Category Archives: Miscellaneous

Catching Up on Emails

I have been busy and haven't even looked at this project in months. It's time now to dust the cobwebs.

Since I have not even read the emails I have been getting, that's where I am going to start.

If you sent me an email this summer, I'll try to reply to you in the next few days. If you don't hear from me by October 1, drop me a line.

Update: I just realized I have emails from Spring to answer as well.

No Comments

I am sick and tired of the weird comments posted by various people as well as those who feed the trolls.

I do not have the time or energy to actively monitor and moderate comments.

Therefore, there will be no comments allowed here any more.

Personal Journey

I have had myself, my wife, my daughter, my parents, and my sister genotyped by 23andme.

From time to time, I explore my personal and family data on my other blog. If you are interested, you can read about it under the Genetics category there.

My latest post is about figuring out how my inbred genome has passed on to my daughter.

Affiliate Links

As you can see, I now have affiliate links on the sidebar. If you order a test following those links, I get a small amount for referring you.

Right now, I have FTDNA and 23andme listed there.

Project Anniversary

It has been one year for the Harappa Ancestry Project. I announced it on January 17, 2011 and then moved it to its own domain on January 19.

It started out fast and furious with participants sending their data every day and I was blogging it multiple times a day. Now it has slowed down quite a bit with only one South Asian unrelated participant (not counting any Romany) in the last 2 months.

Speaking of participants, there have been a couple of complaints.

The decision to include non-South Asian participants from countries that do not neighbour the Subcontinent contradicts the Harappa Project's original inclusion criterion.

I concur with DMXX. While I'm certainly not anyone to tell Zack how to run his own show, I think the project is losing it's original focus. Accepting folks from West-Asia was also fine, given that South-Asians derive a lot of ancient ancestry from the area and thus may be deemed a secondary focus area. The same could also be said for those with partial Roma Gypsy ancestry. But, some of the runs seem to be almost entirely dominated by non-South Asian participants, who have absolutely no connection with the subcontinent. I can't help but ask on what basis these Brazilian, Belizean, Mexican, Hispanic, Somali, African-American and European participants were accepted into the project.

My approach has been to make it clear to any potential participants that my focus is on South Asia. Thus any Admixture components I have computed have been with a heavily South Asian dataset. Also, a number of PCA and clustering analyses that I do are at times limited to South Asians etc. On the other hand, I have accepted any participant who has asked to be included. I run a basic Admixture run for everyone which is a fairly automated process and sometimes include them in other analyses.

Let me illustrate with an example. I am working on a new Admixture calculator. For computing the components, I am using all the South Asian project participants in addition to reference datasets. I am going to select the data for that in such a way that we get Admixture components which gives us a better idea of South Asian genetic ancestry.

While participation in the project has slowed down, the research on South Asian genetics has picked up. We had the Metspalu et al paper and dataset. Also. 1000genomes is expected to release 400 South Asian samples (100 Lahori Punjabis, 100 Bangladeshis, 100 Sri Lankan Tamil and 100 Indian Telegu) over the summer.

My Phased Genome

I released my 23andme raw data last year. Since I had my parents also genotyped, I am now releasing my phased genome.

I haven't done anything with it yet. So if you have any ideas of what use I can put it to, chime in.

Happy New Year

Hope y'all have a great 2012! And that we see another fruitful year for personal

I have been away over the holidays driving around the country and am just getting back to try to catch up with my email. I owe several people IDs which I'll send out by tomorrow.

Another 23andme Sale

23andme is having another sale till December 31: $23 off per kit (from $99 up front). The code to take advantage of the sale price is TPHG6P.


UPDATE: Here is another link for a $23 discount for 23andme.

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.

Zack's Genome Public

I have released my 23andme version 3 genome into the public domain.

I challenge y'all to find anything interesting about my chromosome 9 (which is 93% homozygous)

Also, I got my parents' 23andme results last night.