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Browsing isolated population data

Mancosu, Gianmaria and Cosso, Massimiliano and Marras, Francesca and Cappio Borlino, Cesare and Ledda, Giuseppe and Manias, Teresa and Adamo, Mauro and Serra, Donatella and Melis, Paola and Pirastu, Mario (2005) Browsing isolated population data. BMC Bioinformatics, Vol. 6 (Suppl 4), p. 1-5. ISSN 1471-2105. Article.

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DOI: 10.1186/1471-2105-6-S4-S17

Abstract

Background. In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships. To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies. Results. The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects. Availability. PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com.

Item Type:Article
ID Code:176
Status:Published
Refereed:Yes
Uncontrolled Keywords:Isolated populations, genealogical research, PedNavigator, Sardinia
Subjects:Area 05 - Scienze biologiche > BIO/18 Genetica
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > CNR-Consiglio Nazionale delle Ricerche > Istituto di genetica delle popolazioni, Alghero
Publisher:BioMed Central
ISSN:1471-2105
Deposited On:18 Aug 2009 10:01

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