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Posted by rmlpereira on 01 Mar 2011 at 17:02 GMT

It seems that the researchers developed a marker panel based on the criteria “allele frequency close to 0.5 in the European population” [1] and are using it for both paternity testing [2] and as “a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms” [3].

The very same panel good for kinship testing and as validated AIMs? Markers selected to have allele frequency close to 0.5 in the European population as validated AIMs?

At least from my point of view the criteria preferred for the two purposes are completely different. Definitely, markers with high degree of polymorphism in different population groups for human identification and kinship testing. Definitely, markers with high divergence between different population groups to be used as AIMs and thus assessing admixture proportions.
Publicizing the same panel for both purposes is in my opinion erroneous.

Quoting [1]: “We accessed their data base (http://research.marsh&#64...) and identified 40 polymorphisms that fulfilled the following criteria: widespread chromosomal location, increasing amplicon sizes that allow multiplex analysis, and allele frequency close to 0.5 in the European population”.

Quoting [2]: “We developed a panel of 40 multiplexed short insertion-deletion (indel) polymorphic loci with widespread chromosomal locations and allele frequencies close to 0.50 in the European population. (…)The average heterozygosity (gene diversity) per locus was 0.48…”

Quoting [3]: “Using a panel of 40 validated ancestry-informative insertion-deletion DNA polymorphisms we estimated individually the European, African and Amerindian ancestry components of 934 self-categorized White, Brown or Black Brazilians from the four most populous regions of the Country. We unraveled great ancestral diversity between and within the different regions.”

References:

[1] Bastos-Rodrigues L, Pimenta JR, Pena SD (2006) The genetic structure of human populations studied through short insertion-deletion polymorphisms. Annals of Human Genetics 70: 658-665.

[2] Pimenta JR, Pena SD (2010) Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms. Genetics and Molecular Research 9: 601-607.

[3] Pena SD, Di Pietro G, Fuchshuber-Moraes M, Genro JP, Hutz MH, et al. (2011) The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected. PLoS ONE 6: e17063.

Competing interests declared: I work in a related subject.