///The Encyclopedia of mtDNA Origins – Geno 2 Samples & Maternal Origin

The Encyclopedia of mtDNA Origins – Geno 2 Samples & Maternal Origin

I am continuing my work on the Encyclopedia of mtDNA Origins from my last post… This is a project that will create mtDNA pages for all named subclades. One part of each page will hold a table of results from National Geographic's Genographic Project's Geno 2 results. The combination of academic sample collection and public participation, the Genographic database is one of the largest sources of mtDNA result with maternal ancestry information.

Geno 2 Sample Requirement

From the first post, we have a user story –What the user wants. As a user with mtDNA results, I would like Maternal Origin information from Geno 2.0 tested samples.

Encyclopedia of mtDNA Origins - Geno 2 and Genbank Requirements

Encyclopedia of mtDNA Origins – Geno 2 and Genbank Requirements

Just what are Geno 2 results? What maternal origin information is available?

Geno 2 Background

Truckin'
…you got to play your hand sometime
the cards ain't worth a dime
if you don't lay em down — Robert Hunter

The original Genographic Project launched in 2005. The first public participation tests were either Y-DNA for men or mtDNA for women. In 2012, National Geographic relaunched their website with new features and a new three-part test. Based on a microarray chip, the test included autosomal and mtDNA results for women. For men it included autosomal, mtDNA, and Y-DNA results. Along with testing, participants could answer demographic questions.

Three of those questions are birthplace, mother's birthplace, and maternal grandmother' birthplace. From them, it is possible to derive a recent maternal origin. Of course, the origin will be too recent to exclude the migrations and Diasporas of recent origin in the Americas. That will need individual analysis.

Normalizing Origins

My first step was to download demographic and genetic information from the Genographic DAR, the researcher portal to results.

Encyclopedia of mtDNA Origins - Fetching Records from the Genographic DAR

Encyclopedia of mtDNA Origins – Fetching Records from the Genographic DAR

From there, I imported the results into Excel.

Encyclopedia of mtDNA Origins - Import Results to Excel

Encyclopedia of mtDNA Origins – Import Results to Excel

I next removed unneeded columns and added Hg IDs for record keeping. Note, every Genographic participant has a private ID (the GPID). There is a different ID used for the research database. Thus, the Hg ID creates a double layer of removal from the participant's ID.

Encyclopedia of mtDNA Origins - Cleanup Columns

Encyclopedia of mtDNA Origins – Cleanup Columns

I then replaced the empty fields and the places where the answer was Unknown with Unspecified. For places where the answer was not a country, I changed it to the appropriate country and corrected misspellings.

Encyclopedia of mtDNA Origins - Cleanup Data

Encyclopedia of mtDNA Origins – Cleanup Data

Finally, I create the Maternal Origin column. It follows these rules:

  • If the Maternal Grandmother's Birthplace is not Unspecified, then it is equal to her birthplace.
  • Otherwise, if the Mother's Birthplace is not Unspecified, it is equal to her birthplace.
  • If neither of those, it is equal to the participant's birthplace.

I made some minor adjustments in the column name. Note that Geno 2 results currently use Phylotree Build 16.

Encyclopedia of mtDNA Origins - Add Maternal Origin

Encyclopedia of mtDNA Origins – Add Maternal Origin

Building the Geno 2 Sample Database

With the data prepared, I built the content type to hold it in the database. For the past mtDNA Stories and Phylotree Branches, I have used the PODs framework to create custom content types. These let me add special fields and options to each. For Geno 2 data I knew I wanted something more though. Custom content types are part of the WordPress data structure. For large sets of records with many fields, it can become unwieldy.

Thus, I decided to use PODs Advanced Content Types. These place the records and associated fields in their own table within the database.

Encyclopedia of mtDNA Origins - Creating Geno 2 Advanced Content Type

Encyclopedia of mtDNA Origins – Creating Geno 2 Advanced Content Type

The first five fields hold the data I prepared. The next two are relationships. As I mentioned, Geno 2 results use Phylotree build 16. For the initial launch I have linked each haplogroup to the corresponding mtDNA Story using the Build 16 Hg field. When I convert results to build 17, I will add the right relationships to the Build 17 Hg field and change settings to use that field.

Meanwhile, I visited my PHPmyAdmin interface, and used SQL to load records into the database.

Geno 2 Sample Templates

The first template is Get Geno 2 Profiles. Unlike the template for the Phylotree log, wrote this one to only return the rows for the table. This is because in some cases there will not be results for the branch. Creating the table elsewhere ensures that the lack of records is shown by an empty table and not an empty space on the page.

Encyclopedia of mtDNA Origins - Get Geno 2 Profiles Template

Encyclopedia of mtDNA Origins – Get Geno 2 Profiles Template

Second is updating the mtDNA Stories template.

Encyclopedia of mtDNA Origins - Add Geno 2 to the mtDNA Story Template

Encyclopedia of mtDNA Origins – Add Geno 2 to the mtDNA Story Template

I save both, and am done.

JQuery DataTable

After looking at the Geno 2 dataset, it was clear that there would be many cases where there were hundreds and sometimes thousands of records for the branch. Making this user-friendly needs a bit more than a table of all results. I decided that the requirements should be extended to include pagination, column sorting, and searching.

One of the top code libraries to add those features to tables is DataTables.

Encyclopedia of mtDNA Origins - DataTables.net Example

Encyclopedia of mtDNA Origins – DataTables.net Example

Integrating it could take some time, so I checked to see if someone else in the WordPress community had already done so with a plugin. Yes! WP jQuery DataTable does exactly that.

Encyclopedia of mtDNA Origins - WP JQuery Plugin

Encyclopedia of mtDNA Origins – WP JQuery Plugin

After a few style and setting adjustments, it was ready.

Looking at Results

With all of that done, it is time to check out the results. Here is how it looks for K1a12a.

Encyclopedia of mtDNA Origins - Gene 2 Section

Encyclopedia of mtDNA Origins – Gene 2 Section

Not bad. To be continued…

2017-02-03T12:35:24+00:00 July 9th, 2016|Categories: News|Tags: , , |
  • Roger Guiles

    My mother was orphaned and my quest is to find out her parents so I can complete a family tree for my children. I have utilized familytree. com and took the DNA test for the general family search. What would be your suggestion for a next step?
    Thanking you in advance,

    Roger

  • Debra Katz

    You cannot be sleeping at all to be getting so much done on this project!! I think Google should buy the sight as you deserve to get rich off of so great—-and useful!—an effort. (And no, this is not your mother or bookie). (-;

    • Thank you, but they cannot have it yet. I am having too much fun.