (or otherwise utilize) my results or reserve the right to do so. This is the case with both 23andMe and Ancestry.com, and to be clear, they have never claimed otherwise.
And oh, I forgot to mention…I am just so relieved….I have a decreased risk of baldness….
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I have been planning to blog on my results from Promethease. I found Promethease worth the $5. I compared 23andMe, Geno 2.0, AncestryDNA, and FTDNA results. Using 23andMe health results and comparing them to Promethease, Promethease looked at a lot more SNPs than 23andMe. In one case, 23andMe gave me 1.44x higher risk factor based on one study. The study used one SNP that hadn’t been verified as being a known SNP for the condition, but was in the same general area as other SNPs known to be a factor. My Promethease results from 23andMe looked at 130 SNPs, including 14 from a 2007 study, that was known to be relevant.
My question to 23andMe is why they used one unproven SNP when they tested 130 and many of those would affect my risk factor. It wasn’t an isolated case as many other conditions in my Promethease report showed a lot more SNPs than what 23andMe reported or considered.
Let me know, or post here, where you do your blog. I’d be very interested and I think others would be too.
Did you mean to say familial tremor? You said familiar tremor. Pesky typo?
Yes, thank you. It was all too familiar:)
Hi Roberta,
I run an independent facebook users page that talks about Promethease. Anyone who wants to post any interesting results, comments or questions are welcome to do so. https://www.facebook.com/PrometheaseUsersGroup.
Great Gary. Thanks.
Just finished. Well worth the $5. Fun to do. An inexpensive way to get the first letter of your mitochrondial Haplogroup. They gave me mine, which is U. Actually, I paid a lot of money to get the full mtdna and my group is U3a1b. I have the fat gene!*? Good gripes! I am 70 and weigh only 115. I have increased risk for lung cancer, but have mitigated that since I have never smoked or been overweight, etc. My report was 941 pages. Not interested in printing that out. Thanks, Roberta, best $5 I have ever spent!
how did you see mtdna?
I don’t believe that you do. Sort for mitochondrial.
I did free promethease, which takes about 8 hours (Since my machine runs 24×7, I didn’t mind giving a try). I am still going through results one by one, but it is interesting what it can give you.
BTW, have a question for you, in case you know. Is there any way to ‘compare’ 2 or more datasets from 23andMe? I would like to compare mine and DW’s with DS’s.
Thanks in advance.
Not that I know of, but ask on the Promethease Facebook group. Maybe someone there will know.
GEDmatch.com has a one to one comparison tool.
Go directly to SNPedia to download and install Promethease and run it for free (as noted above, free runs take a few hours) or opt to pay $2 via Amazon and the application will cache the SNP data and run much faster (10 minutes or so). Results are the same other than an interface option (“V2”) that didn’t seem that great to me. $5 for running online is pretty cheap… But if you have a bunch of kits to run, the free or $2 options are worth knowing about!
Sorry, forgot link, it is direct from SNPedia.com at http://snpedia.com/index.php/Promethease
Are those $5 for creating only a single report, or do they cover many runs by a single user ?
One run.
Roberta I clicked on the link but it only offered info from 23 and Me. I don’t think I have ever did anything with them. I have Ancestry and DNA.
The only thing necessary for evil to triumph is for good men to do nothing – Edmund Burke
Wilbur G. Corbitt US Army (Major) Retired) US DOJ/DEA (Investigator) Retired Lake City, Fl 32025 386-867-1687
I used both Family Tree DNA and Ancestry files too.
There are two green boxes when you click on the link. One says use 23andMe files and the other says “upload from your computer.” Select that one if you’re not doing 23andMe and then upload your file from either Ancestry or FTDNA from you system.
Boy, one can spend a week searching through the SNPs and the links SNPedia offers. I saw that under “Topics” I had 462 SNPs under NatGeo and 365 under Haplogroup, almost entirely without reference notes (except for 6 under NatGeo and an R1b under Haplogroup) Do you know if these are referenced SNPs for some of the branches of the haplotree?
I don’t know Mark, but if they are Y SNPs you might check the ISOGG tree and see if they are referenced there.
I ran the test. Where do I see my haplogroups? Especially interested in mitochondrial haplogroup. Thanks.
I’m not at all sure that Promethease gives you haplogroup information. It’s medical, not genealogical in nature. For haplogroup information, I would test at Family Tree DNA. There is a separate Yline (paternal for men) mitochondrial DNA test.
