DNA.Land

Posted on December 7, 2017 by Roberta Estes

DNA.Land first launched in October of 2015, a free upload site whose goal is to encourage sharing to enable scientists to make new discoveries including the initiative to understand what is needed for a cure for breast cancer by 2020.

Their purpose, as stated by DNA.Land in their FAQ:

DNA.Land is a place where you can learn more about your genome while enabling scientists to make new genetic discoveries for the benefit of humanity. Our goal is to help members to interpret their data and to enable their contribution to research.

DNA.Land has invested a lot of effort into providing tools for genetic genealogists in order to encourage them to upload their autosomal DNA testing results to DNA.Land and participate in research in exchange for having access to their tools.

Let’s step through the process and take a look at their offerings.

If you’re interested in participating, the first thing to do is to register and the next step is the consent process.

Consent

If you are considering participation, or uploading your DNA to utilize their ethnicity or matching services, you must sign their consent form. Needless to say, you need to fully read the consent form before clicking to authorize, at DNA.Land and anyplace else.

Please note that you can click on any image to enlarge.

Upload Your File

After you click to approve and continue, you’ll be asked to select a file to upload. I chose Family Tree DNA Build 37.

Research Questions

Given that the focus of DNA.Land is medical research, you’ll be asked questions about yourself and your ancestry, such as your birthdate, as well as that of your parents.

I joined the Breast Cancer research and authorized researchers to contact me.

You are then asked, “Is this file your file?” DNA.Land wants to be absolutely sure you are providing information for your own file, and not someone else’s.

DNA.Land then asks questions related to your family and breast cancer. I answered the questions, agreed to be contacted if there are questions and joined the study.

You’ll answer questions about whether your parent, full siblings or children have been diagnosed with breast cancer, as well as questions about yourself.

I was excited to see that I was the 7,456^th person to join the breast cancer initiative, but then I realized that their goal is 25,000 by the end of 2017. They have a LONG way to go. Please consider joining.

Your Personal Page

Your personal page includes your file status, the research projects in which you are participating as well as reports available.

Your file status is shown at the bottom of the page, including links to learn more.

About Imputation

DNA.Land was the first vendor to attempt imputation. I wrote about imputation in the article, Concepts – Imputation. I also wrote about matching with a vendor who utilizes imputation in the article Imputation Matching Comparison.

Imputation affects your matches, segment sizes and the quality of those matches. If you’re not familiar with imputation, I would strongly suggest reading these articles now.

While I’m incredibly supportive of the breast cancer and research initiatives, I’m less excited about the accuracy of imputation relative to genetic genealogy. Let’s take a look.

My Reports

Now that I’m done with setup and questions, I’m ready to view information about my own DNA results according to DNA.Land. Remember that these results include imputed information, meaning data that was imputed to be mine in regions not tested based on my DNA in regions that have been tested. My Family Tree DNA file that I uploaded held over 700,000 tested locations, and DNA.Land imputes another 38 million locations based on the 700,000 that were actually tested.

You can select from various My Reports options:

Find Relatives
Find Relatives of Relatives
Ancestry Report
Trait Prediction Report

Let’s look at each one.

Find Relatives

As of today, just over 70,000 individuals have uploaded, an increase of 10,000 in just under two months, so the site is rapidly growing.

The first page is DNA Relationship Matches. The match below is my closest match to cousin, Karen. I wrote about dissecting this match in the article Imputation Matching Comparison.

You can show or hide the chromosome table at far right. Segments are divided into recent and ancient based on the segment size. I’m not sure I would have used the term “ancient,” but what DNA.Land is trying to convey is that more often, smaller segments are older than larger segments.

I have 11 High Certainty matches and 1 speculative.

The information page explains more. Click on the “Learn more about the report” link in the upper left hand corner, which displays the following example information.

All reported segments are 3.00 cM or larger.

Very beneficially, my closest match, Karen, showed her GedMatch kit number as her middle name. I utilized her file at GedMatch and her results at DNA.Land to compare raw data file matching and imputed file matching. You can read about the findings in the article, Imputation Matching Comparison.

Based on imputed matching, I’m not sure that today I would have much confidence in matches to the relatives of relatives, but let’s take a look anyway.

Find Relatives of Relatives

Relative of relatives is a big confusing. Think if it as an alternate to a chromosome browser. Here’s what their information page says about this feature.

This is a bit confusing. The “via” relative is the person on your match report.

The first person listed, or the “endpoint” relative is the person related to them.

