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Using Promethease

There isn’t a week that goes by that The Legal Genealogist doesn’t get the question from a reader somewhere.

It’s usually someone dealing with an unknown parentage situation, but not always.

And the question is very simple: “how do I get information about my health history using DNA testing?”

That’s an easy question.

It hasn’t got an easy answer.

Oh, you can go to your doctor, discuss doing genetic testing, and pay the associated lab and doctor fees for whatever testing you can convince the doctor to order and get the information that the doctor or a genetic counselor is willing to explain to you.

That’s probably the easiest way to do it, and certainly the recommended way for anyone who has a specific identifiable health concern that needs to be addressed.

promethease2016But for those of us who are just curious… who just want to see what information may be lurking in our genes without any particular need for an answer right now… DNA testing does offer some options.

One choice is to test with the genetic testing company 23andMe. Its $199 Health + Ancestry Service option provides some health reports that let you get information (at the moment) about some 41 carrier status variants, 22 trait variants and seven wellness variants that the company reports on. The carrier status variants include things like cystic fibrosis; the trait variants things like sensitivity to bitter tastes; and the wellness variants things like lactose intolerance.

But there’s another, much less expensive option, and it’s open to anyone who’s tested with any of the genetic genealogy companies.

It’s called Promethease: “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.”1

I’ve written about this option before,2 but it seems a good time to revisit the issue now that 23andMe is offering an Ancestry-only version of its test.

So… what is Promethease? It’s “a computer program developed by the SNPedia team which allows users to compare personal genomics results against the SNPedia database, generating a report with information about a person’s attributes, such as propensity to diseases, based on the presence of specific single-nucleotide polymorphisms (SNPs) within their genome.”3

It “builds a personal DNA report based on the scientific literature cited in SNPedia and a file of genotype (DNA) data. Customers of DNA testing services (23andMe, FamilyTreeDNA, Ancestry.com, Complete Genomics, …) can use it to retrieve published data about their DNA completely independent of whichever company produced the data.”4

SNPedia, in turn, is a wiki devoted to the medical consequences of DNA variations, including software to analyze personal genomes. It describes itself this way:

SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being.

 

Our genes are important, and the variations in them help define our uniqueness. Yet at the same time they help forge links between us, as many of us carrying certain variations find ourselves facing similar medical issues. SNPs are those variations. SNP stands for Single Nucleotide Polymorphism and means variation in the same place (polymorphism) within the DNA sequence.

 

SNPedia is based on a wiki model, in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. We anticipate that as the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we’ll all want to know more – a lot more – about the meaning of these DNA variations. And SNPedia will be here to help.5

What Promethease does is compare your raw autosomal DNA test data — and you can use your raw data from any of the three major test companies (Family Tree DNA, 23andMe and AncestryDNA) — to information collected from peer-reviewed scientific journals at SNPedia to “create a personal report linking your DNA variations to the information published about them.” It’ll cost you a whopping $5.00 to get each report.

Among the specific DNA markers (called SNPs, or single nucleotide polymorphisms6) it looks at are ones now believed to raise the risk of Alzheimer’s disease, influence baldness, determine sensitivity to anesthetics, trigger obesity and type-2 diabetes, impact the risk of coronary heart disease, or result in lactose intolerance.

There are currently 87,905 SNPs in the SNPedia database and — depending on which genetic genealogy testing company you tested with — a Promethease report will give you links to any scientific studies on markers in your DNA. According to SNPedia:

• Ancestry.com uses Illumina OmniExpress Plus, reporting all SNP’s on that chip for $99. Current users will receive data for about ~47,000 of the SNPs in SNPedia. ~25,000 of these are in ClinVar. Prior to May 2016, Ancestry customers received data for around 13,000 of the SNPs in SNPedia with only a few hundred from ClinVar. This test is currently available in the USA, Canada, Australia, and the UK.

 

• 23andMe $99 “ancestry only” product, which does allow downloading of full results, e.g. to Promethease to get a report, or, $199 “ancestry + health” product, which includes carrier status reports (and also full data download). One time payment, lifetime membership. Both products uses the (same) customized Illumina chip which covers 25695 of the 87905 SNPs in SNPedia. Less than 2,000 of these are known to be in ClinVar; presumably some of the proprietarily named “i-SNPs” correspond to ClinVar/SNPedia entries as well but 23andMe does not reveal which publicly or to its non-corporate users.

