Downloading Ancestry’s Autosomal DNA Raw Data File

Posted on March 21, 2013 by Roberta Estes

Well, the big day has finally arrived. Ancestry has at last allowed us to download our raw data files. To download yours, sign on to your Ancestry account and fly over the DNA tab. You’ll see the selection, “Your DNA Home Page,” Click on that.

Then click on “Manage Test Settings” to the right of the orange “View Results” box. You’ll see the following screen.

ancestry download 1 Click on “Get Started” in the right hand box under “Download your raw DNA data.” You will then be prompted to enter your password to receive an e-mail to allow the download.

The e-mail will arrive, and you will need to click the link in the e-mail, shown below, to activate the download.

Clicking on the e-mail link “Confirm Data Download” takes you to the next step on Ancestry’s website, below.

Clicking on the green “Download DNA Raw Data” link shows the following:

Shortly, your browser will do whatever it does to ask you if you want to save or display the file.

I use Internet Explorer and download files are automatically saved in the “download” folder. I renamed it and moved it to someplace where I can find it, hopefully. The good news is that if I “lose” it on my computer, it’s easy to repeat this process.

Now, what can you do with this file today? Not a lot. You can compare raw data segments with others who might download their files too, but life will be a lot easier when tools like GedMatch can accept these files and do something with them. There were also rumors last fall that Family Tree DNA would support uploads as well when Ancestry released these files, the same as they do with 23andMe raw data files. Let’s hope so.

However, today will be the first day these organizations see the raw data too, so expect a bit of lag time before anyone can process or incorporate this information. Of course, it goes without saying that we have to address issues pertaining to file layout and compatibility.

I’m hopeful that since Ancestry has the raw data files for everyone who has tested there, that they will do what the other two major players have done and create a chromosome browser where you can see who matches you on which segments and download that comparative information as well. It’s not just the raw data we need, it’s the integrated tools to use it. Hopefully we’re at the crawl before you walk stage and we’ll be walking soon!

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The Autosomal Me – Start, Stop, Go – Identifying Native Chromosome Segments

Posted on March 18, 2013 by Roberta Estes

This is Part 7 of a multi-part series.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets. Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis. In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering. We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7 – “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, takes a deeper dive and focusing on the two chromosomes with proven Native heritage, begins by comparing those chromosome segments using the 4 GedMatch admixture tools. In addition, we’ll be extracting Native segment chromosomal start and stop addresses that we’ll be using in a future segment.

Using Doug McDonald’s tool and the 23andMe results, we can begin with the following two Native segments, one each on chromosome 1 and 2. These will be our reference points, because according to both sources, these are the largest and most pronounced Native segments, the strongest indicators, so they will be our best yardsticks.

	Chromosome 1	Chromosome 2
23andMe	165,658,091 to 175,711,116	86,316,174 to 103,145,426
McDonald	165,000,000 to 180,000,000	90,000,000 to 105,000,000

On all of these admixture graphs, my results are shown first, then mother’s, then the comparison between the two where the colored regions show common ancestry and the black shows nonmatching segments – in other words those contributed by my father.

Please note that Native contribution in this analysis is being evaluated by a combination of geographies. In some cases, one individual will show as “Native” meaning in the case of MDLP “North Amerindian” and the parent (or child) will show as something similar, like “Actic,” “South American” or “MesoAmerican.” In order to normalize this, I have combined all of the geographies that are Native indicators.

MDLP

On the MDLP graph below, the legend indicates that these 4 regions are relevant to Native ancestry.

Army green – Mesoamerican
Lime Green – Arctic
Emerald – South American Indian
Grey – North Amerindian

Chromosome 1 – Native Segment

On the graph below, you can see that mother has more grey than I do from about 162-165, but then I have some grey that she does not at about 170.

A detailed analysis of the segment of chromosome 1 between 158-173 shows the following admixture:

On my results, the putty green, MesoAmerican, is scattered between about 158 and 173, in three segments. The putty green in my mother’s segments are from 159-160.5 and then 167-170.5. Therefore, my father, by inference has a segment from about 162-165 and from about 170.5 to 173.

My teal, North Siberian, ranges from 162-163 and from 168-171. My mother carries no teal in these segments, so this is inferred to be contributed from my father.

My dark grey, North Amerind, ranged from 162-165.5 and then from 168-169.5. My mother’s range is from 161-165.5. Therefore my grey segment at 168-169.5 is either recognized as MesoAmerican or Arctic Amerind in my mother.

Chromosome 2 – Native Segment

Chromosome 2 is quite interesting. You can see that on my chromosome, the North Siberian begins at about 80. Mom has none at that location. My North Amerind begins at about 95 and extends to 105, where Mom’s begins in the same location but then transitions to a large segment of MesoAmerican which I do not carry. I do have MesoAmerican, but mine begins about where hers ends and extends to about 105. Mom’s North Amerind ends about 101, while mine continues to about 105. She looks to have trace amounts beginning about 105 and extending through 115.

Eurogenes

The next graph shows the same chromosomes using Eurogenes. Regions relevant to Native ancestry include:

Red – South Asian
Brown – Southwest Asian
Yellow – North Amerindian and Arctic
Putty – Siberian
Emerald – East Asian

Chromosome 1 – Native Segment

The difference between my chromosome 1 and my mother’s in this region is quite pronounced. My mother’s is drenched in beautiful red South Asian, while I have absolutely none. Some of the area where I have North Amerindian shows as South Asian on hers, but in other areas, there is no correlation. It is expected of course, that there are areas where she has some ancestry and I have none, due to the fact that I only inherit half of her DNA, but she has a significant segment of East Asian between 163 and 164, and I look to have received only a very small portion. The same is true of her Siberian segments at 163-164, but then I have Siberian that she does not at 169-170 and she has some that I don’t at 160-161.5. Some of this difference can likely be explained, especially between the yellow North Amerindian and the red South Asian by slight differences in the DNA read and how it is categorized, but in other cases, the difference is real. Looking at mother’s red segments from about 166.5 to about 168 and then looking at my corresponding region, you can see that I have nothing that hints at Native. In that region, I clearly inherited from my father as well as my mother’s North European.

Chromosome 2 – Native Segment

As different as our chromosomes 1 were, one wouldn’t expect chromosome 2 to be so similar. In the graph, I included my large South Asian segment surrounding 80, where Mom has a trace, although that is beyond the area indicated as Native by 23andMe and Doug McDonald. In the range of interest, beginning at about 80, we find nothing until about 94 where mother and I both have North Amerindian segments that stretch through about 105. Mom’s goes slightly further than mine, to about 105.5. It’s interesting to note that in part of this region, on either side of 101, her Siberian and my North Amerindian are the same shape at the same location, so obviously the same DNA is being read and categorized as two different regions, probably due to my father’s admixture.

Dodecad

On the Dodecad graph of the Native segment, you can see the Native colors are in shades of green.

Putty – West Asian
Yellow-green – South Asian
Emerald – Northeast Asian
Light Green – Southeast Asian

To use Dodecad in an equivalent manner as the rest of the tools, it looks like Northeast Asian is the closest we would get to Native American since that is where Native Americans lived just prior to crossing Beringia, so the greens should probably be evaluated as a group. As can be seen on chromosome 1, they do clump together. Even though West Asian is also found with this group, it seems to be outside the range, so I am not including it in the evaluation.

Chromosome 1 – Native Segment

You can see another example here of one segment being called South Asian in Mom’s and Northeast Asian in mine at about 170mb.

