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From: Anders Pålsen <>
Subject: Re: [DNA] OmniPop caution received from FamilyTreeDNA
Date: Wed, 14 Mar 2007 18:49:53 +0100 (CET)


I noticed earlier this abstract refered to at Dienekes Anthrpology Blog regarding use of FTDNA's autosomal panel 1 using STRUCTURE 4.1 software to assign individuals to population groups, do STRUCTURE software and OMNIPOP offer different ways to assign individuals to population groups?

"Use of Forensic Markers in the Assessment of Population Stratification Population Stratification.

Assignment of individuals to population groups is important to genetic case control association studies, admixture mapping, medical risk assessment, genealogy, and forensic studies. Polymorphic sequences can be used to infer ancestry but their utility for such an application is related to the number of alleles and relative frequency differences of these alleles between the population groups under study. Multiple study designs differing in numbers and types of polymorphic markers with differing levels of informativeness make comparison of studies difficult. The use of commercially-available highly-informative markers that are used internationally in forensic applications could provide a universal first tier analysis for assignment of individuals to population groups prior to inclusion in association and admixture studies. We evaluated the utility of the PowerPlex kit of 16 markers from Promega for this purpose. Multiple population groups including African, Bengalis,
Chinese, Japanese, Koreans, Crypto Jews, Sephardic Jews, and Dutch were genotyped using the PowerPlex kit. The data were analyzed with STRUCTURE (Pritchard et al.) using an admixture model, correlated alleles and 3 clusters. Africans, Asians (Bengalis, Koreans, Chinese and Japanese), and Caucasians (Dutch, Sephardic Jews, and Crypto Jews) were clearly delineated. Individuals showing admixture were detectable and their removal resulted in more discrete clustering. An independently collected and genotyped set of Dutch individuals was indistinguishable from the original Dutch group providing reproducibility across data sets. The sensitivity conferred by the number of markers used in the analysis was assessed by removing markers. Delineation of population groups was apparent when 14 markers were used, although clusters were noisier; however it was not possible to delineate population groups when only 8 markers were used. The use of forensic markers is a promising strategy for
clustering individuals into population groups and will be an inevitable outcome of their forensic use. "

Source: http://dienekes.blogspot.com/2006/11/ashg-2006-abstracts.html

TJ




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