Monday, March 9, 2015

I-CTS10228 "Dinaric" samples in Estonian Biocentre Data

The Estonian Biocentre released 307 Y chromosome sequences as mentioned in Dienekes' blog.

The sequences are from all over the world and especially from places not covered in the 1000 Genomes Project, for example, Eastern Europe. You can see a summary of the samples by clicking Y_data_metainfo.xlsx which is the file at the bottom of this directory

There are 13 samples in haplogroup I: 5 samples listed as I1 (from Russia(2), Belarus, Ukraine, and from an Aboriginal Australian). There is one sample listed as I3 from the country of Georgia. There were seven samples listed as I2a, and they all belong to CTS10228 "Dinaric":

The I-P37 project obtained the sequences for the seven I2a samples and compared them to Big Y results and we are in the process of comparing them to the samples from the Hallast study.

See the YFull tree
our most recent I-L621 tree
and the STR results page of the I-P37 project

Estonian Biocenter samples #18357 & 18359 from Belarus have CTS10228>Y4460>Y3118>Y5598>CTS5779
Two kits in the I2a Project have this result, and when we compared these four I-CTS5779 sequences, we found no shared SNPs below CTS5779.

Samples #18429 from Bosnia and #20364 from Herzegovina have CTS10228>S17250*. They share some novel variants with each other that were not tested in Big Ys. There are several Big Y results in this I-S17250* group, but we found no shared SNPs below S17250.

Sample #18440 from Russia (Chuvash) has a I-CTS10228* result. There are only two known I-CTS10228* people in the I-P37 project, one is from Poland and the other belongs to the "Jewish Dinaric cluster". Sample 18440 shares two novel variants with the person in the Jewish Dinaric cluster. The positions (Chr Y: 13203040 and 9853064) are close to the centromere and it may be difficult to design primers to test these SNPs individually. We have asked a related Jewish Dinaric cluster member to test 13203040 at

Sample #21452 from Russia (Vepsas ethnic group, from north of St. Petersburg) has CTS10228>Y4460* (ie. Y3118- S8201-). A Big Y result (ancestry Riga, 1600s) shares two positions with 21452: 21835651 and 22669350. Another shared NV is at 22271330, but it is inside the 125bp repeat region.

Sample #21481 from Lithuania has CTS10228>Y4460>Y3118*  (ie. Y5598-) result. There are three Big Y results in I-Y3118* but we found no additional shared novel variants.