The Native, or in this case, Northeast Asian/Southeast Asian begins at about 162.5 where Mom’s and mine are very similar. However, we diverge at about 164.5 where Mom begins with large segments of South Asian. I have a little bit, but not much. Beginning about 168, I have a large Northeast Asian segment, but she shows with South Asian there, although the segments are not exact.

Chromosome 2 – Native Segment

Chromsome 2 is quite simple using Dodecad. Only two of the three groups appear. Southeast Asian is absent, South Asian is present only in trace amounts except for one small area between 79.5 and 80 on my chromosome. As expected, Northeast Asia is more prominent. Mother has a few areas that I don’t, which is to be expected.

HarrappaWorld

Last, we have HarrappaWorld. American and Beringian are the Native American categories here. Regions relevant to Native American heritage would be:

Teal – American
Periwinkle – Beringian
Lime Green – Siberia
Emerald – Northeast Asia

Chromosome 1 – Native Segment

You can see both Beringian and American embedded again at about location 169. In mine, this entire block reads as American.

There is one large chunk of Northeast Asian showing for both results, but part of that region of my chromosome, between 163-164 shows as American instead of Northeast Asian. The Beringian is scattered through the American, which I would expect. The American runs either strongly or weakly through this entire segment from 163 to 175 in mine or to 179 in mother’s. Surprisingly there is no Siberian at all. I would have expected to see Siberian before Northeast Asian.

Chromosome 2 – Native Segment

Where on chromosome 1, we saw no Siberian, on chromosome 2, we find Siberian instead of Northeast Asian. I have no Beringian, but mother has 4 segments. Three of her 4 segments are embedded with American segments. Two may simply be categorized differently in my results, but two, I did not inherit.

Analysis Discussion

What have we learned?

When we are dealing with small amounts of minority admixture, they may or may not be able to be picked up directly by the testing companies. Of course, part of this has to do with their thresholds for what is “real” and reportable, and what isn’t. Aside from that, lack of identification of minority admixture probably has to do with which segments were inherited and their size, if they have been isolated and identified as Native by population geneticists, and the robustness of the data base sources the data is being compared against.

We can also see how difficult it is to sort through threshold matches, meaning what is Native, Asian, central Asian, etc. Many of these differences are probably not actually differences between groups, but similarities with slight categorization differences. Of course, it’s those differences we seek to identify our ancestral heritage. Combining similar geographies may help reveal relationships masked my reporting and categorization differences.

Given that multiple sources have indicated Native ancestry, and on the same two chromosomes, I have no doubt that it exists. Had any doubt remained, the exercises creating the MDLP Chromosome Map Table and reviewing the segments on chromosome 1 between 160 and 180mb would have removed any residual concerns.

The following table shows the results for the Native segments of chromosomes 1 and 2 beginning with the 23andMe and McDonald results, and adding the start and stop segments from each of the 4 admixture tools we used.

	Chromosome 1	Chromosome 2
23andMe	165,658,091 to 175,711,116	86,316,174 to 103,145,426
McDonald	165,000,000 to 180,000,000	90,000,000 to 105,000,000
MDLP	162,000,000 to 173,000,000	80,000,000 to 105,000,000
Eurogenes	162,500,000 to 171,500,000	79,000,000 to 105,000,000
Dodecad?	162,500,000 to 171,000,000	79,500,000 to 105,000,000
Harrappaworld	163,000,000 to 180,000,000	79,000,000 to 104,000,000
In Common	165,658,091 to 171,000,000	90,000,000 to 103,145,426

Although the start and end (or stop) segments vary a bit, all resources above confirm that the region on chromosome 1 between 165,658,091 and 171,000,000 is Native and on chromosome 2, between 90,000,000 and 103,145,426. Those are the areas “in common” between all resources, which is shown in the last table entry.

The concept of “in common” is important, because while any one resource may report something differently, or not at all, when all or most of the resources report something the same way, it is less likely to be a fluke or reporting issue, and is much more likely to be real. We’ll be using this methodology throughout the rest of the articles in “The Autosomal Me” series.

In the next segment, Part 8, we’ll be extracting the actual start and stop addresses of the Native only segments, referred to as the “Strong Native” method, and the combined Native indicator segments, referred to as the “Blended Asian” method and looking at how we can use those results.

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The Autosomal Me – DNA Analysis – Splitting Up

Posted on March 12, 2013 by Roberta Estes

This is Part 6 of a multi-part series.

In this segment, Part 6, “DNA Analysis – Splitting Up” we’re going to focus on specific aspects of those tools and begin our analysis of our minority ancestry.

Analysis. Sounds like I’m climbing on the shrink’s couch. But I’m not, I’m saving all my dollars for DNA kits! Besides, I don’t want to stop! This analysis, we’ll do by putting several pieces of data together and sorting the wheat from the chaff. And yes, we’ll be splitting up…well…splitting our DNA up into pieces contributed by our father and mother.

Let’s start with looking at the DNA segments that mother and I share that are Native.

According to Doug McDonald, we have significant Native matches on chromosomes 1 and 2, with third party tools confirm that finding. Unfortunately, the only company where Mom’s DNA resides is Family Tree DNA whose test did not reveal the Native ancestry. 23andMe did confirm Native segments in my DNA in those locations.

I’ve used several third party tools at GedMatch to see where Mom and I both have Native heritage, where she has it and I don’t, and equally as important, where I have it and she doesn’t? What is that so important? Simple, it means my father had Native heritage too, and tells me on which chromosomes his Native DNA is located This could, when matching people in the future, on particular segments, help to isolate who our common Native ancestor was, or at least which line. That is the ultimate goal we are working towards with this entire process.

In this case, to identify my father’s Native lines, if Mom and I neither or both have Native markers at a particular chromosome location, the values are irrelevant, because the Native lineage came from mother. I did notice in a few cases that I had more than mother, and of course, in that situation, it means that my father contributed some too, or my mother had a misread in that region or a categorization issue exists. For that reason, I am looking for patterns, not single instances. We’ll discuss using patterns in a future segment.

Using the MDLP chromosome mapping tool, as MDLP appears to be the most comprehensive, I created a spreadsheet using my results as a base. I then added mother’s values in the spaces where I had no values, and then I highlighted my results in the locations where mother had no value. The essence of this is that the red, bold, underscore values mean Mom had a Native result here, but I didn’t receive it. A yellow highlighted cell means I got the entire amount from my father, because my mother has no percentage showing. In other cases, of course, it’s possible that both mother and father contributed Native ancestry on some adjacent chromosome segments. The MDLP mapping tool with my additions is shown below for chromosomes one through eight. Chromosomes 9-22 are similar, but the chart is too big to display as a whole. This provides an example of how to do this analysis with your own results.

The results were very interesting.

My two primary regions, North-East-Europe and Atlantic-Mediterranean-Neolithic, were represented on every chromosome for both my mother and myself. No surprises there. The other regions would be considered minority admixture.

In 2 categories, North-European-Mesolithic and East Siberian, only my father contributed genetic material on some chromosomes and there were no chromosomes where my mother alone contributed.

In 1 category, Melanesia, only my mother contributed genetic material on some chromosomes and there were no chromosomes where my father alone contributed.

In all other categories, both parents contributed on some chromosomes where the other didn’t. This is important, because it will allow me to associate a match with a particular segment of a chromosome on a particular parent’s side with Native ancestry.

