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Monday, November 14, 2011

7 months of MDLP project: alpha phase is over

We would like to announce that the project has been active for more than 6 months, i.e fairly long to accomplish some of the posited goals. The main goal of the project's preliminary (alpha) phase was to collect a statistically reliable sample for obtaining the statistically significant results. The current dataset (MDLP v2) includes 531 unrelated individuals (379 males, 152 females) with 310652 SNPs, of those 183 individuals (48 Romanians, 2 Russians,17 Chuvashes,12 Uzbeks,16 Turks,18 Armenians,15 Lezgins,20 Georgians,19 Hungarians,8 Lithuanians,8 Belorussians) from Behar et all (2010) dataset.41 individuals from HGDP (25 Russians, 16 Adygei), 175 individuals from the 1000 Genomes Project (83 British, 92 Finns) and 62 individuals from Yunusbayev et all. (2011) paper (14 Mordovians, 16 Nogays,13 Bulgarians,19 Ukrainians).

 The ethnic distribution of the whole set would look as follows (ethnic groups in red need more participants/samples )


Belarussian 18
Adygei 16
Armenians 18
Aszkenazi 2
Bulgarians 13
Chuvashs 17
Finns 92
British 83
Georgians 20
Hungarian 20
Latvian 1
Lezgins 15
Lithuanians 27
Mordovians 14
Nogays 16
Ossetians 14
Norwegians 2
East Germans 7
Others  8
Poles 18
Romanians 14
Russians 36
Swedish 2
Turks 16
Ukrainians 30
Uzbeks 12

Another interesting characteristics of sample is that one of average inbreeding coefficient in each particular population,  based on the observed versus expected number of homozygous genotypes in given population.


FID F-coefficient
Lithuanian-average 0.0158738
Finn-average 0.01375742
GBR_Orkney-average 0.013074288
Lezgin-average 0.012808472
Belorussian-average 0.011024444
GBR_Cornwall-average 0.010527961
GBR_Kent-average 0.009641047
Georgian-average 0.00949285
Turk-average 0.0093435
Hungarian-average 0.007138795
Adygei-average 0.006826329
Romanian-average 0.006763092
Russian-average 0.006179208
Uzbek-average 0.005255747
Armenian-average 0.004329326
Chuvash-average 0.004147971



The following characteristic of  MDLP - an average number of shared IBD segments per population is especially valuable for evaluating the genomic structure of population. I've limited the results to Slavic populations only.



Poles 0.878788
Belarusians 0.722008
Ukrainaians 0.676113
Russians 0.561878
Lithuanians 0.548961


 

1 comment:

  1. I would like to ask something: I made the Admixture Proportions test, and i have about 15% caucasian. What does it mean? What are the caucasian genes (haplogroups?)? Thank you...

    ReplyDelete