March 04, 2009

Geographical affinities of HapMap samples

PLoS ONE doi:10.1371/journal.pone.0004684

Geographical Affinities of the HapMap Samples

Miao He et al.

Abstract

Background

The HapMap samples were collected for medical-genetic studies, but are also widely used in population-genetic and evolutionary investigations. Yet the ascertainment of the samples differs from most population-genetic studies which collect individuals who live in the same local region as their ancestors. What effects could this non-standard ascertainment have on the interpretation of HapMap results?

Methodology/Principal Findings

We compared the HapMap samples with more conventionally-ascertained samples used in population- and forensic-genetic studies, including the HGDP-CEPH panel, making use of published genome-wide autosomal SNP data and Y-STR haplotypes, as well as producing new Y-STR data. We found that the HapMap samples were representative of their broad geographical regions of ancestry according to all tests applied. The YRI and JPT were indistinguishable from independent samples of Yoruba and Japanese in all ways investigated. However, both the CHB and the CEU were distinguishable from all other HGDP-CEPH populations with autosomal markers, and both showed Y-STR similarities to unusually large numbers of populations, perhaps reflecting their admixed origins.

Conclusions/Significance

The CHB and JPT are readily distinguished from one another with both autosomal and Y-chromosomal markers, and results obtained after combining them into a single sample should be interpreted with caution. The CEU are better described as being of Western European ancestry than of Northern European ancestry as often reported. Both the CHB and CEU show subtle but detectable signs of admixture. Thus the YRI and JPT samples are well-suited to standard population-genetic studies, but the CHB and CEU less so.

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7 comments:

South Central Haplo said...

Japanese and Cambodians together
that is surprising

Polak said...

>>Japanese and Cambodians together
that is surprising

Not surprising, because they're not together.

South Central Haplo said...

good eye.

antoine1706 said...

What is striking is the significant level of middle eastern acestry among the 3 Italians populations which seems to be around 10%

antoine1706 said...

..and also the central asian and middle eastern ancestry for a total of about 10% among the French !

Maju said...

Have you checked the bidimensional graphs at figure 2? That is surprising!, especially if compared with previous studies that appeared to show geographic patterns.

Take for instance graph C (European populations). You see some curious tight clusters:
· Barcelona-London-Zaragoza-Emilia-Romagna
· N. Norway-Valencia-Limburg
· Caceres-Strasbourg
· Netherlands-Asturias
· Sweden-Umbria
· Ljubliana-Moscow
· Lausanne-S. Ireland

Overall the whole geographic structure looks totally (or at least largely) messed, with Athens and Turkey clustering with Stuttgart and Central Norway, and Finland with Portugal). CEU nevertheless does appear to be intermediate between London and Denmark, as expected (though Madeira and Asturias are closer matches).

Apart of that again some frustration at finding that the French sample only includes Parisians. Please, France is the largest state of Europe after Russia and has a very diverse regional structure if we are to judge from history!

sardiniankid said...

we sardinians seem to have the highest middle eastern dna in this sample? i wonder what it woud look if they samples some greeks and other southern italians?