DTC genetics

Brianne Kirkpatrick Quoted in WebMD Magazine Articles on At Home DNA Testing

Brianne Kirkpatrick Quoted in WebMD Magazine Articles on At Home DNA Testing

I recently spoke with Sonya Collins who writes for WebMD Magazine. I shared my thoughts and advice on at home DNA tests based on years of both personal and professional experience, and I was pleased to see TWO articles come from it!

Please read, especially the second article! It will equip you to be a savvy chooser of a DNA tests you might purchase online and you can find more detailed advice than what made it into the article HERE.

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!

Resource for Learning about Medical Genetic Testing

If you are a blogger, writer, or speaker who covers the topic of genetic testing, and the topic of medical genetic testing or consumer-based testing with medical implications ever comes up, please stop and read this!

Over the past year, I've been working with a group of genetic counselors on behalf of the National Society of Genetic Counselors to gather, summarize, and explain the various aspects of genetic testing that commonly lead to confusion and concern.

We developed a summary document called the "Genetic Testing Resource" listed in the section of the website aboutgeneticcounselors.com. See the screenshot below for where to find it.

Find the document at http://aboutgeneticcounselors.com/Genetic-Testing, where the orange arrow points. 

Find the document at http://aboutgeneticcounselors.com/Genetic-Testing, where the orange arrow points. 

The aim of the document is to address in everyday language the common questions (and myths) about genetic testing for medical purposes. Some of the many topics addressed in the 16-page document include:

·      Types of DNA that can be tested

·      Different DNA technologies and their usefulness

·      What exactly is “informed consent” for genetic testing?

·      Where do genetic counselors fit in the picture?

If you write about DNA online or in books or speak to audiences, please be extra cautious about the advice you give to others regarding medical information from consumer DNA tests (and especially the raw data to come from them). You are welcome to use quotes from this document as long as you cite it as your source.

Reports produced from raw data files from the consumer testing market and clinical genetic tests are not the same, and it’s critical that if you choose to comment on health topics, you understand how, and why. The “Genetic Testing Resource” will give you a good start.

I’m a consumer of at-home DNA testing many times over. I understand the appeal, and I understand the desire to gather medical information from any test where it’s possible.

I’m also rooted at the intersection medical genetics and consumer testing and see the benefits and limitations from an insider perspective. I don’t discourage people from pursuing information that is important to them, but I encourage everyone to learn as much as possible about the differences between types of testing and the results to come from them.

There is a lot of information that can mislead and confuse. I want you to get accurate and useful medical information, whether you chose a test from the consumer market or opt for a clinical-grade test.

Want to learn more? I've written more about "raw data" topics herehere, and here. Check out those posts if you want to learn more! 

 

Newsreporter shares DNA journey on ABC27 news

Kendra Nichols is a news reporter for ABC27 news, based in Harrisburg, Pennsylvania.

She recently decided to go on a DNA journey, given the limited information she knew about her birth father who was not a part of her life growing up.

I sat down with Kendra the day she swabbed her cheek to talk about a DIY genetic test and to help her prepare for the journey.

Click here to see what Kendra learned about the process, and the risks to be aware of before you sign over your DNA. 

If the link above does not work, try pasting this URL into your browser: http://abc27.com/2017/07/13/what-to-know-about-dna-testing-kits/

Alzheimer's disease - key points to know in light of the new 23andMe reports

Alzheimer's disease is a complex and devastating condition. Genetic factors are only one piece of puzzle, as today's post will explain.

This guest blog post is written by Jamie Fong. Jamie is a board certified and licensed genetic counselor. She provides genetic counseling to people and families with or at risk for inherited neurodegenerative disease, including Alzheimer’s disease, frontotemporal dementia, prion disease, Huntington’s disease, amytrophic lateral sclerosis, and ataxia.

I'm grateful for Jamie taking the time to highlight the key points for my readers. The points she makes in #11 and #12 are especially helpful: you can participate and contribute to active research on Alzheimer's disease, and you can find a genetic counselor near you specializing in risk assessment for the condition. 

