Wednesday, February 25, 2015

Hunter gatherers or farmers

Using the raw data from 23andme and uploading it to Gedmatch you can determine whether you're ancestors from the New Stone Age were hunter gatherers or farmers.

Below is the composition of my genome for each chromosome from Gedmatch.

12000 years ago my Neolithic ancestors were mainly Baltic hunter gatherers, then Mediterranean farmers and Anatolian farmers. This is the composition of my genome they left.

Tuesday, February 24, 2015

Disease risk from Prometheus/23andme

If you download raw data from 23andme and upload the data to Prometheus (5 dollars cost) you can get a report on your disease risks that is based on the collection of SNPs in SNPedia.

Here are some of my results that I found interesting:


In total I have 292 'bad' SNPs, 3636 'good' SNPs and 14516 'neutral' ones. 292 SNPs are thus associated with some phenotype that is considered 'bad', but I have 3636 good SNPs that are beneficial.





I have 17 SNPs that are associated with heart disease and 17 protective SNPs for heart disease so I guess it is a photo finish there. And considering that I have family and relatives that suffered a heart attack this finding is not surprising.





I have AA genotype on rs1667394 that is associated with blond hair and blond eyes. Not very surprising when looking at my photo as a child bellow (with my mom).





I have T allele at rs2180439 and increased risk of baldness, which will obliterate my beautiful blond hair.



I have increased memory performance and higher IQ, obvious.







I have increased proneness to anger,  ##*!!!!*#*!#*!*`';!~":!@



I have increased risk of sexual dysfunction when takes antidepressants, and increased risk for depression which in combination is not a very good outcome.







Monday, February 9, 2015

First glimpse on my 23andme analysis

So these are my results from 23andme genome analysis service named Ancestry Composition. The majority (77.2%) of my genomic variants are specific for the Balkan region (as expected since I am from Serbia).





Additional 7.7% of the variants are Broadly Southern European, 6.6% are Broadly European.

6.8% are Eastern European variants that reflect the migration of Slavs to the Balkan peninsula in the 6th century.

1.2% are Northern European variants that could be remnants of the ancient Celtic settlements of Southeastern Europe.

0.4% are Italian variants that most probably represent a local migration between Italy and Balkans few hundred year ago.

Even though Serbia was part of the Ottoman empire for several centuries. there was no mixing with Turkish variants, I have 0.0% of Middle Eastern variants, which includes Turkey.

In total, I contain 99.9% European variants.

0.1% of East Asian variants could represent either 40000 year old variants that reside before the time of separation of European and Asian population, or could represent variants that were left behind the Mongol invasion of Europe in the 13th century that also encompassed Balkan regions.






I have estimated 2.7% of Neanderthal DNA.



Tracing back my maternal and paternal haplotypes to 40000 years old maternal ancestral haplotype and 23000 years old paternal ancestral haplotype.

My maternal haplotype is H, which is over 40000 years old, that originated in the Near East and then expanded after the peak of the Ice Age into Europe, where it is the most prevalent haplogroup today. Some of the famous people with haplotype H: Luke the Evangelist, Marie Antoinette, Napoleon Bonaparte, Prince Philip, Susan Sarandon.



My paternal haplotype is E1b1b1a which arose over 23000 year ago in in eastern Africa and spread into the Mediterranean region after the Ice Age, 8000 years ago from Near East. Today it is one of the most common haplogroups in Southern Europe.


Tuesday, February 3, 2015

Finding files in Unix

Command find is quite useful for finding the right file you want in Unix.

For example I remember I had a file with chromosome sizes of the human genome but I couldn't remember where, so I tried to search for it with regular expression *hg*size* and find command:

find . -name *hg*size*
./Sazonova et al/COOCCUR/hg19_chromsizes.tab

And I found the subfolder where the file was placed.