The intersection is the set of intersecting matching segments between you, your match and their match that (apparently) also matches you, or they would not be on this report.

Here’s a Relatives of Relatives match with my strongest match, Karen.

The problem is that the person shown as Karen’s match, Shelley, is not shown as my match. The common matching segments between the three of us, shown above and below, are very small. Even though Shelley is a match to Karen, Shelley apparently only matches me on smaller segments, not large enough to pass the DNA.Land threshold for a match.

The problem is that all of the above matching and triangulating segments above are imputed segments and don’t show up as legitimate matches at GedMatch between me and Karen, so they can’t be a valid three way match between me, Karen and Shelley.

In other words, these aren’t valid matches at all, even before the discussion about whether they are identical by descent, chance or population. Therefore, these have to be matches on imputed regions, not through actual testing.

The certainty field is also confusing. I initially though that the “high” certainty pertained to the three way match certainty, but it doesn’t. Certainty means the certainty of the match between your match (the via relative) and the endpoint (their match) and has nothing to do with the certainty of the segments matching the three of you being relevant.

If you’d like to utilize this information, please read the information pages VERY CAREFULLY and be sure you understand what the information, is, and isn’t, telling you.

Ancestry Report (Ethnicity)

The Ancestry report is DNA.Land’s ethnicity report.

Looking at the map, it’s difficult to compare the DNA.Land results to other vendors, because they have Scandinavia divided into half, with the westernmost part of Scandinavia included in their Northwest Europe orange grouping, the light green designated as Finnish with the olive green as North Slavic. Other vendors include Norway and all of Sweden as part of Scandinavia.

One nice thing is that the population reference locations are shown on the map below, even for non-matching reference groups.

In my case, DNA.Land missed my Native American entirely.

The chart below represents my known and proven genealogy as compared to the DNA.land ethnicity results.

You can see how DNA.Land stacks up against the rest of the vendors, below.

Trait Prediction Report

The trait report requires an additional consent form. In essence, DNA.Land wants to make sure you really want to see your traits, that you understand what you are going to see and that you understand how traits are calculated and displayed.

DNA.land offers several traits you can select from.

But there’s a hitch.

Before you can see your traits, you get to answer a survey. In all fairness, DNA.Land’s purpose is medical research, and the reports participants receive are free.

My eye color is accurate, BUT, I also just told them that my eye color is dark brown during the questions. Not terribly confidence inspiring – but my confidence increased after reviewing all of the information they provided about the science behind my actual trait prediction.

The eye color map, above, is something unique I haven’t seen elsewhere. I find this kind of information quite interesting.

Even though I did provide DNA.Land with the “brown eyes” answer, this chart makes me feel much better, because they shared the science behind my result with me. Therefore, I now feel much better, because, based on the science, it’s apparent that they didn’t just parrot my result back to me.

There is also a “what if my result is wrong” link. After all, science is all about continuing to learn and to think we know everything there is to know about genetics is foolhearty.

Yea, I like this a LOT!

If you’d like to read more about how genetic research takes place, read the interesting article titled Is there a Firefox Gene? Yes, that’s the Firefox browser, and yes, this is a real study. Take a look. It’s really quite interesting and written in plain English.

Summary

DNA.Land has a different purpose than other DNA matching and ethnicity sites. As a nonprofit, DNA.Land offers their matching and ethnicity services as an enticement to genetic genealogists who have paid to test elsewhere to upload their results to DNA.land and in doing so, to participate in medical research.

DNA.Land is absolutely up front about their mission. The features are “complimentary,” so to speak, meant to be enticements to consumers to participate and contribute their DNA results.

Given that, it’s difficult to be terribly upset with DNA.Land’s features and services.

DNA.Land has a nice user interface and some nice display features. Their eye color mapping isn’t found elsewhere, and other similar features would make great teaching tools. Their help pages are informative and educational.

Imputation concerns me. Imputation for medical research doesn’t directly affect me today, although it may someday, given that imputed data is used for research.

Imputed data does affect your results at Promethease if you choose to utilize your imputed results as input for any application that reports your academic and/or medical mutations. You can read about that in the article, Imputation Analysis Using Promethease.

Imputation affects matching for genetic genealogy negatively. While I didn’t discuss matching quality in this article, I did in the article Imputation Matching Comparison, which I would encourage you to read if you are attempting to utilize the DNA.Land matching function seriously for genealogy. I would encourage genetic genealogists to simply match at the vendor where they tested, or at Family Tree DNA which accepts uploads (Ancestry V1, V2 and 23andMe V3, V4) from other vendors, or at GedMatch for serious match analysis.

