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.

Paternal and Maternal Lines

We men inherit the Y chromosome from our fathers who got it from their fathers. So the Y chromosome can be used to trace your paternal lineage. Different sequences of alleles and mutations can be assigned to haplogroups where a haplogroup signifies common descent on the uniparental line.

According to my 23andme results, I belong to the paternal haplogroup R1a1a. This group is very common in Eastern Europe as well as South Asia. The distribution of R1a1a can be seen in the map below.

Similarly, we all inherit mitochondrial DNA from our mothers. The sequence of alleles and mutations on the mitochondrial DNA (mtDNA) is also organized into phylogenetic tree.

I can trace my maternal line to Egypt (my great-grandmother) and thus I expected a maternal haplogroup common in the eastern Mediterranean. It turns out I belong to haplogroup H, which everyone and their mother belong to in Europe as can be seen in this map.

According to Wikipedia,

Haplogroup H is the most common mtDNA haplogroup in Europe. About one half of Europeans are of mtDNA haplogroup H. The haplogroup is also common in North Africa and the Middle East. The majority of the European populations have an overall haplogroup H frequency of 40%–50%. Frequencies decrease in the southeast of the continent, reaching 20% in the Near East and Caucasus, 17% in Iran, and <10% in the Persian Gulf, Northern India and Central Asia.

Since 23andme didn’t tell me which subgroup of H I belonged to, I used mthap by James Lick:

Your rCRS differences found:

HVR2: 263G
CR: 750G 1438G 4769G 15326G
HVR1: (16519C)

Best mtDNA Haplogroup Matches:

1) H
2) H26
2) H(16192)
2) H35
2) H24
2) H10
2) H25
2) H(195)
2) H33
3) H19

Amber’s maternal haplogroup is M4a, which is mainly found in South Asia.

You can see the Y-DNA haplogroup tree and the mtDNA tree online.