In the minority categories for Native American, Mesoamerican, Arctic-Amerind, South America Amerind and North Amerind, grouped together, both parents contributed on some chromosomes where the other didn’t, and in two categories, on 3 chromosomes, I carry more than my mother, indicating an additional contribution from my father.

This is a repeated occurrence, with Native ancestry for my parents and I combined showing on a total of 42 chromosome locations across 4 geographic/ethnic categories, and in at least three cases, both parents contributed.

In the African categories, South African, Sub-Saharan and Pygmy, I had contributions from both parents on a combined total of 18 chromosome segments. The African admixture, in total, was less than the Native, and they are assuredly below 5% combined. If they were present at higher levels, I wouldn’t need to go through these genetic gyrations to prove or disprove the heritage and which parent contributed, because it would be evident in the testing results of all companies.

In our next segment, Step 7, we will be further scrutinizing Chromosomes 1 and 2 for additional information about Native heritage and assigning specific Native segments that I carry on various chromosomes to either my mother or father’s lineage.

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The Genomics Revolution 13 Years Later – Bennett Greenspan

Posted on March 9, 2013 by Roberta Estes

On April 29, 2013, from 11 AM-12 noon, Bennett Greenspan will be the featured speaker in the CSE Distinguished Lecture Series in the Georgia Tech Auditorium located in the Technology Square Research Building, 85 Fifth Street, Atlanta, Georgia, 30332.

Bennett will be speaking about bridging the gap between traditional genealogy and genetics, and will be discussing the various kinds of testing and when each is important. He will also be talking about new technology, exome and full genome sequencing and how that will be important to individuals.

Always a man with his eye on the horizon, thankfully for genetic genealogists, Bennett says the genomic revolution has just begun.

Bennett is speaking at the Bremen Museum on Sunday, April 28^th at 2PM about using DNA to settle family disputes, connect to long-lost relatives and to garner an appreciation for where your ancestors came from and where they journeyed since our departure from Africa.

For those who have never heard Bennett speak, he is an exceptional speaker and makes genetic genealogy not only understandable, but very attractive to the novice. Being a genealogist before genetic genealogy, a field established by Family Tree DNA, he brings a very powerful personal story to the table. He has a way of speaking and simplifying the complex that resonates with people.

This is also a rare opportunity to hear someone personally who has directly caused a technology revolution. Bennett founded Family Tree DNA in 2000, actually, almost by accident, as a result of the process he went through trying to answer one of his own long-standing genealogy questions.

I hope you’ll have the opportunity to attend one or both of these presentations. Even though I’ve heard Bennett many times, if I were anyplace to close to Atlanta, you can bet I’d be in the audience. Hearing Bennett speak makes me fall in love with genetic genealogy all over again!

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Personal Genetics – Coming out of the Closet – Ostriches, Eagles and Fear

Posted on March 6, 2013 by Roberta Estes

While most of the people subscribing to this blog are here because of genetic genealogy, genetic genealogy is only one piece of the picture of the future of personal genetics. Ironically, it’s genetic genealogy that gave low cost genetics a push into the mainstream, some 7 or 8 years before 23andMe, the first personal health genetics company, launched in 2006.

This week, the magazine, ieee Spectrum, of all places, has an absolutely wonderful article, The Gene Machine and Me, about the future of personal genetics. Many of these types of articles are sensationalized and full of what I call “fear-mongering,” but this one is not only excellently written, it’s accurate and interesting – a triple hitter home run as far as I’m concerned.

I’d like to talk for just a minute or two about the high points in this article, about this emerging technology, what it means to us and about fear. I’ll be sharing my personal journey down this path.

For those who would like to know how next-generation technology works – by the way – that’s the chip technology employed by Family Tree DNA for the Family Finder product, 23andMe for all of their testing and the National Geographic Geno 2.0 project – this article has a very educational description that is understandable by regular air-breathing humans. The next-next generation sequencing, discussed here and offered shortly by Ion Torrent, will certainly revolutionize personal genetics much as the Illlumina genotyping chip technology has today.

The benefit of full genomic and exome sequencing, the new technology on the horizon for consumers, is in the information it will tell us about ourselves. And I’m not referring to genealogy here, although that assuredly will be a big beneficiary of this new world of personal genetics. For genealogists, there is mention of soon-to-be capabilities of sequencing from one single molecule of DNA. For those of us with hair brushes and toothbrushes that we’ve been jealously guarding for years now, waiting for the technology to improve to the point where we can obtain the DNA of our dearly departed loved ones, this is going to be our ticket. As excited as I am about that, that’s not the potential I’m talking about. I’m talking about information about our own bodies and the potential future foretold in those genes. Notice the word potential.

The information in our genes is seldom a death sentence. In rare cases, it is, such as Huntington’s Disease. If this disease runs in your family, you already know it and testing should be done in conjunction with genetic and/or medical counseling. For these people, DNA testing will either confirm that they carry that gene, or relieve their mind that they do not.

For the vast majority of us, the information held in our genes it much less dire. In fact, it’s a good news message, as it will provide us ample warning, an opportunity, to do something differently with our lives to prevent what might otherwise occur. So it’s not a death sentence, more of a life sentence. For me, it was an epiphany. Yes, I took positive action and made dramatic life changes as a result of my DNA test results. In essence, this is my “coming out” story.

I was one of the first people to order the new 23andMe test when it was first offered, mostly for the genealogy aspect, but as you know, it includes health traits and information. When I received the results of that test a few years ago, in black and white, where I could not possibly ignore them, the reports indicated that I was at elevated risk for certain conditions. Those conditions were certainly beginning to manifest themselves in my life. I was on medication for two of them. My weight, at the time, was certainly a contributing factor to the development of those conditions. My sister had died near the age I am now as a result of those conditions. She looked like me, was built like me, was heavy like me, and very probably carried those exact same genetic risk factors. Our grandfather died of the same thing about the same age. Our father had it too, but he died in a car accident – caused by a coronary episode, at age 61. Seeing this, in black and white, and knowing my family history, I decided to do something to prevent that future, or at least to delay or mitigate it as much as possible.

I lost over 100 pounds and yes, for almost 5 years now, I’ve maintained that weight loss, well except for a pesky 10 or 15 pounds that I fight with regularly. But still, the 100 pound loss is far more important than the 10-15 pounds I battle with. I am off of all medication related to those and related conditions. I’ve changed what and how I eat, and a benefit I really didn’t anticipate is how much better I feel. You have no idea how much I hate these old pictures of me when I was heavy. This was taken at National Geographic Headquarters in Washington DC, in 2005, at our DNA Conference.

This next photo is me at one of our Lost Colony archaeology digs about five years later wearing one of my favorite t-shirts that says “Well Behaved Women Seldom Make History.” All of the genealogists should be laughing about now. No one wants well-behaved women because you can’t find them in the records. If my clothes look a bit large, that’s because they are, but that t-shirt was too small before the weight loss. I could never have done the physical work on those digs, or survived the heat, before losing the weight and going from a size 22 to a 12 in the photo below. These kinds of activities were all unforeseen benefits of the weight loss. My sister’s untimely death was not wasted on me, but served as a warning bell, well, more of an unrelenting siren actually, when I saw those DNA results.

I also took my 23andMe results, at least some of them, the ones related to the conditions I was dealing with, to my physician. I really had to think long and hard about this. So now, let’s talk about the fear part of the equation.

Fear of genetic results falls pretty much into two categories. We’ll call these the Ostriches and the Eagles.