My suggestion to DNA.Land for matching would be to eliminate the smaller segments entirely, especially if they are a result of imputation and not actual matching DNA segments. In my limited experiment, DNA.Land seemed to do relatively well on matching and utilizing larger segments.

Ethnicity results at DNA.Land, called Ancestry Results, are divided oddly, with Northwestern Europe including all of the British Isles, western Scandinavia along with the northwest quadrant of continental Europe. This division makes it extremely difficult to compare to other vendors’ results.

DNA.Land seems to report an unrealistic amount of Southern European, but again, it’s somewhat difficult to tell where the dividing line occurs. It would be easier if their ethnicity map were overlayed on a current map of Europe showing country boundaries. DNA.Land missed my Native entirely.

It would be interesting to know how much of the ethnicity results are calculated on actual DNA and how much through imputation. Ethnicity results tend to be dicey enough in the industry as a whole without adding the uncertainty of imputation on top. Having said that, given how popular ethnicity testing has become, offering another ethnicity opinion is probably a large draw for attracting people to upload and participate in research at DNA.Land.

Some of the trait information is quite interesting and new traits will probably be equally so, although I wonder how much of that information is imputed as well. In other words, I don’t know if the results are actually “mine” through testing or could be in error. The good news is that DNA.Land provides the genetic locations where the trait analysis is compiled, allowing you to utilize a service like Promethease which provides the ability in some cases to confirm imputed data if you upload your actual tested files from testing vendors.

For all results, I would very much like to see a toggle where you can toggle between actual match results and match results derived from imputation.

I would also like to see some research about the accuracy of imputation as compared to non-imputed results. Clearly this would be available through research efforts like my own at Promethease, exome and full genome sequencing.

In a nutshell, DNA.Land provides an interesting free service so long as you don’t want to take the results terribly seriously for genealogy research. If any of the results are important or you want to depend upon them for accuracy, verify elsewhere with actual tested data.

It’s important to remember at DNA.Land that their real goal isn’t to provide a product or to compete with the testing vendors. Their features are a “thank you” or enticement for consumers to contribute their autosomal data for medical research, some of which may be “for profit.” Companies aren’t going to participate in research initiatives that don’t hold the potential for profit.

I really didn’t need an enticement, but I’m grateful nonetheless.

Additionally, DNA.Land has provided an important first foray into imputation and allowed us to compare imputed data with tested data. I know that wasn’t their goal, but I’m glad to have the opportunity to learn and work with real life examples. My own. I would encourage you to do the same.

Be Part of the Cure

The last thing I have to say is that I truly hope and pray that the Breast Cancer Deadline shown as 2020 is a real and achievable goal.

I welcome the opportunity for anything I can to do help eliminate that horrific scourge that has affected so many women. Breast cancer has taken the lives of my family members and friends, as I’m sure it has yours, and I would like nothing better than to participate in some small way in wiping it off the face of the earth. DNA.Land is one way you can help, and it costs you absolutely nothing.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Genos – A Medically Focused DNA Exome Test

Posted on November 27, 2016 by Roberta Estes

Update: As of July 2019, this test and my results are now at https://genos.co after Genos was sold. Original article follows below.

On June 21, 2016, I placed an order for a DNA test with a new company, Genos at http://www.genosresearch.com. The first week of October I received my results.

Genos is a new type of testing company, focused not on genealogy, but on the human exome and medical conditions. Of course, that doesn’t mean that the genetic genealogy community might not find a way to utilize these tests in the future – but today this test is not useful genealogically.

A typical genetic genealogy autosomal test tests between roughly 500,000 and 900,000 locations to compare to others to determine kinship. These are the most variable locations in our genome, the ones most likely to differ from each other and be genealogically useful.

Exome testing, on the other hand, tests 50 million locations – the ones most often medically relevant and the ones we know the most about. Testing the 99% or so of our genome that is exactly like every other human is pointless, for either genetic genealogy or medicine.

What is an Exome?

What is the exome? Genos explains.

Let’s step through the ordering process, then look at my results. They are very interesting.

What is Genos?

Before ordering, I did a bit of research on what Genos offers, what makes them different, and what kind of potential they might have to help me understand my own genes and conditions that makes me unique.

Let’s take a look.

Founders

Genos was founded by these two men.

The next tab is Values, and I’m really impressed, especially with number 4, below.

And the Genos Vision:

Let’s move to the Product page.

