The Iranian Genome Project

By Razib Khan | February 7, 2012 1:54 am

A friend pointed out that the Iranian Genome Project site has been around for half a year. The research team is reputable. You can see the rationale at their blog. Though there are several Middle Eastern populations in the HGDP, and you can get other data sets as well, the total number of markers tends to be modest in comparison to the HapMap, let alone a full genome sequence. If you’re going to look for associations with particular traits (e.g., diseases) then it is best to have as many variants as possible (even if you have enough markers so that you can localize the region of the genome where there is an association, that is less useful than having the exact functional variant of interest pegged).

 

On a minor note the Iranian Genome Project blog keeps  using the word ‘Caucasian’ as if it is exclusive of Middle Eastern populations. This is amusing because one of the Caucasian people, the Armenians, are unquestionably Middle Eastern. The ethnic terminology used in the medical literature can be rather ill-suited to the task of biological taxonomy. When it comes to social surveys I don’t have much hesitation checking ‘Asian American,’ but it really gets on my nerves when that category pops up in medical contexts. Asian American as a social category which is inclusive of East, Southeast, and South Asians, has some leg to stand on, even if you think it is artificial. But as a biological category it is not defensible.

But the bigger issue which I’m wondering about is the impact of high levels of consanguinity on attempts to smoke out genome-wide and population-wide associations. If Middle Eastern populations are strongly structured because of recent endogamy then it may be that genetic drift may result in a situation where many of the diseases susceptibilities are highly particular to small segments of a given population. Of course this doesn’t mean that you can’t start somewhere. But it does suggest that the utility of these projects is sensitive to the particular evolutionary genetic parameters which characterize a given population (e.g., the homogeneity of the Chinese vs. the diversity of the Yoruba, the high levels of inbreeding in the Middle East vs. low levels in Europe).

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  • Ryan G.

    “If Middle Eastern populations are strongly structured because of recent endogamy…”. This may sound like a stupid question, but what do you mean by ‘recent’ here? Does this mean that the various groups of the Middle East only started marrying along strongly ethnic/tribal lines within the past, say, 10 centuries, or the past few millenia? For example, in what timeframe did Arabs in Arabia start marrying strongly along tribal lines, Jews start marrying other Jews, or Persians strongly start marrying other people who were Persian speakers? (By this, the past, say, 1000 years could be considered ‘recent’ when measured against something else…)

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #1, hundreds of years. in many muslim nations there is a custom of children of brothers marrying. this results in rapid increase in inbreeding over the generations.

  • Syon

    Razib:”On a minor note the Iranian Genome Project blog keeps using the word ‘Caucasian’ as if it is exclusive of Middle Eastern populations. This is amusing because one of the Caucasian people, the Armenians, are unquestionably Middle Eastern.”

    Yeah, that is really annoying.

  • Michael

    How are Armenians “unquestionably” ME? Armenians are a European ethnic group under any definition with a diaspora in the ME as a result of the Armenian Genocide of 1915. Prior to the Armenian Genocide the Armenian population in the ME consisted of a few monks in Jerusalem.

  • Josh L

    Syon: Yes, I thought Iranians were adamant in proclaiming their Caucasian status. “European” would have been a much better word to use.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #4, perhaps you come from another culture, that’s fine. but to most americans anatolian turkey is middle eastern.

    http://en.wikipedia.org/wiki/Middle_East#Territories_and_regions

    don’t start a retarded argument over semantics.

  • Onur

    I classify Armenians as a West Asian and, more specifically, as an Anatolian/Armenian Highlander people.

    As for the Middle East, it is territorially a very disputed term, so I avoid using it.

    Finally, I never use the term Caucasian to mean Caucasoid, as that is a pretty silly practice, especially for people living in or nearby the Caucasus like me. I only regard Georgians and the various small ethnic groups of the Caucasus (except Nogais) as Caucasian.

  • Donn

    Homogeneity of the Chinese? Are you specifically referring to Han Chinese here?(not trying to be facetious, am genuinely curious)

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Homogeneity of the Chinese? Are you specifically referring to Han Chinese here?(not trying to be facetious, am genuinely curious)

    genetically east asians are rather homogeneous. especially in relation to africans. i thought this was common knowledge? if you want confirmation, go to google scholar and look up ‘hapmap’.

  • Donn

    ^Not doubting your expertise at all, I know very little about haplogroups and stuff, sorry if I came off as flippant.

    RE my post on “a personal note” since for some reason it won’t allow me to post. That whole example I brought up regarding Mustafa was meant to ridicule that notion of miscegenation.