In April, the direct to consumer test company 23andMe announced it received FDA approval to offer testing for 10 genetic risk factors. Each of the 10 genetic risk factors is associated with a particular health condition. Alzheimer’s disease is one of these conditions.

That a genetic risk factor associated with Alzheimer’s disease is among the tests included in 23andMe’s Genetic Health Risk Report is no surprise, as Alzheimer’s disease has considerable impact on our society. This is reflected by the large (and growing) number of people with the condition as well as by the skyrocketing number of caregiving hours devoted to and healthcare dollars spent on patients. Alzheimer’s disease appears to rank among the most popular conditions for which people seek direct to consumer genetic testing.

From 2011 to 2013, 23andMe previously offered genetic testing for Alzheimer’s disease. At the request of the FDA in 2013, the company stopped offering it, and the recent announcement heralds the test’s relaunch. You may have questions about 23andMe’s Alzheimer’s disease test or about what test results mean. The following are some points to consider.

1.     Everyone has a chance to develop Alzheimer’s disease, a progressive brain disorder that affects memory and thinking. Age is the biggest risk factor for developing the condition. A person’s chance to develop Alzheimer’s disease increases with age.

2.     23andMe’s genetic test for Alzheimer’s disease determines the chance (or risk) of getting Alzheimer’s disease. The test cannot tell a person whether or not he will definitely develop the condition.

3.     23andMe’s genetic test for Alzheimer’s disease looks at a gene called APOE. ApoE occurs in 3 different versions. Another way to think about this is that ApoE comes in 3 different flavors. Each person carries 2 flavors, which can be the same 2 flavors or different 2 flavors. Only one flavor of ApoE is associated with increased chance to develop Alzheimer’s disease. This is known as the Alzheimer’s risk variant (or flavor), called “E4.” The other variants (or flavors) are not associated with increased chance to develop Alzheimer’s disease.

4.     The effects of having an “E4” variant of ApoE depend on a person’s ethnic background. Among people of European ancestry, having one or 2 “E4” variants of ApoE is associated with increased chance to develop Alzheimer’s disease in his lifetime. However, it is not a certainty that a person with an “E4” variant will get sick.

5.     The "E4" variant is common. About 20% of people with European ancestry have one “E4” variant of ApoE. About 3% of people with European ancestry have 2 “E4” variants.

6.     People with African American ancestry are more likely than people with European ancestry to have an “E4” variant of ApoE. By comparison, people with Mexican American ancestry are less likely to have an “E4” variant. However, African Americans and Mexican Americans have a greater chance to develop Alzheimer’s disease than people of European ancestry, regardless of which ApoE version they have. Other genetic and socioeconomic factors likely play a role in these differences. This highlights our incomplete understanding of the genetics of Alzheimer’s disease among people with non-European ancestry.

7.     A person who has no “E4” variants of ApoE may still be at risk to develop Alzheimer’s disease. In the absence of an “E4” variant, family history of Alzheimer’s disease may be the most helpful tool in determining a person’s chance to develop the condition.

8.     The “E4” variant of ApoE is not the only genetic variant that contributes to Alzheimer’s disease risk. There are numerous other genetic variants involved in increasing a person’s chance to develop the condition. Some of these variants are known by researchers and clinicians, but many have not yet been discovered. 23andMe’s genetic test looks at none of the other Alzheimer’s disease risk variants.

9.     Whether you have 0, 1, or 2 “E4” variants of ApoE, your doctor’s advice to you is constant. This means that your doctor’s recommendations do not depend on your 23andMe’s genetic test result. A heart healthy diet and regular cardiovascular exercise may reduce a person’s risk to develop Alzheimer’s disease. Be wary of claims of the benefits of dietary supplements and/or brain games. Nothing has been proven to prevent Alzheimer’s disease altogether.

10.  23andMe’s APOE test should not be used to confirm or rule out a diagnosis of Alzheimer’s disease. The condition is diagnosed by a multitude of other non-genetic tests. If you are concerned about symptoms, please consult your doctor.

11.  There is hope for Alzheimer’s disease therapies in the near future. Consider participation in research. Check out www.endalznow.org.

