Sunday, August 19, 2012

Introducing the ACD Tool

It is with satisfaction I announce the release of my first ever population genetics spreadsheet for fellow researchers. The Ancestral Component Dissection (ACD) Tool is a piece freeware I have developed to give those with a similar knack for fiddling with ADMIXTURE, Y-SNP and mtDNA frequency data better means to flesh out inter-population differences.


ACDTool (v1.0)
How Does The ACD Tool Work?

The ACD Tool relies on the frequencies of "ancestral components", a general catch-all term for uniparental markers (Y-SNP's, mtDNA) and Autosomal DNA (auDNA). These form the mainstay of much of the work that has been done in population genetics for the past few decades. The advent of "genome blogger" projects has brought the immediacy of these techniques to those who have tested with personal genetics companies, such as Family Tree DNA (FTDNA) and 23andMe. The ACD Tool should therefore be considered a supplementary item by those interested in these results, as well as data procured from current literature.

The level of commonality that occurs between many populations and ethnic groups poses a problem for those interested in investigating what differences arise between them.

To solve this, the ACD Tool works by removing mutual shared component frequencies between sample averages within a region. The idea is to lessen the amount of regional similarity and intentionally exaggerate those differences that exist between neighbours.

This is achieved by removing congruent component values across all populations (using the lowest value as a benchmark), leaving only the differences behind.


What Experiments Are Ideal?

As the ACD Tool is intended for finer inter-population analysis, it is best applied in a regional context. It serves the purpose of better revealing genetic differences which may account for linguistic or micro-regional trends.

Example #1: Northeast Europeans (Dodecad)

Once the Polish, Russian and Finnish Dodecad cohort averages were run through the ACD Tool, I simply used Excel to create the charts. The "Before-After" feature is used to highlight that the tool has completely achieved its' desired goal in amplifying the genetic differences between them:


NE European auDNA (Dodecad) through the ACD Tool



Example #2: West Asians (Harappa)
Using the Harappa Ancestry Project this time, I ran the data of Armenians, Assyrians, Kurds and Iranians (mostly from the Harappa cohort) into the ACD Tool once more and presented the differences as above:

W Asian auDNA (Harappa) through the ACD Tool


Example #3: South-Central Asians (Eurogenes)
A final example pits Pathans, Jatts, the Burusho, Balochis and Brahuis against one another:

SC Asian auDNA (Eurogenes) through the ACD Tool



Are There Any Drawbacks?
The efficacy of the ACD Tool depends on the number of populations, cohort size and cohort specificity. As the examples above show, the level of inter-population component sharing may decrease greatly if groups that are from more genetically diverse regions are compared.

In addition, using the ACD Tool on populations that are too different (i.e. Han Chinese and Yoruba) will not work given the genetic overlap through either ADMIXTURE, Y-SNP's or mtDNA is negligible. Of course, this defeats the point of the tool in the first place.

Lastly, the tool requires Macros to be enabled for the instructions to work.


Disclaimer

The ACD Tool is an open-source free-to-use spreadsheet. Those wishing to modify the spreadsheet for their personal use are welcome to do so. However, any modifications made to the ACD Tool with the intent of subsequent redistribution are kindly asked to contact the creator (myself) before doing so out of common courtesy.

Please also note the ACD Tool is a first attempt at giving back to the genealogy world I have been a part of for several years. Though functional (as shown above), it is not without bugs. In light of this, I am not responsible for any loss of data that may occur from its' use.

Finally, I hope the genealogy world finds some use for this nifty piece of kit.



Acknowledgements

To the Dodecad Ancestry ProjectHarappa Ancestry Project and Eurogenes Genetic Ancestry Project (auDNA used in Examples).

Addentum I [20/08/2012]: ACDTool v1.1 replaces v1.0, Macros smoothened and instructions refined. Eurogenes South-Central Asian example also added.

2 comments:

  1. I would like to download the ACDTool. The file is not there anymore. Is there another way to download?

    ReplyDelete
  2. Nice and amazing post ACD SEE 5.0 Standard i hope this post is become useful to solve all about photo converting and much more problems.

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