June 21, 2008

EURO-DNA-CALC 1.1 released

UPDATE (20 Feb 2011): EURO-DNA-CALC has been superseded by the Dodecad Ancestry Project.

The current version is 1.1.1 Download it if you obtained previous version (1.1) which had a bug for deCODEme data.

A new version of the EURO-DNA-CALC has been released. The previous version (1.0) was described here.

Version 1.1 also uses deCODEme/23andMe data for an individual but outputs a maximum likelihood estimate of his admixture proportions from the three groups NW European, SE European, and Ashkenazi Jewish.

More comments on this dna-forums thread (registration required).

Below are the admixture estimates for Greg and Lily Mendel of 23andMe. An examination of the confidence intervals output by the program suggests that non-NW European admixture in Greg is a strong possibility, while Lily could conceivably have no non-NW European admixture. On the other hand, Lily's 10% Ashkenazi and only 1% SE European admixture imbalance is interesting. As with all genetic tools, the results should be interpreted in the light of other information about a person's ethnic origin and genealogy.

40 comments:

cacio said...

Thanks for the new version. I get 9 NW, 91 SW and 0 AS. Being from Italy (tuscany), that seems on the mark. Which algorithm are you using now?

cacio

Dienekes said...

Just an exhaustive search over all possible admixture estimates (x,y,z) where x,y,z>=0 and x+y+z=100.

If NW,SE,AJ are the frequencies of an allele in the three populations, then an (x,y,z) admixed individual will possess the allele with probability (x*NW+y*SE+z*AJ)/100.

Andrew Yates said...

Dinekes, I've added your tool to the genomics secondary market database. What is your full name so that I may credit you with authorship, or if you would prefer an alias, under what name may I list you?

-Andrew Yates
ThinkGene.com

theghostwoman said...

Does this apply to 23andme v2, or does it only work with v1?

Dienekes said...

Does this apply to 23andme v2, or does it only work with v1?

It should work fine with v2.

pconroy said...

My results:

> EuroDNACalc("23andme")
[1] "NORTHWEST EURO: Maximum Likelihood Estimate=100% Interval=[86, 100]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=0% Interval=[0, 14]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=0% Interval=[0, 9]"
>

Genespool2009 said...

I`m of african-American with multi-mixtures back ground. I would like to find out my European origin, so would the Euro-calu 1.1 works for some like me with only 19%European and 10% asian DNA ? I`m currently uses DNA Tribes, FamilyTree DNA & 23andMe.If not, could you please point me some web sites where i might recieve such information. Thank you.

Ponto said...

This Ponto's EuroDNACalc.

SE Euro 87% [53,100]

NW Euro 8% [0,32]

Ashken 5% [0,28]

I have no know Jews, Ashkenazim or otherwise in my family going back as far as I have checked,which is 1500s. Speaking of Jews, in my country of origin, Sephardic Jews were present not Ashkenazim.

Who are the SE Euros and the NW Euros? I am not of Greek descent.

Dienekes said...

NWE and AJ confidence intervals interesect 0% so I wouldn't give them any particular importance.

ctuemmler said...

I ran my dna file from 23andme thru your calc program.
I got:
NW Euro 65%
SE Euro 15%
Ashkenazi 20%
My father is from Germany and and far as I know he is not Jewish.
My mothers mother is Romanian (both parents from Romania)
and my mothers father ancestors have been here for hundreds of years with a little native american and african in the mix (1/2 % each).
My question is, is it accurate that I am really 20% Jewish?
Thanks!

Dienekes said...

You should look at the confidence intervals and not just the central estimates. Both the minor components have probably intervals that intersect zero.

ctuemmler said...

I didn't notice the intervals only the pie chart. I re ran it and here are the results:
"NORTHWEST EURO: Maximum Likelihood Estimate=65% Interval=[38, 89]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=15% Interval=[0, 52]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=20% Interval=[0, 42]"
As I said, my father is from Germany and my mother is half Romanian and the other half mostly European from the UK.
Can you explain what the Intervals mean? Am I 20% Jewish?
Thanks

tippler said...