12.  If you have questions or want a tailored risk assessment, contact a genetic counselor or other genetics professional. Check out the “Find a Genetic Counselor” feature on www.nsgc.org.

 

Written by Jamie Fong, a board certified and licensed genetic counselor. She works with a multidisciplinary team of neurologists and neuropsychologists at the UCSF Memory and Aging Center, where she is involved in both the Center’s clinic and research programs. Jamie holds a Bachelor’s degree in Molecular and Cell Biology from UC Berkeley, and a Master’s degree in Genetic Counseling from Sarah Lawrence College. 

 

 

MTHFR, and the Watershed DNA approach to DNA testing

There is a growing issue of certain practitioners recommending genetic testing for MTHFR so that they can sell you supplements.  A 2016 article in Forbes magazine highlighted this issue and the inherent conflict of interest it creates. If someone is trying to sell you supplements and is recommending MTHFR testing beforehand, they have likely received biased and incomplete education on MTHFR and its effects on the body.

I have been familiar with the MTHFR gene for over a dozen years, so this is a topic I am used to discussing. My first work with results of MTHFR testing came as a genetic counselor in the prenatal field from 2005-2011. I'm seeing a resurgence of MTHFR results again, due to the push for testing amongst those recommending and pursuing direct-to-consumer tests.

I find it really difficult to counter so much of the information that is being spread about MTHFR on the Internet because there is so much of it. The naturopath community has taken this gene and run with it -- but the conclusions naturopaths, nutritionists, and even some chiropractors are making about MTHFR and recommendations on methylfolate supplementation are not consistent with what research has shown. 

The medical genetics community including the American College of Medical Genetics and the National Society of Genetic Counselors feels the research does not support the claims being made by nutrigenomics entrepreneurs, and there is a divide between the medical genetics and naturopath communities which only seems to be growing wider. Here's another summary by ACMG that lays out the evidence we know about MTHFR and variants found in the gene.

During the time I was a prenatal counselor, we stopped testing the MTHFR gene because we found that the results were not useful. Variations in MTHFR are so common and are associated with (but not directly linked to) a long list of varied conditions. MTHFR can affect homocysteine levels (but not always), and homocysteine is what we are concerned about when it comes to adverse outcomes in pregnancies and risk for other things like blood clots.

We replaced genetic testing of MTHFR with direct testing of homocysteine levels in the blood, and as far as I am aware, this is still the recommendation in the medical/obstetrical community today. 

I'm sharing this information because I feel it is important for my readers to understand the debates going on surrounding nutrigenomics and DNA testing. I continue to educate myself on matters related to MTHFR, new research, and current recommendations and guidelines. I am open to the possibility that there may be something useful that can come from genetic testing for nutrigenomics purposes. However, the more research that comes out, the more convinced I become that the nutrigenomics industry is going in the wrong direction for MTHFR.

It is important not to over-emphasize any one gene to exclusion of others, when there are approximately 20,000 genes and countless environmental factors to consider when considering the way the human body functions. The biological cycle in our cells that controls our metabolism and homocysteine levels involves dozens, if not hundreds, of genes.    

If you have questions about a genetic test result or a health issue that seems to be passing through your family, I would love to work with you. My approach is to focus on the concerns at hand for my clients, and to include a review of personal and family health history. Often times, medical history is more important and informative than the results of any genetic test. 

If you have results already available, I will go through those with you and put all of the test and history information together to create an overall assessment. I offer recommendations on next-steps tailored to you.

For clients who haven't yet had any DNA testing, we'll create a plan that helps you focus testing on your goals. For some people, investigating ethnicity or genealogical connections using an ancestry test is a natural next-step. For others, a health-focused genetic test might be called for. Each person is unique, which means there is no such thing as a one-size-fits-all approach to genetic testing.  

My desire is for all people of the world to find connection and commonality with others and to find meaning and truth in life, whether this ultimately involves a DNA test or not. Navigating all of the information out there is tricky, and I'm happy to use what I know to help those who want to include health, ancestry, and DNA in their personal search. 

