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June 23, 2010

PopAffiliator

Luisa Pereira from IPATIMUP and a group of contributors have developing an internet tool to  predict of an individual affiliation to a major population group, based on information from a small set of autosomal STRs. The application can found here: http://cracs.fc.up.pt/popaffiliator

To calculate the assignment of an individual to a major population group (Asia, Eurasia, sub-Saharan Africa) the values in the form bellow should be provided. The range for the allele size was restricted to the ones published in the Short Tandem Repeat DNA Internet DataBase.

The probabilities are computed using a machine learning model built as described in:
Pereira et al (2010)  PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal STR genotype profile. Int J Legal Med. DOI 10.1007/s00414-010-0472-2. (in press)


Abstract
Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on  genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Keywords: Online calculator, genotype,  profile, autosomal STRs, individual affiliation
Conclusion: So the paper concludes that …our confirmation of an 86% accuracy of individual population affiliation for the common 17 STR genotype profiles shows that this well-known forensic set of STRs has also a considerable amount of information for population assignment, besides being excellent for individual identification. We believe that our online calculator will be a valuable tool in helping forensic researchers to predict population affiliation in a specific forensic casework. However, researchers should always be aware that this information is just a first indication, which should be confirmed by other genetic and nongenetic evidence if the population affiliation is really essential to resolve a case. This is especially true for populations that result from a high miscegenation between population groups, such as populations from the Near East or America, for which, in any case, most individuals will have a real mixed ancestry.

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