It doesn't seem to work for me whenever. I have followed every instruction, up until the part where you open the 23andme txt file on the command prompt.

I get this:
"Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '23andme.txt': No such file or directory"

How do i fix this

Spy said...

Is there any way to reverse-engineer the Frankish-Byzantine-Levantine components from one's "Global Similarity" scores in 23andMe? I'm trying to figure out a multiple-regression set up with the use of many people's results.

SCP said...

I get
Error: unexpected symbol in "23andme"

Any instructions?

Thanks,

Steven

Dragon Horse said...

Genespool2009 :

I'm also African American and no it does not work. It shows me to be 64% Southeast European, 0% Northwest European, and 36% Ash. Jew. LOL This does not at all coincide with 23&me, they say I'm at least 62% African, but likely more because they have serious issues overestimating "Asian" (really Native American) ancestry in New World Blacks.

My Central European girlfriend is shown as having 21% Ash Jew, 40% NW Euro, 39% SE Euro. Based on where she is from and her families name and known time in the area I doubt she has any Jewish ancestry that is in the last 200-300 years anyway...the location of her country makes it typical that she would come out as an even split between NW and SE...so with that it appears accurate and matches up with 23&me fairly well as she is almost equally related to Southern and Northern Europeans.

Dragon Horse said...

On second thought, in regard to my results, it does pare up with 23&me if you make the SE Euro AFRICAN and the Ash Jew "Other" (equally Western Euro and Asian) lol

Jacques Beaugrand said...

My results:
> EuroDNACalc("23andme")
[1] "NORTHWEST EURO: Maximum Likelihood Estimate=45% Interval=[17, 67]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=7% Interval=[0, 45]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=48% Interval=[23, 69]"

On ne peut rien vous cacher.
Merci et bonne poursuite de votre superbe travail.

Jacques Beaugrand

Draggon said...

I can report two results for the Euro DNA Calculator, both for two users on 23andme (images attached):

Dan Draghici (myself)
52% NWE, 48% SEE and 0% Ashkenazi Jewish

Some surprise given that most of my known DNA comes from Romania, in spite of some German blood; however, my Y-DNA haplogroup is U106+ L48+ L47- L148-.

David Blais
84% NWE, 16% SEE and 0% Ashkenazi Jewish

No surprise here, with all known ancestry being overwhelmingly French, with a little English, as well.

Mark Royer said...

Those Europeans baffled by indications of Jewish roots should keep in mind that the early church was populated almost exclusively by Jews, who reached out to their pagan Gentile neighbors and included them in the church. Their children, raised in the same faith, naturally intermarried and with each generation the Jewish genes were spread wider, so I would estimate all Europeans have at least some Jewish roots.

Dienekes said...

The Jews were a small part of the Roman Empire, so even if they were ALL of Jewish origin, and had ALL converted to Christianity, and ALL their genes had spread uniformly across Europe, it would amount to a few % at most, spread evenly across Europe.

ctuemmler said...

I have run two dna files (23andME) through the EuroDNACalc program. I have a new computer with Windows 7 and I can't seem to run a third DNA file on my new computer. Is there a new version for Windows 7 I should use
?
Thank you.

Dienekes said...

ctuemmler, I've ran EURO-DNA-CALC on both Win7 and XP without a problem. The only thing I can think of is to perhaps install the 64bit version of R if you are running a 64bit operating system.

R.Elizabeth said...

23andme for my twin and me

58% European
34% African
8% Asian

EuroDNACalc for my twin and me

[1] "NORTHWEST EURO: Maximum Likelihood Estimate=0% Interval=[0, 10]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=56% Interval=[32, 80]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=44% Interval=[20, 68]"

23andme for our mother

57% European
34% African
9% Asian

EuroDNACalc for our mother

[1] "NORTHWEST EURO: Maximum Likelihood Estimate=0% Interval=[0, 18]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=84% Interval=[57, 100]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=16% Interval=[0, 41]"

Considering that we only about 57-58% European, do this mean that my sister are I are about 25% Ashkenazi Jewish (58 x .44), whereas our mother is about 9% Ashkenazi Jewish (57 x .16)?