I think it’s test based, I got haplogroup for ancestry and myheritage ( k) , my mom’s mtdna confirmed that , but my dad’s Promethease run using Family tree DNA didn’t have the info.
My husbands report has a couple Haplogroups noted so yes it does. I havent been through a lot of the results yet so don’t know about mine
Does the report give you information on methylation and what you might do if your methylation is faulty?
I don’t know if it tells you that or not. You could contact them and ask. It won’t give you any remediation advice. That’s for a physician.
The most useful gene for testing methylation abnormalities is the MTHFR gene. If you have the abnormal 677T SNP (particularly if homozygous TT), or if you have the heterozygous 677CT SNP and also another abnormal 1298C SNP, it is wise to take a supplement called L-methylfolate, particularly if you have any symptoms of clinical depression, anxiety or excessive pain
Hi,
Promethease worked great for my raw data from 23andme. Promethease will not accept my father’s raw data from FTDNA, due to the .csv.gz format. My father is close to 92 years old and lives a fairly active life (alone) and is in pretty darn good health. He is okay mentally, and still drives to wherever he feels like going.
I am trying to figure out how to upload my father’s DNA data to Promethease and see his “good” and “bad” and basically see how his DNA (health-wise) has or has not effected him.
Can anyone tell me how to put the FTDNA .csv.gz file to a .zip or whatever format Promethease will allow me to upload? I primarily use a Mac, but also have a PC if that makes a difference.
Thanks in advance to anyone who can assist with this.
I didn’t have the problem, but I don’t use a MAC. You might try the FTDNA forum at their site or try searching their FAQs.
It’s Mac, not MAC. Just saying. MAC requires un-necessarily holding down the caplock key and besides, in computer terminology means something utterly different.
This blog has been quite thought provoking. I haven’t tried it yet and may not. I’m one of those worry wort types. Still….. “I gots to know….”
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Family Tree’s raw DNA shows 4 links for raw data. Which one do I send? Build 37 Autosomal Raw Data
(GZIP, CSV) Build 36 Autosomal Raw Data
(GZIP, CSV) Build 37 X Chromosome Raw Data
(GZIP, CSV) Build 36 X Chromosome Raw Data
(GZIP, CSV) Printable Population Finder Map
Thanks Kim
It’s definitely no the printable map. I haven’t used the site since I wrote the article. I suggest you visit the site and follow their instructions. That’s what I’d have to do too.
It says the autosomal and there are two of those so not sure which to use.
I bet they can use either. Build 37 is the latest so try it first.
Hi Roberta,
Thanks for this writeup, super helpful.
I wonder if you might make a recommendation on the following criteria that your writeup has helped me solidify:
My concerns are primarily medical and health-related, not ancestral, and it appears that I might potentially have to exchange comprehensive results in order for my data to remain private.
Family Tree DNA = Privacy + Less medical and health-related data
23andme = Slippery Privacy + More medical and health-related data
I wonder if you might be able to recommend an alternative that ticks all these boxes:
1) Private, my data will either not be stored, or not be sold, without my clear and explicit consent
2) Comprehensive medical and health-related data, at least as comprehensive as 23andme, if not more so
I am still researching myself and will report back with an answer if I find it, but thanks for any help!
There is no one that does that all. You would have to roll your own by testing with Family Tree DNA and asking them not to store your results, if you don’t want them stored – default is to archive for 25 years. Then you’ll have to do the health yourself through Promethease.
Hi Roberta,
I was wondering if anyone knows how much of a person’s DNA is deemed “bad” on average. In my report where I used Ancestry raw data, I ended up with 219 “bad” items, and 1344 “good” items, and around 12,000 items that were “not set”. I have no idea where I fall on the standard spectrum as far as risk. Do most people have less bad things or more bad things? It doesn’t really matter, but I’ve been very curious.
Thanks,
Melissa
I don’t have any real data on that – but that sounds pretty much similar to mine.
Many of my “bad” items had other offsetting good items for the same thing too.
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I found your blog by searching for “Yes, but about 3000 medically related SNPs have been removed” from the FamilyTreeDNA data. I want to compare my 23andMe data with FamilyTreeDNA I have of my sister, who died a year ago with symptoms similar to those our mother had. I was highly irritated to discover all but one of the rsIDs I specifically want to compare were among those medically related “removed” from the FTDNA data. Any idea if the 3000 SNPs will be added back in by FTDNA, should the 23andMe vs FDA case ever get resolved in favor of access to our own DNA information?