My brother was an Ostrich. Yep, he was, head right in the sand. He had cancer, his wife had cancer, twice, his daughter, in her 30s, had cancer, yet their decision when offered free DNA testing was to decline – because they didn’t want to know. Fear of the information itself, fear of knowing, perhaps spurred because of a sense of fate – nothing we can do about it so why know about it. He also refused to discuss it, so I really can’t tell you why, and he died, of cancer, last year, so that opportunity is past. Personally, I think knowing about a genetic proclivity would equate to more vigilant monitoring. And knowing the proclivity didn’t exist would set one’s mind at ease. I would think you would be a winner either way, but my thinking and his were obviously quite different.

The other group are the Eagles. They are vigilant and acutely aware of the fact that health based discrimination does exist. It has been worse in the past than it is now. This is the reason I had to think long and hard about taking any of my results to my physician. Once in your medical record, it’s permanent.

Today, GINA, the Genetics Information Nondiscrimination Act, goes a long way to protecting people, especially in an employment situation, but it does not cover everything.

Anyone who has ever tried to obtain health care insurance individually or through a small business knows all too painfully about pre-existing condition exclusions. Well, the good news is that ObamaCare, love it or hate it, levels that playing field for the “rest of us,” those who either were denied or had to make life and employment decisions based on whether or not they had insurance coverage through a group where discrimination related to pre-existing conditions didn’t exist.

The other good news is that you don’t have to take any of your DNA test results to your doctor. It’s entirely up to you. You can test anonymously, using an alias, if you’re really paranoid. Your results through personal genetic testing are yours and for no one else to see unless you disclose them.

Lastly, let’s talk realistically about the types of insurance that still discriminate – which would be life insurance, extended care insurance, etc. They are in the business of odds-making. They are betting you will live and you are betting you will die sooner than later. As you age, the odds shift, cause let’s face it, eventually, you will die – and they will have to pay out. Now the only way they can make money is if you pay more premiums during your life than they have to pay out in the end, or they make the premiums so expensive you stop paying, letting the policy lapse, before you die, so they never have to pay. Of course, if they think the odds are stacked too far in your favor, they simply won’t insure you. So, if you or your family members have Huntington’s Disease, you’re not likely to be able to get life insurance outside of a group policy, with or without a genetic test. In fact, there is a questionnaire about your family history when you apply for individual life insurance.

I bought individual life insurance about 10 years ago. They sent a nurse to the house to draw my blood. They wanted chain of custody, to know the blood sample was mine, which is not the case with personal DNA testing. I had to provide ID. If the insurance company wanted to run a DNA test, prohibitively expensive then, but not in the next few years, they certainly could do so. Let’s just say it plain and simple – everyone has pre-existing genetic proclivities to something – no one is immune. These results are not generally black or white either, but expressed as a range. For example, 4.2 European women out of 100 will develop Restless Leg Syndrome in thier lifetime. My risk is 5.2, so slightly elevated above the average. I’m only “above average” in 5 areas, and below average in most. And the insurance companies are still going to be in the odds-making business – they can’t deny everyone or they won’t have any business – and they will use this new tool as soon as it becomes economically viable. There is no escaping it.

So yes, the Eagles are right to watch vigilantly – but for now – how much you share and with whom is entirely in your control, so you don’t need to be an Ostrich either. There is a great deal of good that can come from personal genetic testing, in addition to genetic genealogy. Knowledge is power.

So now, if you haven’t already, read this great article, The Gene Machine and Me!!!

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The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools

Posted on March 3, 2013 by Roberta Estes

This is Part 5 of a series.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part two gave an example of the power of fragmented chromosomal mapping and the beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets. Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In this segment, Part 5, we’re going to look at various third party tools and what they can do for our search for minority admixture. We will use the download files from either 23andMe and Family Tree DNA and utilize third party tools to analyze the raw data. We’ll see how third party developers put those puzzle pieces together, if the results are consistent and what they tell us.

The Weeds

When dealing with testing companies, particularly any individual source (as opposed to multiple testing company results, as I have done), minority admixture, especially less than 1% may not be successfully recognized. One percent equates to between 6 and 7 generations or about to the 1800 threshold in time. However the history of both African and Native admixture in colonial America goes back another 200 years to the Jamestown era.

The social history in the US means that there are many people looking for this admixed heritage as long ago as 1609 when Jamestown was established and the first European/Native marriages took place (although there were “blonde Indians” reported by Jamestown settlers). In round numbers, that’s about 400 years or between 13 and 16 generations. Of course, a minority ancestor drops below the 1% threshold between 7 and 8 generations (with the first generation being the person tested) and by the time you get to the 12th generation, you’re at .048%. At this level, Bennett Greenspan says we’re “rooting around in the weeds,” and he’s right.

However, rooting around in the weeds for those dreaded IBS (Identical by State) segments in genealogy is exactly what we need when looking for small amounts of minority admixture. What’s an IBS segment you ask? It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment. IBS means that you’re from a common population if you match someone with a very small segment, not necessarily that you share a common ancestor within the past several generations. But how to you tell if a small segment is IBS or IBD?

There is no absolute line in the sand, but often segments smaller than 7cM (centimorgans) or 700 SNPS (some say 5cM and 500 SNPs) fall into the IBS category. This has caused some researchers to discard all segments of this size because they can’t tell the difference. That’s unfortunate, because clearly some of these segments are IBD and the IBS segments can be useful too.

When looking for minority admixture in two people, both of them having these small segments in the same location can provide meaningful information, and can confirm minority heritage. Said another way, if two people have less than 1% Native heritage, both share a common ancestor, and both carry part of their “less than 1%” on the same segment….one might say it’s not likely to be coincidence. Identifying the common segments of your common ancestor can lead to identifying the specific family line those segments came from, especially if you match others as well. This is in essence what Minority Admixture Mapping, or MAP, does. It uses these techniques to look for patterns in these small fragmented pieces that, when taken together, indicate minority heritage. Having said that, some IBS segments will indeed, be simply that, because you share the same base population, but some will be IBD, or more current in time. With the MAP technique, we’re sorting through ways to utilize these small segments, whether they are IBS or IBD.

Using the tools, MDLP, Eurogenes, Dodecad and HarrappaWorld at GedMatch allows us to “root around in the weeds,” to quote Bennett, and find those all-important small IBS/IBD segments that connect us to a particular ethnicity and ultimately, to other relatives who carry these same segments in the same locations.

In general, using these this type of DNA is called BGA, or Biogeographical Ancestry where we use SNPs of autosomal DNA called AIMs, Ancestry Informative Markers. A SNP is a Single Nucleotide Polymorphism, or a mutation that happened in one specific location on a gene. AIMs are generally SNPs, not clusters of markers, found at different frequencies in different populations. We combine all we know about them scientifically with information about population frequencies and then draw inferences about where our ancestors came from based on that information. So a SNP that is useful in determining ancestry is called an AIM.

These SNPs, or AIMs, are the foundation for these BGA tools that we will be using to sort through small segments of minority admixture. So this is a building block process. Scientists identify SNPs found in different populations at different frequencies and identify them as such, then scientists and genetic genealogists create BGA tools that use and combine SNPs/AIMs to suggest populations and ethnicities for those who carry them. Using these tools, majority ancestry is easy to discern. We’re going to use those tools to look at groups of SNPs/AIMs clustered in small, fragmented IBS or IBD segments to do Minority Admixture Mapping (MAP) to confirm our minority admixture and to identify our minority admixed lines, families and perhaps even (in time) our original minority ancestor.

