23andMe Update: Maternal and Paternal Phasing

Yesterday I revealed how I’d nearly exhausted my very limited reserves of patience waiting for my dad’s 23andMe results. If only instant gratification were possible with such tests. Maybe some day in the future there will be DNA test kiosks right next to all the blood pressure machines in pharmacies. In the meantime, it is impressive that 600,000+ genetic markers can be analyzed in just a few weeks, even though that seems like a long span of time for impatient people such as yours truly.

Dad’s results were ready this morning. By afternoon, his results had been phased with mine. Mom tested last month, so now I have been phased with both parents. (More information on the phasing process is available here and here).

Here is a chart of my geographical percentages with and without phasing:

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I had hoped to shed more of the “Broadly” percentages through phasing, but this is as about as accurate as direct-to-consumer genetic genealogy tests can be at this time, at least for someone like me, whose known ancestors migrated to America from their home countries 150-350 years ago.

I will close with a 23andMe-generated graphic of my phased results:

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Tonight’s Dinner, and Anticipation

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I’m pleased when the odds and ends in my refrigerator merge into a handsome dinner.

Currently my mind is full with waiting for my dad’s 23andMe ancestry-only test results. No matter how many times I’ve ridden this sort of testing roller coaster, I am anxious for the results, unreasonably so.

Since Friday I’ve seen “Your results are almost ready!” whenever I check the progress of his test’s processing. Whoever wrote that line does not share my sense of urgency. As Carrie Fisher wrote in Postcards from the Edge, “Instant gratification takes too long.”

Every day “Your results are almost ready!” doesn’t actually become ready, I feel a bit crushed, like a miniature of the deflated hope of each of the eight days I was pregnant past my due date.

It’s not like this test will offer earth-shattering revelations.  Like when my mom tested earlier this year, I am so grateful once again that my family has been so supportive of this interest of mine.

Once my dad’s test is done, my results will be phased with both parents, and this, to my knowledge at least, is the most accurate direct-to-consumer geographical ancestry composition result available currently. Through Dad’s results, I will also be able to see his maternal (mtDNA) haplogroup, which is currently a mystery to me.

And now I must check “Your results are almost ready!” again.

Another 23andMe Update: Maternal Phasing

Right after I published my previous post about wistful anticipation of my impending 23andMe ancestry composition update, I logged into that site to see that my mother-to-child phasing had already been completed. It’s a good thing I saved screen shots of my first ancestry composition. Even though those percentages seem to have been burned into my brain over the past year and a half, I have a memento of that which changed how I thought of myself in unexpected ways.

One of my earliest memories involves thinking that I spontaneously appeared on earth from parts unknown the very moment I first considered that I have a memory. I don’t think that notion was entirely erased until I saw that first 23andMe ancestry composition painting. This was evidence I belonged to a web of people who’d been cast over the earth since time immemorial, and in that belonging I felt profound comfort.

I can’t remember a time when I truly doubted I belonged to God, but I was uncertain that I belonged to any person, despite that I am part of a close and loving family. I really couldn’t ask for better parents, siblings, and close relations. The issue was knowing (and I have referenced this situation before on this blog) that there was an astronomically low probability that my parents could be my biological parents. Two parents with type O blood produce a child with type A blood about one time out of a million.

I’ve made some interesting discoveries regarding my family tree, such as uncovering the identity of my paternal great grandfather who had become a missing person 94 years ago. The odds that I am myself are much more extraordinary. There was a one-in-a-million chance my parents would have me (layered on top of the already slim odds that two parents will produce a particular child, a thought that as a parent myself makes me dread the possibility of time travel, by the way).

Before I close, I will share some screen shots about my maternal phasing on 23andMe. This process did make some alterations to my ancestry composition, and I haven’t had time to judge whether I think the new version is an improvement. More regions were added as trace results, so now I have a map that looks much more like my mothers:

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My old ancestry compostion versus my new phased ancestry composition:

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December 2015 result, without parental phasing
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May 2017 result, with parental phasing . . . there is one more line to the result which I cut off because keeping it involved zooming out to a level that made the text of this screen cap unreadable. The line was “Broadly Middle Eastern/North African < 0.1%”

Since I now have a parent tested with 23andMe, I have a new component to my ancestry report that breaks down their prediction of which regions I inherited from which parent. On the left is my dad’s contribution, and my mom’s is on the right:
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More About 23andMe

My mom and my sister both did the 23andMe ancestry test, and their results were ready in just 15 days from receipt at the lab where their samples were tested. This is the semi-instant gratification for which I longed back when I started genetic genealogy tests in late 2015. All 28 days I waited for my 23andMe results felt like a month a piece. I distracted my impatience by building a family tree on Ancestry; it held more than 2,000 ancestors by the time my results were ready.