Product

Ordering

Your DNA at Genos is yours, entirely, and you can choose when, where and if you want to participate in studies, unlike Ancestry and 23andMe where the consent you MUST AGREE TO in order to activate your kit includes allowing them to sell and profit from your DNA.

Family Tree DNA does NOT sell your DNA. Family Tree DNA does not want the genetic genealogy community to associate genetic genealogy testing with medical testing, because of concerns that it might discourage some people from testing for genealogy.

Before ordering, as with any DNA sequencing product or service, please read the Genos Terms of Service here. The Privacy Policy is here and the Terms of Use are here. These are all actually different parts of one larger document titled “Genos Legal Policies.”

As far as I’m concerned, this is the overarching important sentence:

We do not sell, lease, or rent your User Information without your explicit consent.

Also keep in mind that as with all companies, policies can and do change over time – and it’s the consumer’s responsibility to stay current with the policies of any company you do business with.

A New Business Model

Genos is trying a new business model both in terms of testing the entire exome and in terms of allowing participants to actively participate in selecting research projects, so I decided to be on the frontier of this brave new world. You pay for the sequencing, but the results are yours, forever, whether you participate in medical research projects or not, and Genos doesn’t sell your DNA or otherwise share your DNA results without your permission. You own it and you control it. Period.

I want to contribute to and facilitate research, but I want to select the research projects in which I choose to participate. I don’t feel that it’s ethically or morally right for a company to in essence capture and co-opt my DNA by holding forth the lure of my ancestors as bait. Both Ancestry and 23andMe participate in this unsavory practice. The Genos model very specifically does NOT do that.

Right now, the Genos Exome sequencing product and services are in BETA.

I was the 98^th person to order this test, although I’m sure many more have ordered since June.

Let’s take a look at my results.

My Personal Logo

The first thing Genos does is to introduce you to your genome by creating a personal logo for you, if you select that option. I did, of course.

The circle twirled and locations on my chromosome lit up, like tiny fireflies. I wish I had taken a video.

Next, my unique logo, derived from my DNA, was displayed beside my name.

OK, that was fun, but now, let’s look at the data and what, as a consumer, I receive.

The Four Options

Your results are broken down into 4 categories. You can explore your genome, click on Health Identity, view the News or look at the educational Genomics 101 section.

I first spent a few minutes looking at Genomics 101 which is professional and well written. It includes chapters covering questions like, “What is a gene?”

The News section includes links to articles you may find of interest. Of course, I was dying to see my results, so I quickly moved on to the “Explore Genome” tab, where I saw the Map Your Genome page. So, let’s map my genome.

Map Your Genome

Genos compares your genome of the standardized Genome Reference Consortium reference model.

On the page, below, Genos shows me the 44,154 locations where I vary from the reference model, of which only 773 of these have known medical affiliations or mentions in medical papers. The key word here, of course, is KNOWN. The rest of the variants could be family differences, recently introduced or perhaps from generations back in time. Those locations may not be medically significant, or they may be, but we just don’t know how yet. Time and research will tell.

Out of the 50 million loci (locations) sequenced, I have 773 variants which are certainly of interest and may or may not be relevant medically.

I wondered what happens when a new variant is discovered to be medically relevant or found in a new paper. Would my 773 become 774, or is this a static page, really only relevant to today? I wrote and asked Genos, and discovered that their customer support is very prompt, courteous and helpful. Here’s what they had to say.

At no additional cost to you, as the information in ClinVar (the NIH sponsored database) is updated with new assessments and new discoveries, your data will be automatically updated through our digital experience. This ensures that you are always aware of the latest literature available.

This is great news, making this product infinitely useful (medically) into the future.

You can view all of your chromosomes with the chromosome number and the number of identified variants present on each chromosome, below. Please note that you can click on any image to see a larger version.

Genos allows you to browse your medically relevant variants and what they may mean. The results are broken down into “Conditions” and “Traits,” as seen at right, above.

The Conditions are health related, but just because you have a mutation that may be associated in literature with a particular condition, that does NOT mean you have or will ever be diagnosed with that condition. In fact, as you can see, the literature itself is often contradictory. We don’t always understand what makes one person get a disease while another person does not.

For this reason, nearly every page that involves conditions also contains a link to genetic counselors along with cautionary messages that succinctly warn people against assuming that variant=disease. It doesn’t.

Individual Chromosomes

You can explore each chromosome individually.

I clicked on variant 1, on chromosome 1, above.

If I click on the NEXN with the right arrow, I see the display below.

If I click on the G>A which means the normal G nucleotide at this location has been replaced with an A in my case, I see the following:

I can then read more about this gene and the mutational variant.

