Tag Archives: dodecad

Family DNA Results

I posted my genetic ancestry results. Now, we’ve got my parents, my sister and my wife tested with 23andme. So I thought a comparison would be interesting.

Here’s the ancestry painting from 23andme which uses three reference populations: Yoruba from Nigeria, Chinese and Japanese, and Utahns of Northwestern European descent.

Dad Mom Sister Me Wife
African 0.56% 0.95% 0.96% 0.34% 0.00%
Asian 8.68% 6.63% 8.00% 6.58% 10.18%
European 90.76% 92.42% 91.04% 93.09% 89.82%

You can basically use my wife as a sort of reference for Punjabi ancestry here (which is 3/4th of our ancestry too). Also, my wife and I are unrelated.

As you can see, while our results are close, my mom and sister have more African and I have the least.

And here are the similarity numbers for us with different reference populations.

Dad Mom Sister Me Wife
Central & South Asians 67.13 67.09 67.05 67.12 67.12
Northern Europeans 66.97 66.92 66.92 66.91 66.94
Southern Europeans 66.97 66.88 66.92 66.90 66.85
Near Easterners 66.85 66.76 66.81 66.79 66.72
Siberians 66.59 66.50 66.48 66.52 66.77
Eastern Asians 66.52 66.41 66.42 66.45 66.70
North Americans 66.48 66.40 66.38 66.44 66.69
South Americans 66.46 66.37 66.40 66.40 66.76
Oceanians 66.39 66.41 66.39 66.35 66.62
Northern Africans 66.17 66.10 66.15 66.13 65.94
Eastern Africans 64.08 64.06 64.11 64.10 63.89
Southern Africans 63.96 64.00 64.06 64.00 63.77
Central Africans 63.93 63.93 64.00 63.97 63.74
Western Africans 63.91 63.91 63.97 63.94 63.70

As compared to my wife, we are closer to Africans and farther from Eastern Asians, Native Americans (who are really a branch of East Asians) and Oceanians.That’s expected because of the 25% Egyptian ancestry we have.

Finally, here are our Dodecad Project results.

Dad Mom Sister Me Wife
East_European 4.96% 5.71% 4.59% 4.19% 6.28%
West_European 7.43% 9.59% 8.98% 8.97% 11.10%
Mediterranean 11.10% 9.28% 10.99% 9.24% 5.77%
Neo_African 1.36% 1.12% 1.45% 1.15% 0.26%
West_Asian 23.86% 22.41% 22.88% 23.88% 19.81%
South_Asian 33.94% 37.24% 33.15% 36.57% 45.64%
Northeast_Asian 2.53% 1.64% 1.79% 1.95% 3.22%
Southeast_Asian 3.04% 2.85% 3.95% 2.61% 3.35%
East_African 1.86% 2.18% 3.06% 2.30% 0.00%
Southwest_Asian 7.49% 5.57% 5.75% 6.57% 4.56%
Northwest_African 1.90% 1.49% 2.32% 1.57% 0.00%
Palaeo_African 0.53% 0.92% 1.10% 1.01% 0.00%

Similar results but interesting differences.

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Genome in the Wild

I tested with 23andme in April 2010 and then upgraded to their version 3 chip with almost a million SNPs last Christmas.

Now I am releasing my personal genome in the public domain.

CC0
To the extent possible under law, Zack Ajmal has waived all copyright and related or neighboring rights to Zack Ajmal 23andme v3 Genome. This work is published from: United States.

You can download my genome data in zipped files:

Razib has a list of people who have made their 23andme genomes public.

When Blaine Bettinger released his genome into the public domain, he issued a challenge:

So, I’m challenging everyone who reads this to download my data and analyze it to find the most interesting or surprising results. For example, you could use my most recent 23andMe V3 data.

I’ve already done a fair amount of analysis myself, including the Promethease reports above (and see here), and a recent blog post about my vastly increased Type 2 Diabetes risk. However, perhaps there’s a recent but relatively study that applies, or perhaps there’s a story you can weave with a handful of SNPs. Or, even better, what can you tell me about my ancestry other than mtDNA and Y-DNA haplogroups? Don’t worry about the strength of the study, reproducibility, etc. – I’m aware of the uncertainties associated with this type of research, and my goal here is to make people aware of possibilities.

Please post your findings in the comments below, and in two weeks I’ll pick the most surprising or interesting findings and make them the focus of a new blog post.

Can you surprise me with my own genome?

I have done a fair amount of analysis on my genome. For example, here’s my Promethease report. My ID is DOD128 in Dodecad, PKEG1 in Eurogenes and HRP0001 in Harappa.

My challenge for you would be to find interesting information about my chromosome 9 which is 93% homozygous.

If you analyze my genome, it would be great if you could let me know about what you found as I am always hungry for more information.

Related Reading

Dodecad Oracle

Dodecad has come up with a new version (v3) of its admixture results. Here are my results:

South Asian 37.4%
West Asian 23.3%
Mediterranean 9.8%
West European 9.6%
Southwest Asian 6.2%
East European 3.5%
Southeast Asian 2.4%
East African 2.2%
Northeast Asian 1.9%
Northwest African 1.5%
Neo African 1.1%
Palaeo African 1.0%

Dodecad also has a fun tool to check one’s results against different population averages. My closest populations are:

Population Distance
1 Pathan 7.2021
2 Bene Israel Jews 8.6822
3 Sindhi 10.0479
4 Punjabi Arain 10.0926
5 Kashmiri Pandit 10.5778
6 Burusho 11.179
7 Balochi 11.6705
8 Brahui 13.0208
9 Makrani 15.6735
10 Cochin Jews 18.1403

If I make use of mixed mode, the tool tries to find a combination of two ethnic groups with differing percentages that fits my results best.

