Wednesday, December 16, 2015

Promethease: For Your Health & Insomnia



On Sunday The Legal Genealogist, also known as Judy Russell, posted "All you want for Christmas..." is a DNA test kit. Her post began:
So… if that’s you this year, if what you really want for Christmas is a DNA test kit … which one do you get?
Her answer was very thorough and I will not try to duplicate it here. However, you would do well to read her thoughts. Her analysis of the options is sound, genealogically speaking, and she left very little to be added. Except....


Testing only for health related information:

All of us should know by now DNA testing is definitely not a case where "one size fits all." Judy knew this and she provided many viable options, but she left one out and I believe she did that on purpose. We will get back to what her purpose may have been later in this post.

In the last several days I have been approached three times by individuals asking what DNA test I would recommend for gaining health related information. Two wish to self test and the other is looking for holiday gift ideas for two sons. All of the would-be test takers are middle-aged. If they test they would become the kind of test takers all serious genetic genealogists love to hate. They all know little and claim no interest in knowing more about their ancestry except for how their genes may impact their own health. In addition they all claim not to be concerned about their carrier status for diseases that the FDA now permits 23andMe to report to clients. That really doesn't leave much from which to choose. 

Some information about prescription drug interactions with an individual's genome can purchased through a test offered by Healthspek which I have discussed in previous posts. However, that is only one part of the health related information inquiring minds would like to know about what is recorded within their personal genomes.

Several years ago I took a quick look at Promethease but found it to be not as user friendly as similar information presented by 23andMe. Since the reports generated by both companies were coming from the same source data, I opted to concentrate on those on my site at 23andMe


Hemochromatosis Carriers:

During the holiday season three years ago we offered to gift our children and their significant others with 23andMe test kits. One of the things we learned from this was that both one son and his wife were carriers for hemochromatosis -- which causes one's body to accumulate too much iron. The parents were not flagged as being at risk for developing this disorder but their offspring -- our young grandchildren -- were at elevated risk. I discussed this finding with my daughter-in-law who is a gynecological surgeon and medical school faculty member. I recommended that she relay this information to the boys' pediatrician so that he could make note of it in their files and monitor this possibility. My MD daughter-in-law asked if I would write a long email to the pediatrician that explained this development to him.

I did so but I found this to be ironic (pun intended) since I'm an information doctor not a medical professional. Some of you know that I have never had a biological science course of any description in my life. My insatiable curiosity about DNA was God's punishment of me when She read my transcript and realized my academic deficiency. So much for needing medical professionals to protect and guide us uninitiated civilians as we are introduced to the information in our own genomes. But I digress.


Promethease:

Back in September The Legal Genealogist wrote "A Healthy Choice" as a post to her popular blog. In it she presented a very thorough introduction to Promethease as a source for health related information from our genes.



Rather than trying to repeat her succinct prose my intent is to expand on the personal experiment she reported. Until recently I was unaware that self downloaded raw atDNA results from any of the big three testing companies can be uploaded and processed through Promethease. However, the 23andMe test chip has significantly more health related SNPs than the chips of the other two companies. FTDNA has made conscious decision to stay away to the extent possible from SNPs thought to be health related. This decision was made years ago in order to minimize the potential for regulatory problems with the FDA. As we learn more about our genomes, it is increasingly difficult to avoid SNPs with known health consequences. Ancestry discloses little about its rationale for selecting the SNPs on its chip.


Raw data from each of the major U.S. testing companies when processed through Promethease for three different users: 

23andMe Ancestry Family Finder
Legal Genealogist
Gray 17,613 11,225 10,070
Green 5,281 1,538 1,261
Red 413 255 166
Total 23,307 13,018 11,497
Dr. D
Gray 19,049 11,609 10,348
Green 5,580 1,572 1,296
Red 388 248 153
Total 25,017 13,429 11,797
Dr. D's wife
Gray 18,414 11,245 10,384
Green 5,519 1,491 1,265
Red 429 276 177
Total 24,362 13,012 11,826

Clearly customers get reports on about twice as many SNPs from 23andMe raw data than from the data from competitors. My little study has replicated Judy's. So if your only objective in taking an autosomal DNA test is to learn more about how your genetic component may contribute your future health, 23andMe raw data will give you more to analyze and analyze and analyze. That is what you will be doing if you go this route. Processing raw data from 23andMe or Ancestry only costs $5. Family Finder data costs $7 because xDNA must be downloaded separately and added to the mix to get the most complete picture that can be extracted from those data. If you have raw data from all three companies as does The Legal Genealogist and Dr. D., all your data can be loaded into Promethease at one time and processed for a total of $11.


Alzheimer's risk:

It is easy to drown in the data. In my own report Alzheimer's was associated with 156 SNPs: 56 good; 11 bad and 89 with small associations that have yet to be classified as either good or bad. You cannot look at the predictive power of a single SNP and be confident that you know something about how your genome may affect your future health. The human genome is far to complex for this kind of intellectual short cut.


SNPs currently thought to be related to Dr. D's Alzheimer's risk
If you have that obsessive-compulsive gene and love to pour over all the known data, this may be the test for you. If you have already done an atDNA test, for an additional investment of only $5 or $11 dollars, you can entertain yourself all night!


Holiday sale:

As most of you know 23andMe recently raised the price of its test kit to $199 for U.S. customers. If you are already a 23andMe customer, you recently should have received an offer to order kits for $149. This price is good for purchases completed through 11:59 pm PST on January 8, 2016. What you may not have noticed in the fine print is that you can place up to three separate orders. Each order can be for up to ten kits. This allows one to order as many as thirty kits at this sale price.


Caveat:  

If you are at all interested in using DNA testing to learn ancestry information for genealogical purposes, read Judy's December 6th blog post "Now... and not now" before you order any kit from 23andMe.


8 comments:

  1. Great post, Dave, and I don't disagree except... except... except... I'm not sure any of us knows yet what health data will remain in the raw data we can access once the full switchover is made to the new post-FDA-approval system at 23andMe. So it's not just the lack of utility for ancestry that affected my decision not to include 23andMe, it's also the fact that I simply don't know that we'll get the same utility from 23andMe raw data at Promethease once the dust settles.

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    Replies
    1. Judy, you will have the same access to the raw data in the browser and the download. I have double-checked this with 23andMe staff.

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    2. Thanks Ann. That had been my assumption but it is good to have it confirmed.

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  2. Thanks Judy. I've corrected some of the verb tenses that my low caffeine level let slip in earlier. If only 23andMe would tell us clearly what they are really up to. I know. I dream.

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  3. Great analysis. But I still fail to get which one Judy left out among her viable options.

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  4. CAR,

    In her "All you want for Christmas…" (http://www.legalgenealogist.com/blog/2015/12/13/all-you-want-for-christmas/), Judy listed the options for testing from the perspective of a genealogist -- someone who is testing exclusively or at least primarily for family history information. From that perspective, I have no quarrel with anything she said. She did NOT mention 23andMe as an option in this post except in responses to reader comments.

    My point is that if someone is testing exclusively or primarily for health related information (NOT genealogical), 23andMe should be at the top of the list for consideration.

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  5. Thanks for the explanation Dr. D.

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  6. I'm not sure any of us knows yet what health data will remain in the raw data we can access once the full switchover is made to the new post-FDA-approval system at 23andMe. So it's not just the lack of utility for ancestry that affected my decision not to include 23andMe, it's also the fact that I simply don't know that we'll get the same utility from 23andMe raw data at Promethease once the dust settles.

    ReplyDelete