I bet you thought I couldn’t fit all of those acronyms in one paragraph, but I did:) It is a bit like alphabet soup, but when you understand that this is a building process, it’s much easier to grasp as a whole.

Having at least one parents DNA makes this process much easier, because you can immediately tell if your other parent, by inferrence or process of elimination, has contributed any of the minority ancestry, or if it’s all on one side of the tree. Of course, that’s assuming your parents aren’t related to each other. There’s a test for that too at GedMatch. If you don’t have one parent available, you can “make do” with aunts, uncles and cousins, but it’s a much more tedious process.

Third Party Tools

To use any of these BGA tools, you’ll need to download your results from either 23andMe, Family Tree DNA or National Geographic. Currently at GedMatch, the only supported formats are 23andMe or Family Tree DNA, because the National Geographic test is so new. I used my Family Finder (Illumina Build 36) raw data file.

To download your results from 23andMe, sign on to your account, then click on this link and it will take you to the area to download your results.

https://www.23andme.com/you/explorer/

Save the file and do not open it as the act of opening it sometimes causes corruption and you will have a hard time uploading the file. If the upload fails, download a new copy and start over. If you have an older copy on your computer, it’s always a good idea to use a fresh copy to incorporate any changes made by the vendor since your last file download.

To download your results from Family Tree DNA, sign on to your personal page, click on the Family Finder tab and then on “Download Raw Data.” As I write this, Family Tree DNA is in the midst of a conversion from Build 36 to Build 37 for their autosomal files (in order to facilitate the integration of 23andMe results), so you may need to be a bit patient while this process completes. Files may not be available for download at some points. You certainly don’t want to mix comparisons, meaning using one build 36 and one build 37 file for comparison.

If you’re following this process yourself with your own data, please read all the way through this posting before starting your own processing.

Now, let’s look at the third party tools.

Stanford University

This tool is available at Stanford University. Scientists have collaborated to provide this service and I think it’s quite interesting. This tool is not compatible with any browser except Chrome and it requires a download of your autosomal data in a .txt file. If it can’t load your file, the loading task simply never completes. For me, that meant it wasn’t a .txt file I was trying to load.

http://esquilax.stanford.edu/

Load your file and choose Ancestry, then Paintings, then Hap Map 3 (experimental), then Paint my Chromosomes.

Their legend, above, translates to the regions, below.

ASW – African ancestry in Southwest USA

CHD – Chinese in Metropolitan Denver, Colorado

GIH – Gujarati Indians in Houston, Texas

LWK – Luhya in Webuye, Kenya

MEX – Mexican Ancestry in Los Angeles

TSI – Toscani in Italia

Unfortunately, this isn’t terribly useful. Hap Map 3 utilizes additional regions, including Utah, but this tool doesn’t seem to be mapping them, so my closest match region is Italy, which is midleading since none of my family was from Italy. Hap Map 2 is also an option which does include the Utah population, but it’s not as up to date otherwise as Hap Map 3.

David Pike has figured out how to tweak these settings some. You can read about it at this link: https://www.23andme.com/you/community/thread/8062/. David’s posting on June 20^th shows what he did. However, compared to the other tools available, I find this a poor choice and did not spend a lot of time trying to work with it.

However, a second feature that they provide is fun.

Stanford provides a Neanderthal tool that’s a little different than the Nat Geo or 23andMe ones. Click on Explore, Neanderthal, Look Up Exercise. Then enter your primary ethnicity and click on Look Up Exercise again.

Of a possible 84 Neanderthal alleles, I have 9, partially displayed below.

GedMatch

www.Gedmatch.com is a complimentary (voluntary contribution) site created by two genetic genealogists that includes several autosomal analysis tools. One of the areas of this site is “Admix Tools.” On that page one finds several private or proprietary tools, some written by genetic genealogists, some by researchers, and all free. Let’s take a look at each one and their results. If you want to see any of the results more closely than the photos here allow, you can run each of the comparisons using kit F6656 (mine) as the first kit and kit F9141 (my mother) as the second kit.

Each of these tools offers the same functionality, as follows.

We will be utilizing 4 of these functions for each tool.

Admixture Proportions
Admixture Proportions by Chromosome
Chromosome Painting
Paint Differences between 2 kits, 1 chromosome

We select from the tools as follows:

Let’s take a look at what the tools provide.

MDLP World 22

The MDLP software is sponsored by two genetic genealogists. You can read more about the project at http://magnusducatus.blogspot.com/ and http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html.

MDLP shows several populations. I was interested to see if my mother also shared the African percentage. Interestingly, mother does have a South African segment, but it’s .12, so less than mine. Therefore, I would have obtained part of my African heritage from my father. She also has three different categories of Native American heritage, compared to my one. She carried a total of 1.92% and I carry .58%. Otherwise, our results are very similar.

The next feature is ethnicity mapping by chromosome. While the display is too large to see well it’s interesting to note that indeed, both Native American and African were detected on several chromosomes, not just on chromosomes 1 and 2 as reported by 23andMe and Dr. McDonald. Note that DeCode Genetics showed “East Asian” admixture on several chromosomes.

Here’s a portion of the above chart that you can actually see. The highlighted blue regions are your major ethnic regions.

Another feature is chromosome painting, shown below. This shows the first part of my chromosomes 1 and 2 painted by ethnic/regional breakdown. The legend for each tool is different and above their graph.

These tools also provide the ability to compare one chromosome between two people. On the graph below, my chromosome 1 is on the top, and my mother’s is second, with the third band being our common painting. The black represents non-shared regions, meaning those contributed to me by my father. Unfortunately, North American Native American is dark grey, sometimes difficult to distinguish from black.

The graph below shows that while I do share a large piece of Chromosome 1’s Native region (about 160-180mb) with my mother, there are also segments, 169-170 for example, where I have Native genes that she does not, indicating Native heritage in this location from my father’s side.

Eurogenes K9

Eurogenes was created by another genetic genealogist. You can read more about it at http://bga101.blogspot.com.au/2012/04/eurogenes-admixture-utilities-at.html.

Eurogenes calls me primarily North European with .67 Native American and no African in the percentages above, but below, on the individual chromosomes, some African does show, although not on as many chromosomes as MDLP.

In the charts above and below, you can see that Eurogenes detected small amounts of African along with Native American.

Notice that at about 10mb on chromosome 1, on the graph below in the top band, that the North American Indian (yellow) and the South Asian (red) are imbedded with each other. These appear again together at the beginning of chromosome 2, shown as the second band. This hints at how and why it’s sometimes so difficult to determine and filter Native American from Asian. There is no line in the sand, there is a continuum between populations, the only differentiator being 10,000 to 15,000 years spent apart in which time, they, hopefully, developed enough differentiating mutations that we can tell them apart.

On the chart below, the top band shows the chromosome painting of my chromosome, and the second band shows the chromosome 1 Native American segment (about 160-180 mb) of my mother with the third band showing both matching and non-matching regions, painted black. Looking at the segment of chromosome 1, in the graph below, characerized as Native, we can see in mine, top row, that this is categorized as Native American (yellow), but some of the same regions below, in Moms are categorized as South Asian (red), causing a technical non-match, when in reality, It’s likely a categorization issue, not a genetic mismatch. In future analysis, we’ll be using two methods of comparison, one called “Strong Native” that only matches Native to Native and another, the “Blended Asian” method that allows for grouping of similar ancestral types that together likely indicate a Native heritage.

Dodecad V3

Dodecad was created by an anthropologist. You can read more about it at http://dodecad.blogspot.com/ and http://dodecad.blogspot.com/2011/06/design-of-dodecad-v3.html.