Dienekes said...

Considering that we only about 57-58% European, do this mean that my sister are I are about 25% Ashkenazi Jewish (58 x .44), whereas our mother is about 9% Ashkenazi Jewish (57 x .16)?

This test is meant for Europeans only; non-Europeans will still get 3 numbers that add up to 100%, but they are meaningless.

Danielle said...

I tried to use the calculator on my 23andme results and it is giving me an error. Any thoughts as to the cause?
> EuroDNACalc("23andme")
Error in if (allele1 == "-") { : missing value where TRUE/FALSE needed

David Bernstein said...

hi,

my wife is of iraqi Jewish descent on both sides.

her EuroDNACalc results were as follows: "NORTHWEST EURO: Maximum Likelihood Estimate=0% Interval=[0, 22]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=42% Interval=[13, 64]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=58% Interval=[36, 80]"

Does this mean that she is likely at least 36% Ashkenazi, or does it mean that of her European DNA (excluding her Iraqi/Near Eastern DNA), she is at least 36% Ashkenazi?

Put another way (1) does EURODNACALC only count your European DNA strands; and (2) is Near Eastern/Middle Eastern DNA considered "European" for these purposes?

Zohar said...

I'm Ashkenazi. I just ran the test and it came out

Ashkenazi 92%
SE Euro 8%

with intervals

> EuroDNACalc("23andme")
[1] "NORTHWEST EURO: Maximum Likelihood Estimate=0% Interval=[0, 8]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=8% Interval=[0, 30]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=92% Interval=[70, 100]"

I'd like to submit to DODECAD, but I understand that its closed.

Thanks, Dienekes

Mihai said...

Is the calculator working with 23andme V3 chip results?

I have both V2 and V3 data and I am getting different results.
V2: 83% NWE
0% SEE
27% ASK
V3: 85% NWE
65 SEE
9% ASK

Differences are not huge but still I think that they are significant

quentinbaudier said...

this euro dna is shit ,sorry for the term but how can my father be 54 % SE euro and me only 5 % ? we are both v3 data

Lauren said...

I must be really cumputer stupid, but I cant seem to get this to work for me, I removed all of the comment lines from my 23and me file, but cant get past that. I go to change directory and cant find my data file. I changed the data file to a .R file and still no luck, any help would be appreciated

Dienekes said...

In change dir you are not going to find your data file, you will go to the directory where you saved the '23andme.txt' file.

Dante said...

"Error in row.names(B) : object 'X' not found"

What's gone wrong there? Any help is appreciated!

Dante said...

Ok I figured it out - all I needed was to change the 23andme data file to 23andme.txt instead of the default name.

Thanks for the application Dienekes

Kendjelic said...

My known ancestry on my paternal side is Croat and Italian. Mother was adopted but my guess is NW Europe. My results came back as:

[1] "NORTHWEST EURO: Maximum Likelihood Estimate=72% Interval=[52, 88]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=0% Interval=[0, 23]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=28% Interval=[11, 45]"

Does this mean I have Jewish ancestry or do I take the results with a grain of salt? Thanks in advance.

Dienekes said...

>> Does this mean I have Jewish ancestry

It does not.

initialzero said...

Using R 2.13.1 on Linux (Fedora) I had to first load the RData file.


load("/path/to/EuroDNACalc.RData")
EuroDNACalc("23andme")

Lauraannw said...

[1] "NORTHWEST EURO: Maximum Likelihood Estimate=15% Interval=[0, 42]"
[1] "SOUTHEAST EURO: Maximum Likelihood Estimate=73% Interval=[38, 100]"
[1] "ASHKENAZI JEWISH: Maximum Likelihood Estimate=12% Interval=[0, 34]"

Sounds about right! Though, neither I nor my family knew we had Ashkenazi Jewish in our heritage before 23andMe. Now my dad's mom is less of a mystery :)

steve bee said...

Is it still possible to download this?

I've tried several times but it says forbidden.

Mental Menza said...

How to download this? Need help!