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mandag 21. november 2011

Accurate method for pinpointing autosomal ancestry?

In the earlier post I reported to have found 2 haplotype clusters seen in 6 individuals each. I here look closer at 1 of those 2 clusters to see what can be inferred from them.

The core haplotype

The haplotype identified occured in 6 individuals: 3 Finns, 2 Swedes and 1 Norwegian (no Saamis) and no one else in the population panel. The core of the haplotype is GC with the markers rs6683734 and rs4649296. These are together mutations that can only be found among Fennoscandians. However the spread is very limited only occuring in 6 of 88 haplotypes (or "3" of 44 individuals).

The extented haplotype

The haplotype can be furter extended for all with these markers: rs16858853 rs12087818 rs701177 rs16858884 rs701176 rs701173 rs11800619 rs10489806 rs7546115 rs10910120 rs1033322 rs12124323 rs17752790 rs6697791 rs12140862 rs12130755 rs6683734 rs4649296. The physical distance between the first and last is 75kb or 0.075 Mb. The individual haplotype appears to have gone trough recombination if extending the haplotype further.

The extended haplotypes founder haplotype appears to have accumulated several mutations that appears to have some local variation suggest it has a age and history in Fennoscandia seen in total. Two Finns FI11 and FI12 appears to share what appears to be the founder haplotype. FI10 have accumulated two mutations not seen in anywhere else. The SWE1 and SWE13 haplotypes appears to have separate history from the founderhaplotype seen in the two Finns. Here the SWE1 appears to be the founder while the SWE13 appears as a subfounder. The one Norwegian haplotype NO5 appears to have a history closest to the Finn haplotype.

The mutation diversity suggest a history even its widespread. The founder haplotype is seen in Finland while 4 of 6 mutations is seen in Swedes and a Norwegian. The Swedes even have a sub-node haplotype. This suggest that Sweden is the oldest location for this haplotype with Finland as runner up. It may be youngest in Norway but belong to the Scandinavian cluster in other analysis so it may be grouped with Swedes. More samples could possibly enlight the question of origin.

The ancestral haplotype

It would be of great interest to identify the true ancestral haplotype to the above described haplotype in Continental-Europe to be able to infer the "point" of entry to Fennoscandia.

I managed to extract this possible ancestral haplotypes. Two from Spain and 1 from the French Basque. As seen from these it appears like third last and last SNP mutated in Fennoscandia from AGA to GGC. The Norwegian's AGC may be due to back mutations, error or it could be transition between the third last and and last SNP. If correct this could mean the point of entry was Norway but it is inconsistent with extended haplotype having the lowest diversity but not if we group Swedes and Norwegians.

The SNP before the last tree is the common founder haplotype. I attempted to find sign of diversity for the Iberians for this part but didnt manage to detect any at first screening. The zero diversity of the Iberian group for this part compared to the Fennoscandian suggest the Fennoscandian haplotype are older. The difference is mutated positions for the third last and last SNP.

SUMMARY:  As seen from this posting trying to reconstruct a autosomal haplotype could be complex but give accurate and informative genetic history. The core haplotype appears to be simple and effective in proving Fennoscandinavian ancestry despite its tiny size, while the extended haplotype can provide clues to its age and history.

This method using core haplotypes with limited distributed mutations appears to be very accurate in pinpointing ancestry

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