The Pakistani genome

We’re fast approaching the point where the “first genome” of class X is going to lose its novelty. There are more than 100 people who have had their full genome sequenced, and you can’t really track down a comprehensive list anymore that I can see. Remember, a full genome sequence is a mapping of all 3 billion DNA base pairs. In contrast, what genotyping services offer are a subset, often 1 million base pairs. The 1 million are not random, rather, they are variants which are known to…vary. But there are some important issues which can be addressed only in a full genome sequence. For example, you can see which distinct mutations are unique to you, and separate you from your parents.

In any case, here’s a summary in the Dawn:

The details were revealed to the Pakistani media by Prof. Dr. M. Iqbal Choudhary, Director International Centre for Chemical and Biological Sciences (ICCBS), Karachi University and Dr. Kamran Azim of ICCBS at a press conference at PCMD.

Highlighting the importance of the project, Dr. Choudhary said Pakistan had officially entered into the world of genome mapping and the details of the work would be published soon in a research journal. He disclosed that eminent Pakistani chemist and former chairman of the Higher Education Commission (HEC), Dr. Atta-ur-Rehman was the first Muslim and Pakistani whose complete genome was mapped by Dr. Kamran Azim.

“The important work will pave the way for research on heredity diseases, evolution and the over all genetic make up of Pakistanis which now hold a unique genetic pattern as a nation. In the past many people like Dr. Watson and others urged scientists not to reveal their genome publicly but Dr. Rehman has never put any restrictions for his genome draft,” Choudhary added.

As you might guess, I laud that they’re releasing this data to the public. I do find it rather weird that the Pakistani press is reporting that the first Muslim has been sequenced. Do we talk about the first Buddhist, Christian, or Hindu being sequenced? Muslims are not a clear and distinct class in relation to population biology, but I suppose for many believers this is the biggest point at issue when considering one’s self-identity.

Speaking of populations, The Express Tribune has a rather amusing short article which speaks volumes:

“Our nation is a mix of a lot of races,” said Prof. Dr M Iqbal Choudhary, who heads the project. “Pakistanis are like a “melting pot” ie a mix of Mughals, Turks, Pashtuns, Afghans, Arabs, etcetera.”

You can actually look at a lot of Pakistani genetics thanks to the HGDP data set. There are statistically significant contributions from Africans, West Asians, and even East Asians, to Pakistanis. But on average this is a very low load, less than ~5%. Pakistanis are what you’d expect, just part of the normal range of variation of South Asians. In some of the remarks and press there is the admission that Pakistanis aren’t really genetically discontinuous with Indians, but that isn’t overly emphasized (also, aside from the Baloch, it does look like Pakistanis are discontinuous with Iranians).

To make more concrete about what I’m talking about, let me show you a plot I generated a few days ago. Below are three populations, Iranians, Pakistani Pathans, and Gujarati Patels. Each bar represents an individual, and the color proportions represent ancestry mixes. I’ve labeled the colors for convenience, though they have only rough correspondence with the names I give them. You can find the full results here. The individual sequence above is reputedly a Mujahir, so I suspect they would be somewhere between the Pathans and Patels in their proportions. Note that I also added some friends & family whose samples I have at the right edge of the bar plot.


One thought on “The Pakistani genome

  1. The article in The Express Tribune certainly speaks volumes, but the reader’s comments section has an equally interesting story to tell by itself. Almost every reader is amused by the characterization of this exercise as the the sequencing of first Muslim’s genome, and the affirmation of presence of the “right” races in Pakistani populace. Some comments that stand out…

    “Mashalllah. As per Dr M Iqbal Choudhary we have all the right martial genes but not the genes of Indian. May Allah be with the discoverers as Allah is the greatest discoverer of all.”

    “Irony is a doctor named Chaudhary is not Mughals, Turks, Pashtuns, Afghans, Arabs, etcetera and one does not need dna test to confirm that.”

    Looks like average Pakistani is much more level headed than their so called elites.