A call to all brown gene nerds!

Update II: Several people have emailed me and confirmed that they finally purchased a kit. A little over $100 seems to be a good price point for what is mostly recreational genetics. Tomorrow I will post on what you’ll see in your 23andMe account, and how you have to interpret it if you are brown.

Update: Sale is operative. Limit 5 per person!

Just thought I’d pass on word, tomorrow the 23andMe genotyping service is going to have a sale. The details:

When: April 11th, 12 AM PDT to 12 PM PDT (so 3 AM EDT to 3 PM EDT)

How much: $9/month for 12 months = $108 per year for their analytic service. The kit cost, $199, is waived for the sale.

What you get: Ancestry analysis, trait assessment, and disease risk estimates. I wouldn’t put too much stock in the last in terms of bang-for-buck if you are not adopted…though the last person I explained that to ended up finding over 50% probability of macular degeneration (not a 50% increased risk, a 50% probability of developing the disease!).

For nerds the big deal is that you can get your raw genotype for 1 million markers. There are several personal genetics projects which have been started by people pooling their data. I put up a simple tutorial for those curious, and have started my own African ancestry project. But for readers of this weblog, Harappa is the way to go. Zack has over 80 participants now. Below the fold I’ve placed a tree which shows the genetic relationships in terms of ancestral quanta. I’ve underlined myself (I’m right next to my parents, as you’d expect).hap_1_80_admixture_K12_dend (1).png

14 thoughts on “A call to all brown gene nerds!

  1. Holy shit, this is fascinating… What are some interesting things that you’ve discovered by messing around with the data? Any particular observations that surprised you?

  2. also, a minor technical note.

    if you are not african 1 million markers is really enough for anything you want to do for ancestry inference and genealogical exploration. the law of diminishing returns really kicks in, and the 3 billion base pairs of the total genome will give you hardly anything more than 1 million SNPs. there is a technical issue with ascertainment bias of the markers on these genotyping chips which make me more cautious about saying this for ppl for african ancestry.

    finally, i think a whole genome sequence, and especially getting your whole family sequenced to do intra-familial comparisons, will add a lot in terms of disease/trait understanding. especially variation within the family. so if that’s your interest, hold up about 5 years to have it be totally affordable…though i guess insurance might 1) cover it, 2) and so inflate the price point.

    to recap, this is not a whole genome sequence, a string of letters of your total base pair sequence. rather, it’s your state at 1 million markers which have been found to be variant in europeans (this is the main reason that africans have some issues, they’re way diverse, and, they tend to differ a lot from eurasians).

  3. To Razib:

    I’ve recently read Cavalli-Sforza’s smaller compendium on population genetics, and his research on the Neolithic Farmer’s expansion into Europe. It appears that he was able to show that the spread of farming coincided with the spread of genetic markers quite conclusively. However, I have my deep reservations about this. I personally think that his data fit a little too well. Moreover, I believe that he stated and tried to postulate as to why the European continent has the least amount of variation. I’d appreciate it if you could share with me your ideas/opinions.

    Q1: Dr. Sforza has researched about the Neolithic Farmer’s expansion into Europe, but it’s common sense that these Fertile Crescent Farmers must have spread out in a radial fashion, even coming into Indian Subcontinent around 9,000 years ago. Has any research been done on their expansion into India and the concomitant spread of genes? It seems that he has a very Euro-centric scope to this research.

    Q2: How could Europe have the least genetic variation, when in fact, Pre-Columbian American people should, in theory, have the least theory. They’ve been here for only ~15,000 years, whereas Homo Sapien Sapien lived in Europe for about ~40,000 years ago. One thing that I read from a tabloidal source is that the Great Plague may have had a homogenizing effect on Europe.

    Any and all explanations are appreciated.

  4. re: europe having the least variation, he was constrained by the nature of his data. you are correct, the amt. of variation goes like so:

    african > south asian & mid east > europe & east asian > oceania & new world

    Has any research been done on their expansion into India and the concomitant spread of genes? It seems that he has a very Euro-centric scope to this research.

    http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2009_Nature_Reich_India.pdf

    i believe the “ANI” were middle eastern (anatolian) farmers. i am also coming to believe that “ASI” were bearers of an indigenous farming tradition of some sort.

    re: farmers & europe. i think cavalli-sforza was right, more right than he even knew, but for the wrong reason. there is a technical error in the way he interpreted PC maps. in short, they might be artifacts. but extraction of ancient DNA is giving us very strong hints that there was massive replacement of hunter-gatherers in europe by later peoples.

    btw, u might find my 10 questions for cavalli-sforza in 2006 of interest:

    http://www.gnxp.com/blog/2006/08/10-questions-for-luigi-luca-cavalli.php

  5. Waaaaah! I tried ordering the service last night, but it’s not offered in Maryland. Apparently MD (and possibly New York State too) requires a lab license for analyzing spit samples. Lame. X-(

    Thanks for the info though.

  6. Curses! I missed the sale. I really want to try this but can’t afford the full price. Stink. Keep us updated for when (if?) they have another sale. I would love to do this. (and get my fiance to too!)

  7. Keep us updated for when (if?) they have another sale.

    they have a few sales per year, so yeah, i assume they’ll do it again. though you might want to subscribe to your genetic genealogist in your RSS. she always has the “inside scoop” on impending sales (leaked purposely from 23andme).

  8. Thanks for the info Razib… I have been really enjoying all your posts lately, really interesting.

    For 23andme it looks like you cannot participate if you are in India now. That’s also too bad because my fiance and our group of friends are mainly UPites, which it sounded like it was needed for the Harappa Project. How long will that project be going on?

  9. For 23andme it looks like you cannot participate if you are in India now. That’s also too bad because my fiance and our group of friends are mainly UPites, which it sounded like it was needed for the Harappa Project. How long will that project be going on?

    ain’t the government of india awesome? also new york state and russia. the project will go on for a while until zack’s wife gets sick of it probably :-) and yes, alas UPites are WAY underrepresented still….

  10. Also, I wonder if these genetic tests can decipher when India experienced a great population explosion – if an explosion ever occurred. With genetic science, we can see that there was a population explosion in Europe around 10,000 years ago, and moreover, over 60% of their genes comes from the Middle East. I wonder if the same type of information can be found in India?

  11. . With genetic science, we can see that there was a population explosion in Europe around 10,000 years ago, and moreover, over 60% of their genes comes from the Middle East. I wonder if the same type of information can be found in India?

    yes. we can. need better population coverage. right now the indian gov. throws around a lot of red tape, though the techniques are so cheap and widespread that it is starting to not matter (1000 genomes will release a bunch of indian samples later this year to the general public).