Author Archives: Zack - Page 11

Zack's Genome Public

Posted by on July 27, 2011 2 comments

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).ragrani.ru

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

Harappa Participants Haplogroups

Posted by on July 22, 2011 35 comments

All the ancestry analysis here has been based on the autosomal genome (i.e., the SNPs on chromosomes 1-22) and not on the sex chromosomes X and Y or the mitochondrial DNA. The reason is basically that the autosome provides information about your overall ancestry.

Since the Y chromosome is inherited only from father to son, it is useful for finding out about your paternal line. Similarly, mitochondrial DNA is inherited from mother to child, so that's good for information on the maternal line. Note however that the paternal and maternal lines are not the sum total of your ancestry. In fact, it is quite possible to have very different mtDNA or Y-DNA ancestry compared to your whole genome.

Anyway, many people are interested in paternal (Y-DNA) haplogroups and maternal (mtDNA) haplogroups. AV requested information on the haplogroups of Harappa Project participants and SB created a spreadsheet where project participants can enter their paternal and maternal haplogroups. I am also pulling that information into my Harappa Participants Ethnicity spreadsheet.

If you tested with 23andme, here are the links to their maternal and paternal haplogroup pages.

Now go ahead and enter your information in the haplogroups spreadsheet.

You might also want to take a look at the Harappa Participants Map.

UPDATE: Please be considerate of others' privacy. Only disclose someone else's information (haplogroups, location, or anything else) if you have explicit permission to do so. Thanks!

Admixture (Ref3 K=11) HRP0141-HRP0150

Posted by on July 18, 2011 43 comments

Here are the admixture results using Reference 3 for Harappa participants HRP0141 to HRP0150.

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.

150 and 100

Posted by on July 14, 2011 11 comments

The total number of participants has gotten to 150. The Harappa Ancestry Project has been active for a little less than 6 months.sports74.ru

Of these, depending on how you count, we are at about 100 unrelated South Asians.infolio-rg.ru

Sorry for my absence from the comment section and the slow pace of posting. There's a lot of backlog of work and home errands that accumulated during my vacation.

Admixture (Ref3 K=11) HRP0131-HRP0140

Posted by on July 8, 2011 75 comments

Here are the admixture results using Reference 3 for Harappa participants HRP0131 to HRP0140.

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.

Admixture (Ref3 K=11) HRP0121-HRP0130

Posted by on July 7, 2011 8 comments

Here are the admixture results using Reference 3 for Harappa participants HRP0121 to HRP0130.

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.

Back

Posted by on July 5, 2011 5 comments

I got back yesterday. Due to jetlag and things that accumulated during my absence, it'll take me a few days to get back to regular posting here.ir-leasing.ru

I got about 12 data submissions during my vacation. I'll send everyone their Harappa IDs by tomorrow. If you haven't received an ID from me by Thursday morning, drop me an email to remind me.rpk-tramplin.ru

I have 2 batches of ten to process for Admixture results. I hope to post those by the end of the week but can't make any promises.

If you sent me an email in the last month that required a response, I will try to reply soon. If you haven't heard from me by July 11, please remind me.

Thanks, Razib, for your guest blogging.

Links

Posted by on June 13, 2011 3 comments

According to Cece Moore of Your Genetic Genealogist, there are 3,400 customers of 23andme who identify as South Asian. Now if 10-20% of them would participate in Harappa Ancestry Project!

Also, Konrad Karczewski and others have created a very interesting personal genome analysis website, Interpretome.

Vacation

Posted by on June 7, 2011 2 comments

I am going on vacation. Unfortunately, the rush of work before a vacation means that I haven't been able to finish the analysis of ASI (Ancestral South Indian) that I wanted to present before going.

Since the only computer I am taking with me is my daughter's netbook, I don't expect to work much on the Harappa Ancestry Project during that time.

I will have Internet access, so I might write some. However, there will not be any new analyses of participants. Also, I am more likely to post a travelogue on my regular blog.

In the meantime, I have Razib lined up as guest blogger here. Hopefully, you guys will have some good discussions.

I encourage people to keep sending me their 23andme or FTDNA data which I'll analyze as soon as I am back.

I expect to be back working on the project at the start of July.

Reference 3 + HAP PCA

Posted by on June 5, 2011 3 comments

I had run PCA on the Reference 3 dataset before. Now I included Harappa participants in it as well.

Here's the dendrogram based on the Euclidean distance between Harappa participants in their PCA results.

Since no one liked the IBS nearest neighbors lists, I thought making a spreadsheet with every participants' closest 100 neighbors in PCA space might be more fruitful.

Note that for the Harappa participants, the median distance to their nearest neighbor is 0.2064. So if your nearest neighbor is more than let's say 0.3 away, then you are not close to anyone.