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Open Access Highly Accessed Research article

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification

Emiliano Giardina1*, Ilenia Pietrangeli1, Claudia Martone1, Paola Asili2, Irene Predazzi1, Patrizio Marsala2, Luciano Gabriele2, Claudio Pipolo2, Omero Ricci2, Gianluca Solla2, Luca Sineo3, Aldo Spinella2 and Giuseppe Novelli14

Author Affiliations

1 Centre of Excellence for Genomic Risk Assessment in Multifactorial and Complex Diseases, School of Medicine, Tor Vergata University of Rome, Italy

2 Direzione Centrale Anticrimine, Servizio di Polizia Scientifica, Rome, Italy

3 Dipartment of Animal Biology, University of Palermo, Italy

4 Division of Cardiovascular Medicine, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA

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BMC Genomics 2007, 8:457  doi:10.1186/1471-2164-8-457

Published: 12 December 2007

Abstract

Background

The recent advances in human genetics have recently provided new insights into phenotypic variation and genome variability. Current forensic DNA techniques involve the search for genetic similarities and differences between biological samples. Consequently the selection of ideal genomic biomarkers for human identification is crucial in order to ensure the highest stability and reproducibility of results.

Results

In the present study, we selected and validated 24 SNPs which are useful in human identification in 1,040 unrelated samples originating from three different populations (Italian, Benin Gulf and Mongolian). A Rigorous in silico selection of these markers provided a list of SNPs with very constant frequencies across the populations tested as demonstrated by the Fst values. Furthermore, these SNPs also showed a high specificity for the human genome (only 5 SNPs gave positive results when amplified in non-human DNA).

Conclusion

Comparison between in silico and in vitro analysis showed that current SNPs databases can efficiently improve and facilitate the selection of markers because most of the analyses performed (Fst, r2, heterozigosity) in more than 1,000 samples confirmed available population data.