I must tell you that I feel very empowered by having my own genetic information at my fingertips that was previously entirely unavailable to me, or available only through a medical provider, if at all.

Conditions

Moving now to the Conditions link on the right hand side of the main page, I can see the following conditions, grouped by category.

You can explore the Conditions link for conditions associated with your variants, the Traits or the Variants themselves.

By clicking on the icons, you can see how many variants you have in each category. The first category is allergies.

For example, here is one of my Conditions. I’ve chosen to share this one because you can tell by looking at my picture that I am clearly NOT albino.

Still, I carry at least one mutation associated with this condition.

Almost every single page carries this warning verbiage, which is proven by my albinism mutation and my somewhat younger photo when my hair was still its original color!

Variants

Variants are divided into groups.

Most of my findings are benign. Whew!!!

This is an example of one of my benign variants.

You can see that while this mutation is mostly benign, or green, some papers show it to fall into the other risk categories.

Please note the verbiage at the bottom of the screen.

“What is believed to be true today may be disproven tomorrow.” That’s part of why I’m participating in this type of testing.

The screen for each variant goes on to provide the links to the studies themselves, which may or may not agree, so you can read and digest for yourself. Please, unless you’re an MD, do not attempt to be your own doctor!

Traits

The Traits at Genos are the same traits that are tested and reported by other testing firms as well.

Like other genetic values, variants and results, these may or may not be accurate. My hair is very thick, as you can see from my photo, I taste bitter very well, unfortunately, and my skin is not light…at least not for someone primarily Caucasian. Some of these traits are clearly subjective. They make for interesting party conversation.

Health Identity

The next section of the website if for Health Identity. This is where you provide information about yourself and your health history.

If you’re going to participate in this type of endeavor, it’s important to provide Genos with as much information as possible. That’s one avenue for Genos to know who would might be a good candidate for specific kinds of research.

Research

While there aren’t any research projects yet underway today, there will be in the future.

And last but not least…

Genetic Counselors

If you discover something you would like to know more about, or that concerns you, you can make contact with a genetic counselor through the Genos site.

Caveat

I am, personally, very much an advocate of genetic research, when it is preformed ethically, transparently and with full disclosure. As far as I’m concerned, Genos absolutely fits that bill.

However, if someone were prone to anxiety or hypochondria, this type of testing might not be a good fit.

I’m not prone to either, and I have a very high risk tolerance level, but I still am inclined to spend quite a bit of time looking at the variants that aren’t benign. If you are in the “don’t want to know” camp, then don’t test. Bottom line.

Let me say this again.

Don’t test if you really don’t want to know.

You cannot put the genic back into the bottle once it’s out.

Exome testing is different than genetic genealogy testing and has the potential to reveal information which may be frightening or distressing to some people, which is why I shared my results with you in such detail.

Looking to the Horizon

Having said that, I find exome testing absolutely fascinating. I would like to see if my children have the same variants that I do. Did they inherit those from me or did those variants bite the dust in my generation? Are there variants that I carry one of and my children have two, meaning their father contributed one as well? What does this mean, health-wise, potentially, for my grandchildren? What did they inherit?

Of course, today, exome comparisons between individuals are not possible at Genos (or elsewhere), but perhaps in the future?

Could this type of testing be a step forward in identifying conditions and diseases not yet “discovered” as we define them today? Some mutations affect particular individual family lines negatively, and sometimes fatally. Can exome testing help these families, if not today, then tomorrow? Exome testing certainly has that and a lot more potential.

I’m excited about being able to select and participate in research studies with the ability for the researchers to contact me to follow up many years into the future, if need be. The new Genos model allows citizens willing to have their exome sequenced the opportunity to help shape the future of medical understanding and potentially, contribute to treatments and cures – in addition to learning a great deal about their own DNA and literally what makes them tick. Which studies you participate in and what happens to your DNA is entirely within your control.

I hope that a research project (or projects) that I participate in eradicates a disease or diseases so that my descendants will only read about the disease in history books and will hopefully know that their ancestor played a small role in disease extermination.

In the mean time, I’m very actively participating in exome testing to attempt to track and identify a fatal family mutation that has plagued one family for at least 4 generations. Of course, we don’t yet know how successful we will be. However, exome testing, especially at this price, holds promise that was never available before. I hope that what today is literally a life and death experiment will one day be a standard testing routine available to any family with this type of issue. I’ll let you know the outcome in a few months.

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Disclosure

Thank you so much.

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