Dodecad, unfortunately, does not subdivide into Native American, so the Native will show here as some form of Asian. Northwest Africa shows in the percentages above, but more detailed African heritage shows in the chromosome detail below in regions not shown above.

Above, my chromosome painting for the first part of chromosomes 1 and 2.

Below, the comparison showing the Native segments from about 160-180mb. My Native segment (top) compared to mother’s (middle) with the comparison of the two on the bottom for chromosome 1.

HarappaWorld

HarappaWorld divides results into fewer population groups and is focused on Asia. You can read more about it at http://www.harappadna.org/2012/05/diy-harappaworld/.

In HarrappaWorld, Beringian and American appear to be equivalent to Native American. Like Dodecad and Eurogenes, African does not show in the total percentages, but does on the individual chromosome analysis, although in smaller percentages with this application.

Chromosome painting of my chromosomes 1 and 2 are shown below.

The graphs below show the Native region comparison of chromosome 1 between me, top row, mother, middle row, and the third graph showing the common areas, with black representing areas where there is no match.

For each of these tools and their results, we’ll do further analysis in a future segment of this series.

Tools Summary

Now that we’ve looked at these individual tools, and building on the Test Results Chart created in Parts 3 and 4, let’s compare and see what information these tools add.

Test Results Chart Including Third Party Tools

Test/Company	European	Asian	Native	African	Unknown
Pedigree Analysis	75%	0	~1%	0	24%

Testing Companies
Family Tree DNA – Original	100%[1]	0	0	0
deCodeme	92%	5%	Inferred[2]	3%
deCodeme – X	91%	6%	Inferred	3%
Dr. McDonald	97-99%	1-3%	0.5%	0
23andMe – Original	99%	1%	Inferred[3]	0	0
23andMe – 2012 – Standard	99.2%[4]	0	.5%	0	.3%
23andMe – 2012 – Conservative	98.7%[5]	0	.3%	0	1%
23andMe – 2012 – Speculative	99.3%[6]	0	.5%	0	.2%
Family Tree DNA – 2012	100%[7]
Geno 2.0	79%[8]	18%	0	0	0
Ancestry	92%[9]	0	0	0	8%

Third Party Tools
MDLP	86.68%	12.55%	.58%	.17%	0
Eurogenes	94.83%	4.5%	.67%	0	0
Dodecad	85.47%	13.43%	Inferred	1.09%	0
HarrappaWorld	86.56%	12.80%	.65%	0	0

Of the various chromosomes, the breakdown is as follows. Dodecad does not break the categories in a comparable fashion to these other 3 tools, so their results are omitted in the following chart. Please note that how geographies are categorized can make a significant difference.

Minority by Chromosome Chart

Tool/Chr	MDLP Native	Eurogenes Native	Harrappa Native	MDLP African	Eurogenes African	Harrappa African
1	Y	Y	Y	N	N	N
2	Y	Y	Y	Y	Y	N
3	N	N	N	Y	Y	N
4	Y	N	Y	N	N	N
5	N	N	N	N	N	N
6	Y	Y	Y	Y	N	N
7	N	N	Y	N	N	N
8	Y	Y	Y	Y	N	Y
9	Y	N	N	Y	N	N
10	Y	N	N	Y	N	N
11	Y	N	Y	Y	N	N
12	Y	N	Y	N	N	N
13	Y	N	Y	N	N	N
14	Y	Y	Y	Y	N	N
15	Y	N	N	N	N	Y
16	Y	Y	Y	Y	N	N
17	Y	Y	Y	N	N	N
18	N	N	N	N	N	N
19	Y	Y	Y	Y	N	N
20	Y	Y	Y	Y	N	N
21	Y	N	Y	N	N	N
22	N	N	N	Y	Y	N

From these various tools, it’s obvious that I do have some Native admixture, probably about 1%, and it’s from both parents. I also have some African, but it looks to be an even smaller proportion that Native American.

Join me for Part 6 of this series, where we look at how to analyze and use this information.

[1] 71.5% western European, 28.4% Northeastern European

[2] Inferred that Asian is actually Native in an American with no history of Asian ancestry.

[3] No category, inferred.

[4] 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

[5] 54.6% Northern European, .3% Southern European, 43% Nonspecific European

[6] 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

[7] 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

[8] 43% North Europe and 36% Mediterranean

[9] 80% British, 12% Scandinavian

______________________________________________________________

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The Autosomal Me – Testing Company Results

Posted on February 24, 2013 by Roberta Estes

This is Part 4 of a multi-part series, The Autosomal Me.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets. We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like. The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably. They initially only offered 3 population groups, and one inferred that Asian was actually Native American. Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances. This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry. Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results. This is not a commercial endeavor but a private research project which has been ongoing for years. His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European. His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American. However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data. His results showed no African.

Standard deviation (statistical noise) is about 1%. He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison. I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

Doug indicates that the Native American is found at about the .5% level. Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side. Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current. The vendors have made upgrades too. In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American. This is consistent with Dr. McDonald’s findings.

A second view is available which paints the chromosomes. A split view is also available if one of your parents has been tested at 23andMe as well. That is not an option for me.

The conservative estimate, below, shows less Native at .2%.

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments. Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage. What fun!!!

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available. Thankfully her DNA was stored at Family Tree DNA and was still viable.

Mother’s original results are shown above and her most recent results are shown below. Her results shifted within Europe and her margin of error doubled.

My current results from Family Tree DNA’s updated software are shown below.

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results. They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

It made more sense when I read the information. It’s true, reading is fundamental.

These results are, in essence, more anthropological in nature.

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well. What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches. Recently, Ancestry announced that the percentages may change over time. They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous. Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

Ancestry shows my heritage as only British and Scandinavian.

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted. Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies. There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported. If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture. For many people, it’s this small amount of minority admixture that they are seeking. So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results. We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry. I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.

1. Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2. 71.5% western European, 28.4% Northeastern European

3. Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4. No category, inferred.

5. 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6. 54.6% Northern European, .3% Southern European, 43% Nonspecific European

7. 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8. 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

9. 43% North Europe and 36% Mediterranean

10. 80% British, 12% Scandinavian

______________________________________________________________

Disclosure

Thank you so much.

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Thick Hair, Small Boobs, Shovel Shaped Teeth and More

Posted on February 17, 2013 by Roberta Estes

Yep, there’s a gene for these traits, and more. The same gene, named EDAR (short for Ectodysplasin receptor EDARV370A), it turns out, also confers more sweat glands and distinctive teeth and is found in the majority of East Asian people.

This is one of the results of the National Geographic’s Genographic project. This mutation found at location rs3827760 on chromosome 2 occurred about 35,000 years ago. It apparently has conferred some advantage to its carriers, because it is found in the majority of Asian people today. We don’t exactly know why that happened, but maybe ancient male Asians preferred thick haired, small boobed and sweaty women. Or maybe those women survived when women with more body fat (yes, boobs are fat, sorry guys) and who could sweat less perished.

This New York Times article discusses the experiments performed to verify that this gene in fact does confer those traits. The scientific article itself is available in the journal, Cell although it’s behind a paywall.

Want to know if you carry this trait? If you’ve tested with either Family Tree DNA or 23andMe, you’re in luck.

Download your raw results file and open the file using any tool. Generally, a spreadsheet or Notepad will be your preferred methods. Then using the search function of the tool you’ve selected (ctl+f for Notepad or Excel’s find function) search for rs3827760. You will see two letters comprised of either T, A, C or G. If you have a G shown for either letter at this location, then you carry this particular mutation.

