Promethease

Should people having at-home DNA tests for medical purposes?

Should people having at-home DNA tests for medical purposes?

I’m often asked for my thoughts on whether at-home DNA tests should be used for medical purposes, since they are the only option some people can afford.

This a complex question, but it is one I have thought about and continue to think about.

It’s hard to answer succinctly because of all the moving parts -- access to an ordering provider for clinical DNA tests, additional costs for getting customized support or counseling support, the next steps to take in the medical system if a test is positive, etc. -- I address some of these in my recently published book since I am very close to all of these moving pieces and will write just a bit about it here.

Digging Deeper into a Promethease Finding Before Accepting It as Truth

Digging Deeper into a Promethease Finding Before Accepting It as Truth

I recently worked with a client who was adopted and had used a raw data file and the Promethease tool as an avenue to obtain some health/medical information for herself.

This case gets a little complicated but please stick with it; it demonstrates a lot of the areas where there is weakness in our understanding and communication of medical genetics data.

The case also highlights the importance of doing deeper investigation of findings that show up on a Promethease report, before accepting the report’s summary at face value. I write about 23andMe and Promethease in the summary, but my conclusion is true for any tool (Genetic Genie, Sequencing.com reports, etc.) run on any raw data file (AncestryDNA, MyHeritage, etc).

Open your at-home DNA Alzheimer's report when you're already on the phone with a genetic counselor

at DNA Alzheimer's Report (2).png

June is Alzheimer's Awareness month which seems an appropriate time for an updated post on Alzheimer's disease.

I've compiled resources about Alzheimer's disease genetic testing into one place (see the bottom of this post). I'm also including some direction on how to involve a genetic counselor when you prepare to open your 23andMe report on late-onset Alzheimer's disease risk (or a third-party report run on a raw data file, like Promethease). 

Panic doesn't have to be part of the equation if you find out you have an elevated risk of developing Alzheimer's disease.

The advice and resources included below can help reduce or stop the panic before it has a chance to start.

If you haven't worked with a genetic counselor before, a genetic counselor is a great partner to have when you are deciding to have DNA testing or at the point of learning DNA results that could have a profound effect on your outlook for the future.

I can speak for all genetic counselors when I say we aren't trying to keep you from your genetic information. We aren't trying to meddle with your rights or get between you and knowledge about yourself. Genetic counselors know you can handle what you find out. 

It's our job to get you the correct information and help you locate support you when you need it.

After your results are back but before you open your Alzheimer's risk report, consider finding a genetic counselor to have on call. Schedule an appointment with them*, and open your report together with your genetic counselor on the phone or over video chat.

*Ways to do that include scheduling with me here or someone else in the Genome Medical network here* or searching for someone located near you here. Watershed DNA and Genome Medical services available only to U.S. residents at this time.

You'll have instant access to information, support, and next-steps if you find out you carry an elevated risk of late-onset Alzheimer's disease. If you find out your risk does not appear to be elevated, you can use the rest of the time with your genetic counselor to review your family and personal medical history.

Your genetic counselor can explain other types of testing that might fit your needs.

It might be carrier screening if you're planning a family, or a proactive genetic screen if you're healthy but curious about future risks. Diagnostic testing might be what you need if you already have a medical condition or health symptoms. 

A one-time appointment with a genetic counselor -- whether you're having unexplained medical issues or are healthy without any specific genetic concerns -- can set you on the right path. At-home DNA tests merely skim the surface.

Find a genetic counselor to be your partner, and keep learning about the different tests available. Some DNA tests are medical-grade and some are not, so make sure you've taken the right one. 

Learning about your genetic risks can be empowering if you know what to do with the information you learn.

Your Alzheimer's risk report might be ready and waiting for you, but don't feel pressured to open it right away. Read some of these articles, then look for a genetic counselor to have on the line, if it feels right to you.

Watershed DNA blog post: Should you do a home DNA test for Alzheimer's?

Watershed DNA blog post: Need help fighting the urge to open your Alzheimer's disease risk report?

Watershed DNA blog post by guest writer Jamie Fong: Alzheimer's disease - key points

apoe4.info article: Thinking about testing? APOE4.info is a support organization founded and operated by individuals who have found out they carry an elevated risk of Alzheimer's disease based on genetic results. Not all of the content on the site has been developed or reviewed by medical/genetics providers and researchers. Check with your doctor before you make changes based on what you read on the site.

Article from the Philadelphia Inquirer - highlights one person's experience learning about her elevated Alzheimer's risk and advice and resources for others 

Readers who are in the age range of 60-75 years old, you have a chance to help make a difference for your children and grandchildren by enrolling in the Generation Program. There are some particular criteria for participants, so read more here to find out if you're eligible.

-Brianne

 

Click here to schedule your session with Brianne Kirkpatrick, MS, LCGC.

 

Filtering a Promethease Report: One Genetic Counselor's Strategy

There's no right or wrong way to filter through the results of raw genomic data and no professional standards or guidelines about how to do. So I've come up with my own strategy for how to do it out of necessity. It's a common request I receive, and in my quest to help people get proper genetic counseling and the appropriate follow-up testing and/or recommendations, I'm happy to try to help.

There are many reasons you should not rely on a Promethease report or consider raw data to be accurate health information, which I've written about in prior blog posts (and posted a video on YouTube) in the past:

https://www.watersheddna.com/blog-and-news/8-key-points-about-a-raw-data-file

https://www.watersheddna.com/blog-and-news/raw-data-what-is-it

https://www.watersheddna.com/blog-and-news/thirdpartyversusclinicalreport

https://www.watersheddna.com/blog-and-news/thoughts-on-promethease

But don't just take my word for it! Also consider the warnings from the companies and tools themselves, like this fine print on one page of the 23andMe website:

"This data has undergone a general quality review; however, only a subset of markers have been individually validated for accuracy. As such, the data from 23andMe's Browse Raw Data feature is suitable only for research, educational, and informational use and not for medical, diagnostic or other use."  