So in what order are the builds 37, then 37x or vice versa, which of these 2 is the newest
My Dad’s Promethease report had several things that said 100% seems Parkinson’s and it said like 15 or 20 times yet he didn’t have Parkinson’s thank God. Please help me understand that…
I can’t find their Facebook page. I bought the Promethease for myself, my daughter, mo dad and stepdad. The icons to reread don’t work later 🙁 Has anyone had that problem? Thanks Kim
I’m not a doctor and I can’t interpret them for you – but it’s normal to have some things that have an elevated prediction and others that don’t. Very few things are an absolute. Just having a raised elevation does not mean you have or will get the disease.
Best I remember you only had access to the info/report Promethease provided for only 30 days. You could have printed it out. You must have missed the fine print.
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I am trying to found out info about my deceased father who never knew who his parents were, the folks always lied to him. What would be the best DNA test to find out his ancestry? Through my brothers Y chromosome, we would like to find out his genetic ancestry, and what what lab would be suggested ? With much appreciation
Eleanor
This article will help you. http://dna-explained.com/2012/10/01/4-kinds-of-dna-for-genetic-genealogy/
The only lab that does the Y DNA testing is Family Tree DNA. Their link is on the side of my blog page.
FTDNA gives you 4 data files to download, Build 36 autosonomal, Build 36 X, Build 37 X and autosonomal. Which one do you download to Promethease for medical purposes? I am not very educated in Genetic Testing. Thanks
Which file do you download from FTDNA and upload to Promethease? There are 4 data files, Build 36 and 37 with X and autosomal data files. I do not know much about DNA testing yet. Thanks Wendy
I would read the instructions for Promethease. It’s been a long time and I don’t remember exactly what I did. They will tell you. It’s the same data, just aligned differently for reading.
i was printing copes of my Promethease analysis report, with I suddenly lost the web page. How do I find my data?
I’m sorry, but I don’t know for sure. I believe they kept a copy online for something like 30 days. You’ll need to contact them.
My report showed my daughter at highest level positive for Brca2 and I took the report to her insurance and they retested her and she is negative. That was very scary.
I hope you took it to a doctor, and preferably one that deals with these kinds of issues. I wonder how she could be negative in one and positive on another for the same allele. Did you ask? Or did the second test test more? It would be very frightening but I would want to be positive which test was accurate.
The highest level positive for BRCA 2? What was the number? I did not know how to read mine. The person doing my mamo said BRCA can only be tested with a Blood test, not saliva. Did your daughter have a blood test. Just looking for more info. Many thanks.
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I’ve received Promethease.com’s offer of exome sequencing. Would the results include all findings and not limit them on some Promethease scaryness scale? I would not pay for results that would be censored.
Would this exome fee also include all of the level 1-9 findings from the Ancestry/23 and Me data?
Frankly, I think Promethease should provide all results, (scaryness levels 1-9), to users who uploaded data from Ancestry or 23 and Me. Promethease could require users to certify that they have read the pros and cons of knowing their genetic risks and what to do after learning worrysome facts.
You’ll have to ask Promethease these questions.
in 12/2013 you note “Family Tree DNA intentionally removed some medically relevant data in order to avoid any FDA type of issues.” you also note how Prom. could read 8k SNPs from the FTDNA raw file vs 10k ancestry and 20k 23andme. did you find that those 8k SNPs had the same key health SNPs typically analyzed i.e. SHMT, ACAT, CBS, MTHFR, MTR, BHMT, MAO-A, SUOX, NOS, VDR-TAQ, COMT?
for mutations and nutrigenomics, which $99 raw file service would you pick today in 2017, if you could only pick one for the key SNP array noted (in case any of them have removed more SNPs)?
which of the top five $99 kits has the most 3rd party nutrigenomics potential? do enough support FTDNA or heritage yet?
I am interested in this issue. Briefly, Is it now (April, 2017) possible to get the health information FTDNA stripped out in 2013? I am very interested in a comparison of my deceased sister’s FTDNA data and my 23andMe data.
Not that I know of.
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I didn’t get bad or good news section. Also I don’t know how to interpret numbers on medicines & medical conditions. Can you pls help. Thanks I’m reading on my phone
You’ll probably need to read this on a real screen.
Have FTDNA raw data enough snps to interpret blood types?
I don’t know. For $4.95 you can try and see.
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My daughters results came back with positive for Brca 2 gene at the highest level. We had her retested through our insurance company and the results were wrong. She was negative for Brca2 gene. That was scary!
Did you inform them? I wonder if her original test was wrong or the interpretation was wrong.
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