More resources for you on MTHFR:

MTHFR summary by 23andMe

http://www.genetics.edu.au/health-professionals/mthfr-dna-test

https://rarediseases.info.nih.gov/diseases/10953/mthfr-gene-mutation

Differences between third-party DNA reports and clinical genetics laboratory reports

This post assumes the reader already knows the meaning of certain terms like "raw file" and "third-party tool" and "VCF". Apologies to DNA newbie readers. 

People are using third-party tools that give consumers information they interpret as health information on themselves.

What comes out of these third-party tools is not actually a genetic health report, but it kinda "looks" like one. The people who manage one such third-party tool, Promethease, have explained in places like the comments section on Judy Russell's blog that they try to help people understand what Promethease is and isn't.  But based on the questions I have coming to me about this and other third-party tools on a regular basis, many people still have questions.

I'll keep on trying to help others understand what third-party tools can and can't tell them about potential health risks and will continue to point out the limitations of third-party tools. No matter how well curated the SNPedia database becomes (and there are many people admirably working toward this goal), it does not change the inherent limitations of the tool itself.

I acknowledge that people are going to use third-party tools no matter what an expert in genetic testing says. If you are going to do this, I support you and will offer guidance as best as I can.

But I would be remiss not to point out what an actual genetic health report from a clinical laboratory includes. 

A genetic health report from a clinical laboratory includes information that genetics professionals can use to gauge the utility and validity of test results. In other words, the details on a clinical report help to answer questions like "Are the results accurate?"  and "Are the results useful?" The type of info I'm talking about are things like testing methodology, for example. There are many different TYPES of genetic testing and different methods to test DNA, and none is anywhere near perfect yet.

I need details to put a genetic result in proper perspective, and a lone VCF file rarely gives me everything I need to assess the results. Clinical laboratory reports fit medical purposes better. These reports provide me with data such as whether confirmation studies were done on positively-identified genetic variants. Why does this matter? Because when you re-test a variant using the same or a different genetic testing method, sometimes a variant no longer shows up. If you repeat the entire test, something might show up that wasn't seen before.

That's right, genetic tests can be wrong! There I said it, and it didn't feel good, but it's true. Genetic tests can be wrong because going from a biological tissue to a computer file is a complicated process and failures can happen at many points along with way. Good news is that most of the time failures don't happen, and clinical laboratories have safeguards in place in case they do. 

Clinical laboratories include info to allow genetics professionals to judge whether the lab is adhering to standards and guidelines to try to cut down on the inevitable errors and mistakes. By including CLIA and CAP certification numbers on a report, for example.

All of this data is important me. I know that when I hold a clinical report in my hand (or, in these in modern times, see it on a screen), that data has come from a place where I can call up and ask questions to laboratory scientists, research scientists, and genetic counselors. Questions like, "Were you able to find a lot of studies or database entries of this rare genetic variant found? If the studies had conflicting results, how did you decide which one to believe? What is your rate of false-positives?" 

The details on a clinical report help me assess how well the DNA results have been analyzed, how confident I can be in telling someone they do or do not have a risk or a predisposition or a disease-causing genetic variant. Many people view certifications and regulations as roadblocks, hurdles, something to bypass or overcome. I view these things as necessary, important, and valuable.

A final note on raw data files at this time...

Raw data from an ancestry company (and raw data from a direct-to-consumer exome sequencing company for that matter) have not gone through quality checks. The data hasn't gone through confirmatory analysis. It's also representing just a smidgen of your entire DNA and only from one type of cell in your body - cells that slough off in your mouth. It's far from perfect, but this is where we are right now.

We'll get to that future of reliable genetic health information at low cost, eventually. But please don't expect that right now because we still have a lot of work to do to get there. 

Virginia Association of Genetic Counselors hosts one-day genetics conference

Virginia is for genetics lovers! The Virginia Association of Genetic Counselors hosted its 10th annual meeting for genetics education in beautiful and historic Charlottesville, Virginia on May 16th, 2016.  Watershed DNA founder, Brianne Kirkpatrick, engaged a rapt audience as she presented on opportunities for genetic counselors to meet the needs of home DNA test customers.

The conference sold out two weeks beforehand, so make sure to book your registration early next year! 

VaAGCmeetingpostcard