Tag Archives: genome

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.

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.

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).ragrani.ru

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


Human Genome Diversity Project (HGDP) is the best resource for a diverse set of genomic data. It has 1050 individuals from 52 different populations.

I got the Stanford University data which has data for 660,918 SNPs from 1,043 samples. It is claimed that the forward strand is given but that turned out not to be true and I had to flip strands and make sure I didn't include any ambiguous A/T or C/G strands in my dataset.

I followed the recommendations of Rosenberg (spreadsheet) in excluding some atypical samples and relatives, leaving me with 940 samples.

I also excluded the Native American samples because we are not interested in them and they are very closely related either due to recent endogamy or ancient bottlenecks. (yeah I had the nerve to write that.)

Of the total of 876 samples, here are the numbers for our populations of interest:

Balochi 24
Brahui 25
Burusho 25
Hazara 22
Kalash 23
Makrani 25
Pathan 22
Sindhi 24
Total South Asians 190

These samples have about 541,560 SNPs in common with 23andme v2.


I am using several datasets in the public domain for my reference population samples. HapMap is one of those datasets.

According to its website,

The goal of the International HapMap Project is to develop a haplotype map of the human genome, the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors. The information produced by the Project will be made freely available.

In the first phase, it genotyped

30 Yoruba adult-and-both-parents trios from Ibadan, Nigeria, 30 trios of U.S. (Utah) residents of northern and western European ancestry, 44 unrelated individuals from Tokyo, Japan and 45 unrelated Han Chinese individuals from Beijing, China.

In their HapMap phase 3 release #3 (NCBI build 36, dbSNP b126), there are 1,397 samples with about 1,457,897 SNPs each.

I removed related individuals as well as individuals whose genomes were too similar. This left me with a total of 1,149 samples with about 474,606 SNPs in common with 23andme's version 2 data.

Since we are not interested in Native American ancestry, I also removed 58 Mexican samples, thus leaving me with 1,091 samples.

Here are the samples I am using from the HapMap data:

Ethnicity Region Count
African Americans Africa 48
European Americans (Utahns) Europe 111
Han Chinese East Asia 137
US Chinese East Asia 106
Gujaratis South Asia 98
Japanese East Asia 113
Kenyan Luhya East Africa 101
Maasai East Africa 135
Tuscans Europe 102
Yoruba West Africa 140

The region assignments are mine to aid me in the analysis, by including/excluding samples by region or by aggregating results by region to find patterns etc.

It was easiest to use the HapMap data since it's available for download in Plink format.

Participants So Far

While I am analyzing the data, checking for errors and making sure the results I am getting are valid, here is some information about participants till now.

So far I have got 11 participants send me their raw data. Of these eleven, ten have some South Asian ancestry.

The regions/ethnicities they cover are:

  • Punjab
  • Bengal
  • Bihar
  • Tamil Nadu
  • Telegu
  • Anglo-Indian

Of these, Punjabis are the only ones I have multiple samples of. So I definitely need more samples of the other ethnicities. And there are lots of ethnicities/regions I haven't gotten any participants in.

It would be great for this project if we got a few participants from each state/province of India and Pakistan. So if you know someone who is from our target regions and has tested with 23andme, please spread the word.

If you tested with 23andme during their Christmas sale, I am hearing that results are going to start coming in starting today.