Two Population Mix Distance
1 17.3% Palestinian + 82.7% Sindhi 3.0122
2 17% Morocco Jews + 83% Sindhi 3.1181
3 17.3% Palestinian + 82.7% Punjabi Arain 3.1228
4 17.2% Egypt + 82.8% Punjabi Arain 3.1846
5 82.9% Sindhi + 17.1% Egypt 3.288
6 17% Lebanese + 83% Sindhi 3.4994
7 16.7% Jordanians + 83.3% Sindhi 3.5238
8 16.7% Jordanians + 83.3% Punjabi Arain 3.5608
9 15.8% Samaritians + 84.2% Sindhi 3.6356
10 16.9% Ashkenazi + 83.1% Sindhi 3.7077

This actually fits reasonably well with my actual ancestry (75% Punjabi + 25% Egyptian).

Related Reading

Dodecad Project II

I talked about the Dodecad Project last time. Dienekes also did some cluster analysis using mclust.

When he classified everybody into 48 clusters, I showed up almost all alone in cluster 21. Only one other member who is a Bihari Brahmin had a 50% chance of belonging in my cluster.

With 56 clusters, I am classified with 9 Sindhis (out of a reference population total of 24) and the same Bihari guy (who now has 99% chance of belongign in this cluster).

It looked like I was an outlier and when Dienekes tested for outlier data samples he found me among them.

With 64 clusters, I am again an outlier, though I am classified with a few Punjabis and 20/24 reference Sindhis and 10/22 reference Pathans. I am likely making their cluster not a good tight fit.

For 63 cluster analysis, the outlier status remains and the story is about the same as with 64 clusters.

More interesting was when Dienekes analyzed just South Asians. In his cluster analysis, I was classified with the 3 Punjabis in his project as well as the following reference population samples: 2 out of 25 Singapore Indians, 1 out of 24 Balochi, 18 out of 24 Sindhi, and 9 out of 22 Pathan.

His admixture results for me in this South Asian analysis were:

Pakistan 39.8
Indian 22.4
West Asian 16.3
Dagestan 11.8
European 2.8
North Kannadi 2.2
Southeast Asian 1.9
Irula 1.8
Siberian 1.1

An interesting pattern I have noticed is that my European admixture percentage is generally lower than other Punjabis. When the European is divided into North and South, I have less North European admixture than a typical Sindhi, Punjabi or Pathan but more South European than those groups.

The final analysis from Dodecad is a fun one:

Using Pakistani Punjabis from Xing et al. (2010) and Behar et al. (2010) Egyptians as references requires me to drop the number of markers to ~38k, but the result of the supervised ADMIXTURE analysis is 77.4% Punjabi and 22.6% Egyptian, which seems compatible with what he expected.

Basically, Dienekes used only 25 Punjabis and 12 Egyptians as reference and then tried to estimate my proportion of these two populations. Of course, the assumption is that these two are my only ancestries. Interestingly, this is very close to what I expected. I plan to do this same analysis with several different reference populations and see what I get.

Related Reading

Dodecad Ancestry Project

I asked Dienekes to include me in his Dodecad Ancestry Project and he gave me the following results:

Ancestral Component Percentage
South Asian 44.9%
West Asian 33.7%
Southwest Asian 5.7%
North European 5.5%
South European 3.7%
East African 3.4%
Northwest African 2.1%
West African 0.6%
East Asian 0.4%
Northeast Asian 0.1%

You can see the results of all the project participants in a spreadsheet. You can also check out the admixture results for the reference samples he used.

Below is a bar chart showing the ancestral population percentages for me (DOD128) along with some other Dodecad participants (those starting with DOD) and some reference populations. I selected those individuals and populations that were somewhat closer to me in their admixture results. Also, as initially sorted, the list goes from most similar to me to least similar from top to bottom.

You can sort the bar chart by the different ancestral components by clicking on the legend on the right.

A word about the ten ancestral components (South Asian, West Asian, Southwest Asian, North European, South European, etc): Admixture results in this case gave 10 ancestral components. These do not necessarily correspond to “pure” ancestral populations and they are not labeled, only defined by their allele frequencies. Dienekes looked at the admixture output for his reference populations and assigned the 10 components different names based on which region it is most common in. Thus calling an ancestral component “West Asian” just means that it is found at highest frequencies in the reference populations living in Western Asia nowadays.

I used hierarchical clustering on the Dodecad results to find out which participants are most similar to me. A tree below shows the section including me.

Closest to me are a Punjabi Brahmin and a half-Sindhi half-Balochi guy, then three Punjabi Jatts.

Through all these investigations, some things have cropped up again and again.

One is that I have a minor amount of African admixture (4% East + West African). Most of it seems to be East African, which is why it doesn’t show up in 23andme ancestry painting. This is consistent with a quarter Egyptian ancestry. An average Egyptian reference sample is 14.7% East African and 4.1% West African. A quarter of that would be 3.7% and 1.0% respectively. Compare that to my 3.4% and 0.6%.

Also, while I am not very similar to Punjabis, they are the group most similar to me. Since there are no Punjabis in the reference data, Sindhis are the next closest. I am in fact more similar to Gujaratis than I am to Turks or any Central or West Asian groups.

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