    And with the light skinned vs dark skinned thing, it’s something I’m seeing more on race realism websites with remarks of the inherent stupidity of “black people”. I’m not saying I’ve seen that here(which I haven’t at all), but your political axes remark made me curious of that. I know racial categories have zero biological use, but it’s social use is very much alive. 5 year old mentality notwithstanding.

  • http://www.parhasard.net/ Aidan Kehoe

    I know racial categories have zero biological use, but it’s social use is very much alive.

    I do hope you’re not a medical professional or close to being one.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    I know very little about haplogroups and stuff

    the standard chestnut of wisdom, with great truth, is that there is more genetic variation within a group of bushmen than in all of the populations outside of africa. from that, you can immediately infer why i’d say chinese are homogeneous in relation to yoruba.

    I know racial categories have zero biological use, but it’s social use is very much alive. 5 year old mentality notwithstanding.

    i disagree that racial categories have zero biological usage. and yeah, if you made me bet i do think that different populations have different distributions of traits. the main reason i don’t talk about it much is 1) most people are stupid, so talk about it stupidly (e.g., most ‘race realism’ blogs talk about genetics without knowing jack-shit about genetics, just like most anti-racist blogs do the same), 2) i’m not too interested in those issues too much now, and i tend to blog about what i’m interested in.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    i tried to find your comment in ‘spam’ and it is not there. no idea what happened. also, i have no idea if monad was serious or not. if he was serious, then i’m going to ban him, as he left that douchey comment on a post celebrating the birth of a mixed-race person (my daughter).

  • Hephaestus

    Razib, please don’t use “retarded”. It is an offensive word that has strongly negative overtones.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #14, i wanted to indicate a strongly negative attitude.

  • Donn

    @Razib:

    Thanks for filling that in, I try to avoid bringing up the issue due to the reaction I usually get. Though I’m not afraid to admit I’m still learning this stuff. No disrespect intended to anyone here.

    @Aidan: “biological value” as in there aren’t distinct races of humans based on pigment. What I’ve been learning is that the term used more now(for health, identification and other applications) is “Ancestry”(though this may be mere semantics to avoid negative connotations). However, continue to insult me as you will.

  • Sandgroper

    “meant to ridicule that notion of miscegenation” – You’ll find plenty of support here, I’m certainly not the only ‘miscegenator’ among regular commenters, and not the only one who will have been offended that someone was moronic enough to make such an idiotic and tasteless comment on a thread celebrating the birth of Razib’s daughter, attempted joke or not. But the reason that the commentary on this blog is usually so good is that people keep it technical and objective, and usually avoid the extremes of stupidity, thanks to the hand of the gatekeeper.

    “I know racial categories have zero biological use” – when applied to ancestral geographical populations, they don’t. If anyone is using them any other way, you can assume he’s a moron.

  • Hephaestus

    Razib, I’m sorry that I didn’t make myself more clear. “Retarded” is a term that is offensive to those with mental issues and their families. Calling someone retarded as an insult is offensive to the mentally impaired in the same way that insulting someone by calling him a nigger, spic, hebe, chink, jap, wop, gook, or camel jockey denigrates everyone from that culture.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #18, mental issues? schizophrenia is a mental issue, but they’re not retarded. anyway, ok, they were being as stupid as a mentally disabled person. happy?

  • Donn

    @Sandgroper:

    Absolutely, that’s one of the reasons I like this blog so much, as much potential for stupid as could be had the author and the posters are usually pretty damn good on keeping an open, level discussion.

    re: racial categories, yeah the way I phrased that wasn’t the best. I meant that it was invalid as a legitimate biological classification, not that it can’t be used for anything(whether left as race or changed to “ancestry it can certainly be used for genomic/medical/forensic anthro applications among other things.)

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #20, arguably aside from individuals no biological level of classification is clear and distinct. i’m including species. a lot of the argument gets down to semantics. i don’t particularly care if someone believes if race does, or doesn’t, exist. rather, i would challenge people on various propositions as to inter-population differences, and see which ones they assent to or dissent from. for example,

    1) can you assign an individual to a population rather easily from a few hundred markers? yes. if you select highly ancestrally informative markers you can push the number down to 10-20. this is fact.

    2) are differences between populations trivial or not? this is more contentious, and we need to ask what ‘trivial’ or not is, but i don’t think the differences between populations inferred in #1 are trivial.

  • Donn

    @Razib: Great questions and it looks like I have a lot more studying to do while thinking about those.(at least the second one s as I have nothing to contend with the first proposition) I just finished on the origin of species so got a loooong way to go

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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