In the intervening 18 months, I’ve grown attached to that initial chromosome painting. While the science behind it simply isn’t refined enough to guarantee its accuracy, it still seems the best of the geographical estimates I’ve done:

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Now that my mom’s results are ready, the company will phase our results against each other, sharpening the estimates. Once this phasing takes place, I will no longer see the chromosome painting above in my account. I hope I can let go of it easily in favor of a result that will likely be a bit more accurate.

Through the DNA tab on the DNA relatives tool on the site, I have been able to see a chart where my siblings and I have matching DNA, both half identical and fully identical. I have made a screen cap of our first 11 chromosomes (including more would have made the details too tiny):

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My sister is in purple while my brother is in orange. The deeper tones indicate where we are fully identical (i.e. inherited the same stretch of genetic sequences from both Mom and Dad, in the same order). There’s a significant stretch of chromosome 9 that is darkened on both bars. On these segments, we are “triplets” to each other. There are other shorter stretches where all three of us are identical, yet I also see some lonely double gray segments where we inherited entirely opposite segments from our parents.

Among the major testing companies, 23andMe has the best combination of clarity and accuracy. It genealogy features are thin compared to AncestryDNA, but my experience with the information on Ancestry leads me to think that a significant amount of the information related to distant matches there is unreliable or coincidental. Since both of my parents have tested there, I have checked their matches with some of my Shared Ancestor Hints and found that a significant number of them are misleading. For example, some of my paternal tree hints are actually matched to my mother. That my tree intersects with that match on the opposite side of my family tree is just coincidence. Worse yet, it’s impossible to see the family trees of your matches without a pricey Ancestry subscription or individual invitations to match trees.

Now that 23andMe offers an ancestry-only test at a price that is equal to that of AncestryDNA, I’d recommend starting with 23andMe if you haven’t already taken such a test and are interested in trying one. I’ve noticed that many people who enjoy their first test end up testing with both companies anyway, if my matches are any indication. I see many familiar names across both sites.

On 23andMe, there is a world map in the Ancestry Composition section that broadly represents where your ancestors were living around 500 years ago. My mom had more of the world painted in her map, and this curiously reflects how much more broad her perspective seems compared to mine at times:

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Back to Reality

I refer to reality in the title of this post solely because I lack the mental focus to invent a more topical title. My husband has the album Master of Reality by Black Sabbath in his car at all times, and the sight of it has inspired me to comment entirely too often that reality really is the hardest thing to master.

I have survived my first week back from medical leave. Aside from soreness due to some quadricep exercises for physical therapy, I haven’t had any struggle in meeting the physical demands of this transition. Instead, I have had a hard time adapting to the sudden expansion of the company I keep. I spent seven weeks in solitude seasoned only by people who understand me implicitly. This was such a heaven that my reaction upon the prospect of conversing with “mixed company” was to fantasize for a moment about what it would feel like to walk back to my car and drive home, where I would stay indefinitely in a reverie of dessert recipe trial-and-error, family tree research, and books partially read.

Alas, the cost of living prohibits me from such a retirement, so I pressed onward through the week. I ended my week with a dinner loaded with enough grease and refined flour that I’d be sure to fall asleep while binge watching Father Brown.

In other news, I am excited that my mom and my sister are going to do the 23andMe test. After a flurry of testing last year with both that service and AncestryDNA, I felt I needed a break from waiting for test results, a span that can be oddly unpredictable. For example, my results were ready in 27 days, but my brother’s took 11 weeks! If you, dear reader, also decide to take part in direct-to-consumer genetic testing, be prepared for discrepancies in testing times that aren’t explained well at all by the companies involved. You could have your results in as little as three weeks, but the whole process could take three months.

However long the wait will be for these two tests, I will be pleased to see them. I think that 23andMe has the best admixture test and matching, and these aspects of the test are greatly enhanced when a parent is tested and a parent/child phasing takes place. Both of my parents have been tested through AncestryDNA, but that service does not do phasing. Now that the price of 23andMe is half what it was last year (at least for an ancestry only test), we have a better opportunity for phasing (and I hope I can talk my dad into doing this test, too). This will also be the first time my sister has tested anywhere, and she is the only hold out among my first-degree living relatives.

I really enjoyed seeing the DNA segments that my brother and I have in common:

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I am eager to see the matrix of overlapping segments between me and both of my siblings. We will also be able to see which parts of my mom’s DNA we inherited, and I am sure there are a few spans of her genome that were passed to none of us. One of the most curious things I noticed with having so many family members tested is how some segments are not passed while others can pass through many, many generations. There are also oddities such as I have a cousin who has segments in common with my dad that I do not have. Likewise, my great uncle and one of his sons have tested, and half of the matches I have in common with my great uncle are not a DNA match with my first cousin once removed.