If you carry this mutation, you’ve probably already headed for the mirror. You’ll know already if you have small breasts, if you’re a female, believe me. You may never have thought about thick hair shafts, which isn’t to be confused with lots of hair. And your level of sweatiness is just what it is. I’ve never even considered that there were different sweatiness levels. But what about Asian teeth? Well, that trait is called sinodonty and here’s a nice wiki article and another nice article, with examples, here. If your teeth are shovel shaped, meaning the backs of your upper 4 teeth are shaped like a spoon as opposed to straight, then you have this trait.

So are you wondering what this might have to do with genetic genealogy? Well, if you carry this gene, then you obtained it from some Asian ancestor. If you’re in America and not of Asian ancestry, then there are pretty much only two routes. One would be Native American ancestry and the second would be the population or invasion of Europe by Asian groups, such as the Mongol Hordes and the Huns. Your genealogy will have to be your guide as to which source contributed this gene to your ancestors, and ultimately to you.

Oh yes, and one last thing, this mutation isn’t the only one involved in at least some of these traits, specifically the teeth. I don’t carry the G and I do have some of the Asian teeth characteristics. I don’t have thick hair shafts which makes sense since EDAR is primarily associated with this trait. And, well, I’m just not discussing the boobs and sweaty traits (and my husband is utterly forbidden to comment)…..TMI:)

______________________________________________________________

Disclosure

Thank you so much.

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The Autosomal Me – Who Am I?

Posted on February 13, 2013 by Roberta Estes

This is Part 3 of a multi-part series.

This series focuses on answering the questions of identity through autosomal testing, in particular, for minority ancestry. By minority, I mean any small, elusive amount of any type of ancestry you are seeking to discover in your heritage. In my case, that’s both Native American and African.

This segment, Part 3, focuses on using pedigree charts to gauge expected results, how autosomal ethnic groups are determined and how fragmented minority admixture mapping is different from other techniques. This leads us into Part 4 which shows the various results from different testing companies and how they differ.

Part 5 features third party analysis tools and Part 6 begins the analyses of the data that parts 3, 4 and 5 provide.

Let’s hope that with all of this information, we can answer at least part of the question: Who am I? Who am I really?

A lot of who I am has to do with who my ancestors were, where they lived, what they did, choices they made. Did they fight in the American or French Revolution? On which side? Were they Native? Were they African? Were they slaves? So, who were they?

One of the reasons I began with genetic genealogy more than a decade ago was to confirm or disprove the persistent family history of Native American heritage that I had been unable to resolve using only traditional genealogy tools. I have made inroads with that, in unexpected ways and places, because of and in addition to genetic genealogy. Genetic genealogy and traditional genealogy go hand in hand.

It’s difficult tracking down each line to perform mitochondrial or Yline DNA tests. Sometimes, it’s beyond difficult and it’s impossible. Lines die out, people refuse to test or you simply can’t find the right people. We need other tools.

Enter autosomal genetics. From the beginning, early in genetic genealogy, we had the CODIS type forensic and paternity type tests. I reviewed the results of those early tests relative to my pedigree chart in a paper I wrote, Revealing American Indian and Minority Heritage Using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis published in JoGG in the Fall 2010 Issue. We’ve come a long way since then.

In that article, I dissected my pedigree chart to determine how much of different types of ancestry I carried and how that compared with the testing that had been performed at that time.

Using the end of line ancestors pedigree analysis method described in the paper, which determines the percentage of ethnicity that each end-of-line ancestor contributed to me, my origins totals were as follows:

Geographic Origin Chart

(1) The ethnic heritage of several lines could probably be inferred by surname or ethnicity of marriage partner. However, I have avoided the temptation to make inferences within the United States, as the Native or African ancestry may well lie with one of these ancestors. These are in fact the perfect candidates and to eliminate them from consideration by inferring origins would be a disservice.

In broader categories, and combining those that are similar, we find:

This is a useful exercize, not just for minority admixture, but to help evaluate the results you receive from the various testing companies. For example, you might notice that there is no Scandinavian showing in my pedigree chart, which makes Ancestry’s 80% British and 12% Scandinavian suspect right off the bat. It also makes results as high as 25% Native American reported in one of the earlier tests impossible. This pedigree analysis tool helps you understand what is reasonable to expect in terms of ethnicity breakdown.

Now that we know what the majority ancestry looks like and any minority ancestry that we are aware of, let’s take a look at the various types of autosomal testing available.

Tests and Population Markers

In the paper, I reviewed the older results from companies using either CODIS or proprietary markers. These low resolution tests are out of date now (although many are still being sold) and have been replaced by the much more thorough wide spectrum tests using chip based technology, allowing hundreds of thousands of DNA locations to be tested and evaluated. Of course, the word evaluated is the loose cannon in that sentence, because the quality of the evaluation is key here. And the evaluation is dependent upon accurate and widespread data bases to compare DNA results against to determine which populations have higher and lower frequencies of specific alleles (markers) occurring in their populations.

For example, let’s compare a population in Siberia that shows 100% of a specific marker value, let’s say a value of 10 at marker location ZZZ. Now let’s compare that result to a population from Africa at that same marker location, but with a value never found in Siberia, let’s say a value of 7. Each of thousands of markers are evaluated this way, creating patterns. Now, you have a tester who doesn’t know where their ancestors are from, whose results at marker location ZZZ have a value of 10. Would you say they are more likely to have ancestry in Siberia or Africa?

This participant’s marker results for ZZZ go in the “very strongly Siberia” bucket. Of course, other markers they carry might indicate Africa, or Europe, or elsewhere, because we are a Heinz 57 mix of all of our ancestors. But this is, in essence, how our ethnicity is determined by autosomal DNA testing. Needless to say, you can be a lot more accurate with thousands of markers than with the 15 or 21 CODIS markers, or even the 300+ in some of the proprietary tests.

BGA Testing

Using autosomal results to determine ethnicity is called BGA testing, or Biogeographical Ancestry testing. It has been used for years to determine percentages of ethnicity. So, how is what I’m doing different and what makes it unique and new to genetic genealogy?

1. Traditional BGA testing deals in percentages of ethnicity, meaning generally 1% or more. Small amounts are difficult to track in the best of circumstances. When dealing with small amounts of admixture, not all tests will be able to identify the minority ethnicity in question. We’re using these tests, plus additional BGA chromosomal painting tools combined with some spreadsheet comparison techniques to cross that 1% threshold.

2. The prevailing winds in this industry have been that anything smaller than 1% was undetectable, and that any amount of admixture less than 7cM, 5cM or 3.5cM (depending on the source) was usless. While this is relatively accurate (but not always) when determining a genealogical relationship within the past few generations, it’s not true when looking beyond the accepted 6 to 7 generation threshold where the 1% ethnicity issue comes into play. At that point, we know we can’t identify the minority ancestor genealogically, so we have to identify them by their membership in a minority population group. I am using a variety of tools and techniques to reach across that threshold.

3. Instead of using these various tools to try to establish a genealogical relationship with another tester (such as we share a common great-grandfather), I am using these tools to attempt to identify which line or lines carry minority admixture. If you already know who in your family tree contributes that admixture, you don’t need this technique. If you are looking to confirm minority admixture below 1%, searching for the minority admixture contributing line, or trying to figure out which of your known ancestors contributed minority admixture, then this technique is for you.

