Monthly Archives: November 2011

23andme Discount and 198

23andme has a discount just for today, according to Twitter and Facebook:

Happy Cyber Monday From 23andMe! Today only $25 Off Our Personal Genome Service®. Offer ends 12pm PST Click Here:

It says it ends at 12pm PST which is at noonmidnight PST on the US west coast. So you'll have to move fast if you want to get it.

Also, Harappa Ancestry Project is just two submissions away from 200 participants.

Computer Upgrade Delays

I upgraded my desktop last week.

The bad news is that I am having to upgrade from XP to Windows 7 which means reinstalling everything.

The good news is that Ubuntu ran perfectly after the upgrade.

And the best news is that with an Intel Core i7-2600 and 8GB of RAM, Admixture is running about 6 times faster.

Ref3 + Yunusbayev Harappa Admixture Results

The ADMIXTURE results for the Harappa participants (up to HRP0180) for the Reference 3 + Yunusbayev dataset are in a spreadsheet and can also be seen in the bar charts below.

Do take a look at K=12 and K=17 (lowest crossvalidation errors) as well as K=15.

Ref3 + Yunusbayev Caucasus Data Admixture

To my standard reference 3 (list of populations), I added the Yunusbayev et al Caucasus samples which include the following:

  • 20 abhkasians
  • 16 armenians
  • 19 balkars
  • 13 bulgarians
  • 20 chechens
  • 14 kumyks
  • 6 kurds
  • 15 mordovians
  • 16 nogais
  • 15 north-ossetians
  • 15 tajiks
  • 15 turkmens
  • 20 ukranians

These 204 samples increased the total to 4,090.

Then I applied a stricter IBD relationship cutoff than I have before. Previously my focus was on removing relatives, but now I wanted to remove samples that seemed highly inbred or belonged to highly bottle-necked small groups so they would not create their own clusters in Admixture. This process removed the following 164 samples:

  • maasai 30
  • papuan 15
  • karitiana 12
  • pima 12
  • onge 8
  • surui 7
  • luhya 6
  • melanesian 6
  • colombian 5
  • hadza 5
  • koryaks 5
  • sandawe 5
  • san 4
  • turkmens 4
  • african-americans 3
  • east-greenlanders 3
  • great-andamanese 3
  • nganassans 3
  • chenchu 2
  • evenkis 2
  • han-chinese-south 2
  • maya 2
  • mbutipygmy 2
  • mexicans 2
  • utahn-whites 2
  • aus 1
  • bantukenya 1
  • british 1
  • chinese-americans 1
  • gujaratis-b 1
  • iranians 1
  • naxi 1
  • north-kannadi 1
  • samaritians 1
  • she 1
  • tuvinians 1
  • yemenese 1
  • yoruba 1
  • yukaghirs 1

Finally, I added the 165 founders from the Harappa Project participants (up to HRP0180).

The crossvalidation error for the admixture results with K (number of ancestral components) from 2 to 20 is plotted here.

Zooming in,

The lowest crossvalidation errors are for K=17 and K=12.

The admixture results are in a spreadsheet.

In addition to K=17 and K=12, take a look at the results for K=15.

PS. I should point out that the names for the ancestral components are just useful mnemonics based on the current distribution of that component. Also, a component with the same name at one value of K is different from a similarly named component at another K.

Admixture (Ref3 K=11) HRP0181-HRP0190

Here are the admixture results using Reference 3 for Harappa participants HRP0181 to HRP0190.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

HRP0181 is half-Punjabi Jatt and half-English and the admixture results are not too different from the average of the reference British and our other Punjabi Jatt participants.

HRP0183, a Khatri, has fairly high European component, less than the Jatts but higher than most other South Asians.

HRP0186 is the most West Asian (and thus least European) of all our Georgian participants.

HRP0188,a Haryana Jatt, has the highest European component (29%) of all South Asians I think. I am surprised at the results for the two Haryana Jatts. I would not have expected their results to be much different from the Punjabi Jatts. If anything, I thought the Haryanavis would be less European than the Punjabis. Now I want to get a few non-Jatt Haryanavi participants. Anybody know someone?