raw data

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

Should people have 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.

GEDmatch & the Are Your Parents Related tool: What it means if you see a lot of blue

GEDmatch is a free website with tools that enable genealogists to use DNA and family trees to search for relatives. It has been in the news lately because it has recently been used to to identify criminal suspects. Tracing individuals based on their relatives DNA and family trees are only part of what GEDmatch allows DNA researchers to do. Other tools are available on GEDmatch, including one called "Are Your Parents Related?" (AYPR, for short). 

DNA Testing: Ten Tips for Adoptive Parents

DNA Testing: Ten Tips for Adoptive Parents

I’ve spoken with a few parents of children who were adopted, and DNA testing is clearly on the radar for many of these families. News reports and TV shows that highlight adoption reunions facilitated by DNA and health discoveries from genetic research have piqued the interest of many.

I’ve compiled ten tips for adoptive parents based on common questions and issues. The focus is on parents of children under the age of 18, but these points can apply to other families as well, such as those who included egg, sperm, or embryo donation in building their family.

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).

GEDmatch, raw data, and solving violent crimes with genetic genealogy

Kendra Nichols from abc27 News interviewed me about DNA testing, and we chatted a bit about the fine print you agree to when you submit a DNA sample to a consumer testing company.

Although it isn't named in the short news segment, a voluntary site created for genealogists called GEDmatch is the site law enforcement and others are using to solve crimes. Solving crimes has included finding suspected perpetrators and identifying victims (in other words, re-identifying deceased persons whose bodies were found and that police were previously unable to identify; these are referred to as John and Jane Doe cases).

DNA security: my thoughts in the wake of the Golden State Killer case development

The use of the genealogical DNA website called GEDmatch to solve a long history of crimes perpetrated by the Golden State Killer has a lot of people wondering, “Should I be concerned about the privacy and security of my DNA?” There is nuance to this question. One person who asks it might be asking whether a company might give away their information without permission. Another one might be more concerned about whether someone with ulterior motives could 'hack' the system at a company (or at an independent DNA sharing site) and take data not approved by customers or users.

Without getting into the weeds too deeply, my opinion on this in a nutshell is this:

Think of DNA security the way you think about credit cards. 

Some people opt out of using credit cards because they know of theft; it’s happened to them or someone they know. Or they are generally worried about it even if they've not yet been affected personally. Other people may weigh the risks of private information being stolen if they use a credit card (or other digital payment system like PayPal), but then decide the ease of using them is worth the risk. It has become culturally normal to use credit cards and online payment systems, and the risks are understood and accepted. 

It almost seems as if no one expects perfection in credit card security. So it is becoming for DNA testing as well.

There will always be a spectrum of how much risk people are willing to take, and that’s ok. We all are different and have had different experiences that attune us to what ought to be cause for worry. What concerns us is not the same as what concerns others. 

The reports of genetic information being 'stolen by bad guys' are non-existent at this point; however, law enforcement has tried to get genomics companies to turn over information, mostly unsuccessfully. The Golden State Killer case recently in the news was a situation in which the absence of laws and regulations around publicly-shared information about DNA matches meant law enforcement was free to use it in a way that helped them solve their case. This wasn't stolen information, per se, but few people who had uploaded their computerized DNA information to GEDmatch seem to have anticipated this use. Some are okay with it, some are not (and have reached out to request their data be deleted).

Are you okay with the use of DNA from family members by law enforcement to solve cases of murder and rape? There isn’t a right answer to this one, but we should still be asking it and discussing it.

What about DNA being held by private companies, like 23andMe and Ancestry.com? In comparison to third-party DNA sharing sites where 'user beware' is the expectation, genomics companies have it in their interest to keep your information as secure as they can -- their reputation hinges on it, in a way.

So they are trying, but in spite of all efforts including the employment of folks with titles like "Chief Security Officer", it might be possible in the future that their security fails. Or that they slip in some language into the terms of service agreement that gives them more freedom to use and share your DNA information than you fully understand.

So bottom line, do I think you should take a DNA test? 

You probably aren't surprised that my answer is the decision falls right back on you.

If you’re ok with the chance of your DNA being used in unique ways or in going farther than you imagined it would in order to answer other people’s questions, take the test. If not, testing might not be right for you. 

-Brianne

Interested in reading more about the Golden State Killer case and how genetic genealogy was involved? This blog post by genetic genealogy blogger Debbie Kennett compiles many relevant articles related to the case.

Want help in understanding the terms of service before you send in your DNA sample or share your computerized DNA file with a third-party website? I'm a licensed and certified genetic counselor, and "seek informed consent" is one of my mantras. Schedule a one-time session with me, and I'll be happy to help you go through the terms you're being asked to agree to.

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! 

 

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.