 

• FamilyTreeDNA Family Finder uses an Illumina OmniExpress for autosomal ancestry testing for $99, including partial raw data download. It covers 13,193 of the SNPs in SNPedia, with ~2,000 of those being known to ClinVar.7

So in terms of coverage, it’s current AncestryDNA, then 23andMe, then older AncestryDNA, then Family Tree DNA.

To begin in any case, you need to download your raw data:

Steps to download AncestryDNA raw data:

1. Log in to Ancestry and go to your AncestryDNA Home Page (DNA -> Your DNA Results Summary).

2. Click on the Settings link on the right hand side.

3. Choose Download Raw DNA Data from the Actions menu on the right hand side.

4. Enter your Ancestry password and click on the box saying you understand the downloaded copy is yours at your risk. Then click on Confirm.

5. Go to your email account. You’ll get an email with the subject Your request to download AncestryDNA raw data. In the email is a link, Confirm Data Download. Click on that link. It’ll take you back to Ancestry.

6. On the Ancestry page that loads is a link: Download DNA Raw Data. Click on that. Then choose the location on your hard drive to save the zip file that results.

Steps to download 23andMe raw data:

1. Log in to 23andMe and drop down the Tools menu. Choose Browse Raw Data. If you haven’t done so before, choose the Raw Data Opt-In by clicking the I understand link.

2. At the top of the page, find the download link either in the tab at the top or in the sentence “You can view or download your data at anytime…” Click on the download link.

3. At the bottom of the Download Raw Data page, choose what DNA data you want. (For Promethease, you want All DNA) and then re-enter your 23andMe password. Then clock on the Download Raw Data link box. Then choose the location on your hard drive to save the zip file that results.

Steps to download Family Tree DNA raw data:

1. Log in to Family Tree DNA. Drop down the myFTDNA menu in the top.

2. Choose Family Finder and open that menu, then choose Download Raw Data.

3. From the bottom menu, choose the type of DNA raw data file you want to download. For Promethease, the recommendation is the Build 37 Raw Data Concatenated file. Then choose the location on your hard drive to save the file that results.

Once you have your raw data file, head over to Promethease and carefully read the agreement. Read the privacy policy and the terms and conditions before just clicking the check boxes.

If you agree, then check the check boxes, click on I agree, upload your raw data file and pay the $5 fee for the report. You’ll get a notice within about 10 minutes that the report is finished.

Now… this isn’t easy. Interpreting any of these results is far more difficult than getting them. There is a video that will help you understand how to use Promethease and Reddit discussion groups for questions about Promethease in particular and about SNPedia in general.

And it isn’t medical diagnosis — it simply isn’t the same thing as being told you have a disease or condition. I have a whole slew of results, starting with a SNP that provides “an apparent resistance to several diseases such as invasive pneumococcal disease, bacteremia, malaria, and tuberculosis” on the good side, followed by one that poses “an increased breast cancer, type-2 diabetes, and aggressive prostate cancer risk” on the bad side. But these are risks, not diagnoses.

But for anyone who’s just curious about what medical information might be lurking in your genes, it’s a fast and inexpensive option.


SOURCES

  1. “Promethease,” Promethease.com (https://www.promethease.com/ : accessed 19 Nov 2016).
  2. See Judy G. Russell, “A health data option,” The Legal Genealogist, posted 13 July 2014 (http://www.legalgenealogist.com/blog : accessed 19 Nov 2016). Also, ibid., “A healthy choice,” posted 13 Sep 2015.
  3. ISOGG Wiki (http://www.isogg.org/wiki), “Promethease,” rev. 8 Aug 2016.
  4. Promethease,” SNPedia (http://www.snpedia.com/ : accessed 19 Nov 2016).
  5. SNPedia:About,” SNPedia (http://www.snpedia.com/ : accessed 19 Nov 2016).
  6. ISOGG Wiki (http://www.isogg.org/wiki), “Single-nucleotide polymorphism,” rev. 4 Oct 2016.
  7. Testing,” SNPedia (http://www.snpedia.com/ : accessed 19 Nov 2016).
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