I know many people will try to make use of their raw data anyway, so here is my guidance for the folks turning to Pomethease. **Again, I want to emphasize this is only one approach, and until there are standards I am not claiming this guidance as personalized medical advice for readers in any way.**

Brianne's Five Steps to Filtering a Promethease Report

  1. Scroll down to the bottom of the report page and set the visualization tool to the "colorblind" setting.

  2. Set “Magnitude” at a minimum of 3.0 and leave maximum at its standard setting (4+).

  3. Scroll down to the bottom to the ethnicity section (at the bottom right), and uncheck all the ethnicities that do not describe you.

  4. Toggle the “ClinVar” button on and off to see what stays and goes.

  5. Review what is remaining and decide for yourself if the finding(s) concerns you.

The first step is optional, but I recommend it because I've found that viewing the genetic markers listed on a Promethease report using the default color setting (red is listed as "bad" and green as "good") can be psychologically misleading and distressing to some people. This report isn't diagnosing you with medical issues, nor is it predicting your future. The genetic markers ("SNPs" or "snips") are simply risk-adjusters. And on top of that, raw data findings can be wrong. Before you believe what you see, find a genetic counselor and seek out a confirmation test from a clinical testing laboratory for anything remaining and concerning to you after you filter through the data. 

Is your raw data from an Ancestry.com test? If you used a raw data file from recent testing through AncestryDNA (the v2 version of their testing platform), be aware that Promethease/SNPedia is reporting many findings as probable miscalls (in other words, false positives). Also, many of the SNPs appear to be missing from the data for unclear reasons. 

These types of blips with raw data happen with other companies' data as well, not just Ancestry's. Make sure you click on each finding in your report before making any conclusions about what you see. Some of the information, such as whether a finding is thought to be a probable miscall, is only visible once you open up the summary about the genetic marker. 

What next?

If you have any markers still remaining after filtering -- and especially if any relate to conditions already in your personal or family medical history -- I recommend you consider scheduling follow-up with a genetic counselor who is familiar with raw data and third party tool reports. You might have to shop around to find one because there aren't too many of us (at least not yet).

Genome Medical is one service that will see patients with questions about specific SNPs and raw data findings associated with health conditions. Genome Medical offers counseling via phone or video and can discuss the potential impact of that marker on your health and order follow-up confirmation testing if appropriate. They do not currently work with patients to filter data or review the entire raw data file, so you will need to have already done the filtering process yourself. 

Some companies, like Color Genomics, offer affordable testing for some confirmation tests.

If you are someone who prefers an in-person type of interaction, you might search for a genetic counselor at a clinic near you. Start at findageneticcounselor.com and search based on location or the genetic counselor specialty (cancer, cardiovascular, reproductive, etc.). Some geographical areas and hospital systems may have a genetic counselor able to assist you and others may not.

Want help with the filtering process or guidance for what to do next after you're done? I'm happy to assist!

-Brianne

Update on May 5th, 2018: My schedule is back up! Search for available appointment spots and sign up for one here: www.watersheddna.com/schedule. Your state of residence may determine if I can work with you, and if I can't help you (due to a licensing restriction in your state), I'll refer you on to someone who can. I'm unable to serve those who reside outside of the Unites States at this time.

Conflict of interest declaration: I do not profit if any testing company receives business as a result of what I say or write. I am part of the network of genetic counselors at Genome Medical, thus I know and respect the policies they set surrounding DTC testing and raw data. I am not affiliated with Ancestry.com, Color Genomics, or any genetic testing company, and I do not get kick-backs if you test with any of them. Just so you know!

Should you do a home DNA test for Alzheimer's?

Alzheimer's is a complicated disease.

There are early-onset forms and late-onset forms that have different genes involved. The risk to develop Alzheimer's as a result of genetic predisposition varies from person to person and family to family, depending on which form is going on and which gene or genes are involved.

We don't know and understand all the factors that cause Alzheimer's yet, so while genetic testing can be helpful, it oftentimes won't be able to tell the whole story. 

If you have raw genomic data you've downloaded from a consumer DNA test (like Ancestry, Family Tree DNA, MyHeritage, or 23andMe), I want you to know some of the limitations that have come to our attention. 

There are known miscalls (testing errors) happening for some of the Alzheimer's-associated DNA markers. Ancestry's chip (v2) is miscalling the APOE e4 variant as normal in those who actually are positive, for example. 23andMe (v5) seems to be having the opposite issue with falsely miscalling a SNP as positive in one of the early-onset genes.

Also, the markers included on testing at consumer companies change over time, so if you try to run an analysis on your raw data (by using Promethease, as an example), your report can change from one file to the next and vary over time. You might see things pop on one report that don't appear on another, depending on the testing company or the version of testing that was used.

My advice when people ask about results on Alzheimer's genes and the results they get back from testing at home is this: talk with a genetic counselor (like myself or someone else you find in your area) to make sure you are understanding the results, and always follow up a home-based test with a clinical test before believing them as "real".

Interested in reading more? Here are two other posts you can read about Alzheimer's and whether to find out if you might have a genetic risk:

https://www.watersheddna.com/blog-and-news/alzheimers-disease-key-points-to-know-in-light-of-the-new-23andme-reports

https://www.watersheddna.com/blog-and-news/need-help-fighting-the-urge-to-open-your-alzheimers-disease-risk-report