DNA testing – Part 3 – Follow-up

June 5, 2017 at 10:27 pm | Posted in Health, History, Online services, Science | 1 Comment
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I’ve written before on DNA testing. In the first article in 2015, I compared the 4 prominent services for personal DNA testing. I chose 23andme. I then reported the broader results. Now I have some updates to that discussion.

It’s turned out the Y chromosome has had a lot more mutation than the maternal line so they had to update the haplogroup naming conventions last year. The original paternal haplogroup name is no longer current and the tree more complex. In my case, the guys wandered further too.

A few terms for the major testing:
Autosomal is the 22 pairs of chromosomes in the cells nucleus, excluding the pair of sex chromosomes. It’s the broad overview and allows you to match to other family members, etc.

Y-DNA is the Y or male sex chromosome. It traces your male line back: fathers, fathers, father, etc. You need to be a male or have a male member of the family tested for this one.

mtDNA – mitochondrial DNA comes from the mitochondria. It is passed down from mothers to both sons and daughters. It traces the mothers line back: mothers, mothers, mothers, etc.

Haplogroup – those that share a common ancestor based on haplotypes, groups of genes inherited from a single parent. We all have a paternal and maternal haplogroup. Haplogroups can be viewed in a tree structure of sequential mutations.

They can trace these 2 lines back roughly 100,000 years now for well-tested populations.

23andMe
Skip forward 2 years and 23andMe has finally upgraded my data to their new site format as promised. For a while, they were offering health results only to Canada and the UK due to US restrictions on “diagnosis.” With the site redesign, they’ve removed a lot of the more detailed health analysis and focus now on general markers like lactose intolerance, sleep depth, and so forth. Gone are more diagnostic things like Celiac and Parkinson’s markers.

Reporting is more centralized and distributed to tabs to support smaller screens. It surprised me to discover printing the reports (for me to PDF) gave a more complete view.

A new report on the Maternal line (haplogroups) goes back as far as the National Geographic’s “Deep Ancestry” report (below) although the second has slightly more detail.

The paternal haplogroup name was updated but there’s a gap between the tree map in the paternal section and the specific haplogroup named. As I discovered on FTDNA below, it’s also less specific.

Genographic
Meantime, I had also decided to take advantage of a sale on National Geographic’s Genographic Project. I wanted to support their work, and it offers more of a deep ancestry approach.

Here a deviation has taken place. Family Tree DNA used to do all their testing, allowing you to load your DNA test results into FTDNA (below) afterwards for free. However, for US customers, Helix is now doing their testing. They’re using a newer system that is not compatible with FTDNA. If you get the Helix test (white box, spit not swab), you can’t download the genome after either.

But as I’m Canadian, I still got the black, cheek swab kit to send to FTDNA in Texas.

My first impression of the Genographic results wasn’t positive – they didn’t notify me when the results were up. And the first presented report is “Genius” matches. It displayed famous people (not geniuses) who had some unmentioned genetic match. Essentially a pointless report.

The Regional Ancestry report had quite different percents from 23andMe but I suspect was less accurate due to the much smaller testing population.

What I did enjoy was the Deep Ancestry reports. This showed the maternal and paternal lines over thousands of years, migrating across vast distances as the ages changed.

There is also a Hominin report for the percent of Neanderthal DNA. This varied substantially from the 23andMe result as well.

Another disappointment was printing. The reports didn’t print well and the official printable report that summarized much of the above was missing all the maps even though the reports refer to them. I had to use screen captures for the maps and assemble them with the reports myself.

Given that 23andMe now includes very similar reports and has a great deal more other ones, it’s certainly preferable. It’s possible the Helix testing for Americans offers more reports or detail but that’s unclear. I suspect 23andMe would still be superior.

Family Tree DNA
Because I got the old Genographic kit, I could transfer the results to Family Tree DNA for free. This allowed downloading the Genome file and offered a few basic reports.

One of note though was the Y-DNA haplotree. This went much further than 23andMe, offering a Haplogroup that was 15 steps more detailed. And there they offered a further test (at a cost) to take it a few steps further.

From this, I discovered the links between the 23andMe paternal map and their designation of my haplogroup plus further steps that FTDNA named.

One of the bigger differences with FTDNA is their a la carte approach to ordering tests. You send in or transfer one sample and then pay just for the tests you want when you want them. Where the others above include autosomal, mtDNA, and Y-DNA, FTDNA lets you choose. Y-DNA is of no use for women, for example, as they don’t have the Y chromosome.

You can also choose the degree of testing for the mt and Y reports. If you’re a male and test all 3 at the basic level, it will cost you more than these others. But for serious researchers, there is a level of detail available you don’t see in the one-size services.

The site has many “projects” where members discuss details of their research. The one’s I looked at required the Y67 test to join as they were specific to certain haplogroups.

FTDNA offered me a significant autosomal discount, so I ordered the Family Finder test to connect with a few relatives on the system. This gave me the Matches section and Chromosome browser, similar to what 23andMe has. The Origins reports where too general to be of much use. They did not match known family regions either.

Also note they’re using the oldest technology now.

Conclusions
I’d still recommend 23andMe for the overview. Their reports are broader and bring a more complete perspective. They use newer tech and have a larger customer base which increases accuracy and matches.

Family Tree DNA is superior if you want to explore genealogy in greater detail. They have more detailed test options but use older tech and are more expensive. Just understanding the value of their options requires a serious exploration.

National Geographic Genographic Project loses much of it’s advantage as others begin to include deep ancestry reporting. With their migration to the newer tech, it can’t be uploaded to FTDNA nor the genome downloaded for other services.

Ancestry also includes a DNA testing service but this would only be helpful if you use their services already. The family tree building software is sophisticated but is an ongoing expense.

From some of the commentary I’ve read on-line, serious researchers use several of the services for different features and to connect with different populations. As the number tested grows, the detail levels will increase. Added features will make going back in and taking a look around again useful, even for the casually curious.
David

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