Lunch beckons, but I am looking forward to seeing a chart of the genetic connections between me and my siblings. I will see in numbers and graphics what has been so apparent since childhood:

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On Testing With 23andMe, AncestryDNA, and FamilyTreeDNA

Last year my enchantment with the series Finding Your Roots with Henry Louis Gates, Jr. inspired me to get tested with 23andMe. Getting those results reminded me of the time when my most nutrition-minded aunt introduced me to Yoplait strawberry banana yogurt back in the late 70’s. After that first taste of creamy tartness, I felt that the best way to honor thats experience was to sample the many, many flavors of yogurt I encountered in the coming years. Just like I once felt compelled to taste boysenberry yogurt, both in blended and fruit-on-the-bottom style, I also tested with AncestryDNA and FamilyTreeDNA.

The marketing for such tests emphasizes their weakest point, geographical analysis of one’s autosomal DNA (chromosomes 1-22, which are inherited from both maternal and paternal ancestors). The variances between my results from these three companies show that precision of admixture estimates is still evolving. All three show that my ancestry is almost entirely European in origin, but they differ sharply on the sub-continental level:

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23andMe: This test matches my known genealogy the best of all three.
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AncestryDNA: There was a lot of overlap in geographical analysis of my known relatives, except my brother’s results were bizarre in suggesting he is more British than a native-born Brit. In contrast, his 23andMe result strongly resembled mine. Oddly enough, his AncestryDNA results were more similar to my FamilyTreeDNA estimates.
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FamilyTreeDNA: The omission of Germany in their list is telling, as I have strong German ancestry on both sides of my family. This company has great matching tools, but similar tools are available at no cost through Gedmatch. This company offers better testing of mtDNA and Y-DNA, so I would recommend skipping their autosomal test.

After having tested with all three of these companies, I avoid putting too much importance on the geographical results alone, especially in the trace regions. All three of them found a bit of DNA that they didn’t want to assign to Europe, but they can’t agree on what area of the world most closely matches these segments. I am inclined to think that it is not outlandish that I have a trace of ancestry from Asia, as my mitochrondrial DNA (mtDNA) haplogroup is U2d2, which hails from west Asia. This DNA is passed unchanged from mother to child with rare mutations, so my mother’s-mother’s-mother’s mother (back hundreds of generations) was not European.

The matching component of such tests is much stronger, especially at the second cousin and closer levels. Matching is greatly enriched with the testing of close relatives. I have had the great privilege of having key relations test: my parents, my daughter, my brother, my paternal grandmother (who has since passed away), one aunt, a first cousin, and several second cousins, along with both of my maternal grandfather’s siblings.

With matching, there are only two certainties: a child gets 50% of his/her autosomal DNA from each parent and identical twins are a complete match to each other. I suppose that even these two principles aren’t absolutely certain, for each person has at least a few mutations. Of course, there are also trisomies that would prevent the 50/50 rule, too, but that topic is beyond the scope of this blog entry.

Beyond parent/child and identical twins, there are only averages of shared DNA based on distance between two people in a family tree. If you have siblings, you are not related equally to each one, and there can be significant variance between families in this relationship. For example, my dad and my aunt are 10% more genetically similar than I am to my brother.

Going back a generation, the inheritance of DNA from grandparents can be even more haphazard. Through testing of key relatives, I can tell that I inherited more DNA from both of my grandfathers than I did from my grandmothers. In the case of my paternal side, nearly two out of every three genes I inherited from my dad were from my grandfather. I have matches through him that go back nine generations, which is as far as AncestryDNA’s system will automatically find a tree match.

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Before I close this entry, I will briefly discuss two other findings of my testing. First is the revelation that the inheritance of X-DNA is even more unpredictable than that of autosomal DNA. It would stand to reason that a woman should pass on a recombination of her two X chromosomes, but this does not necessarily happen. I passed on the X chromosome I inherited from my mom wholesale to my daughter. My daughter and my mom have the exceptional connection of a complete X match on one of the X chromosomes.

Lastly, do not put too much trust in the rules of blood type inheritance recycled almost as often in soap operas as they are in pop science. Here is the case of my family: Dad O-, Mom O+, Sister O-, Brother O+, and me A+. I definitely have a parent/child 50% match to each of my parents. I read lots of speculation online about people doubting their parentage based on soft evidence while blood type differences are held up as a close second best to DNA matching. My experience tells me that having a so-called “impossible” blood type can sometimes be no more significant than a difference in eye color.