Typically these tools have been used to track segments from known ancestors, like a Jewish grandmother, for example. These segments are large and evident. That’s not the case with small amounts of minority admixture. Using several BGA tools together helps to eliminate the possibility of one tool picking up on these small segments and another one missing it. We are bringing all of the resources from various camps together to bear on the situation. This is the ultimate form of recycling, using the shreds that were left on the cutting room floor and deemed to be usless when in actuality, they are diamonds in the rough. We’re reassembling them and looking at them from a different perspective. It’s a new kind of quilting!

A New Name

As I’ve worked through this process, it seems that Minority Admixture Mapping best suits what we are doing, so MAP it is. It makes sense and you can say it.

I still want to know who I am, so in Part 4, we begin our data analysis by looking at the autosomal ethnicity results of the various testing companies and how they compare.

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Disclosure

Thank you so much.

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The Autosomal Me – The Ancestors Speak

Posted on February 10, 2013 by Roberta Estes

This is Part 2 in the series, “The Autosomal Me.” Part 1 was “The Autosomal Me – UnRaveling Minority Admixture.”

Every Sunday, I write something called a Sunday Story. I’ve done this for years. I send them to my kids and I delude myself into thinking they read them. I’m really writing them for my grandkids someday and hopefully, some as yet unborn descendants I’ll have that will care about finding out about the life and times of their a-few-greats grandmother who lived along with the dinosaurs in the last half of the 1900s and first half of the 2000s. I know, I’m optimistic.

I decided that perhaps I would share this weeks Sunday story with all of you. This way, I know that at least someone will read it. Actually, aside from my husband, it’s my daughter-in-law who comments the most often. So welcome to my Sunday Story! You are all honorary cousins!

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I know that a great deal of what I do with genetics is lost on my friends and family members. That’s OK, because it’s very specialized. However, I wanted to take a little bit of time to share with you an aspect of the genetics I work with that I think is very beautiful in both a literal and a spiritual way.

The point of genetic genealogy, of course, is to learn about our ancestors, who they were and our connection to them. There are various ways to do this, but most of the time it’s through various matches to other people who share a common ancestor either recently or perhaps further back in time.

Of course, therein lies the rub – how long ago are two people related and who was their common ancestor? Some people who carry minority ancestry are at a distinct disadvantage, because the testing that provides matches and ethnicity generally relies on amounts in excess of 1%, which equates to about 6 or 7 generations. While many of us know that we carry minority ancestry, we would be hard pressed to say that our “pure” Native (or other minority) ancestor fell into that 6 or 7 generation bracket. Six or 7 generations equates to about 150-175 years before our birth, or about 1775-1800 for most of us. By then, many Native people were already admixed and many already lived outside of a traditional tribal unit. Some people carry Native heritage from multiple lines, but since it comes from multiple ancestors, it too is often quite fragmented, so it doesn’t really improve the situation much unless some of those fragments happen to fall together to make larger segments.

Therefore, we are looking for very small amounts of admixture that often don’t show on traditional tests, or if they do, it’s in miniscule amounts.

Enter chromosome painting.

Without going in to boring detail, I’ve recently been working with a new methodology of identifying these fragmented and very small segments. I am using several chromosome painting tools. I’ll be blogging soon enough about how all of this is done, but I just wanted to share with you a couple of beautiful pieces of DNA, through which our ancestors are speaking, and we can see them, in a manner of speaking.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted. You can see that both of us have a primary ethnicity of North European, shown by the teal.

The grid shows location 120 on the chromosome. Think of this number as a house number on a street. It’s numbered so we can keep track of where we are on the chromosome. For genealogy purposes, the smallest segment normally considered as relevant is 7 mb or marker segments long. Each tick mark equals one segment or address, so a segment 7 mb long would be from 120-127 which takes you right over to the legend. As you can see, the primary ethnicity has no problem reaching way beyond the contiguous 7 threshold, but the minority ethnicity would not be counted because it’s too small.

However, by the very definition of what minority ancestry is, these small segments are not only present, providing critical information, they are essential in our search and very informative. Let’s see what they are saying to us.

First, let’s talk for a minute about ancestry. There is no line in the sand very often between populations. There are generally only degrees of difference. So in the case of Native American, which is yellow on this chart, we also expect to see it “drift back in time” by being found in conjunction with Siberian (putty), South Asian (red) and East Asian (emerald green). Native Americans were not dropped from alien spaceships, they evolved over time from these other Asian populations, so we would expect to see some of their genetics in Native American people.

So let’s take a look at what we do actually see in the DNA.

The first brightly colored segment in the top band is mine. It includes Native American (yellow), South Asian (red), a big chunk of East Asian (emerald Green), a little bit from the Caucus (ginger) which is the Middle East area, and a piece of West African (light green).

There are two messages from the ancestors in this piece of DNA. First, this segment absolutely, positively does NOT come from mother. We can see this clearly because she has nothing but North European (teal) in that section of her DNA. So, this little gem came from Dad.

The second piece of information is that the ancestor who provided this DNA to Dad was very likely admixed, Native and African.

Of course, if you’re thinking ahead at this point, you’ll be asking, “Which one of your Dad’s other relatives has this same segment?” because, yes, that’s exactly how we will tell which of his lines contributed the Native ancestry. But you’re getting ahead of the story, and well, that is a story for another time. This story today, is about the direct messages of the ancestors and the beauty of our DNA itself.

Let’s look at the next segment of minority DNA. It starts about location 123. Mom’s is much more pronounced than mine and much richer. This tells us that I didn’t receive much of Mom’s. Instead I received mostly North European (teal), along with some East Asian (emerald).

Mom has almost a perfect Native segment here. By perfect, I mean we find a progression from Native back through time through all 4 categories I would expect to find. I consider this entire segment “Native” because it indicates Native heritage. You can see the emerald green (East Asian), putty (Siberian), red (South Asian) and yellow (North American Indian and Arctic) nestled together with no other minority ancestry in close proximity. This means it’s not part of a different kind of Asian segment. Remember, part of Europe was settled by the Mongol Hordes and the Huns, so we do see Asian and western Asian DNA in Europe, along with DNA from the Caucus, but we don’t see isolated segments like this, with just eastern Asian DNA and Native American. So this little beauty is the perfect Native indicator, positively, even though it is only about 4 segments long.

Now take a look at my DNA in that same region in the top row. It’s kind of hard to see the emerald green against the teal, but I only inherited the East Asian (emerald) segments from Mom. Of note, however, is that I also have an East Asian (green) segment that Mom doesn’t have. My East Asian starts about 122 where hers doesn’t begin until 123. So good old Dad contributed a bit here as well. Again, we know this because Mom only has North European at that segment.

And now of course for the kicker. Your DNA looks this same way. How boringly teal it is, or how beautifully rainbow multi-colored depends on how much minority ancestry you have, from how many different lines, and which of your parents you received it from.

I hope you can see why I’m so excited to be developing this new technique to work with highly fragmented DNA to find our ancestors. They are there, they have a voice, and they are speaking to us. All we have to do is figure out how to listen.

I am simply in awe of the beauty of this technique, literally as well as figuratively. While I certainly understand and appreciate logically that matching other people means we’re related, there is something awe-inspiring and tangible about being able to see the painted graphs and view the layers of ancestry nestled together, life forces reaching through time, protecting that DNA with its precious message for us over many generations. All this time, just waiting for us to be able to understand the most personal message from our ancestors, delivered, from them, in our genes, to each of us. This is the voice of our ancestors.

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Disclosure

Thank you so much.

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