Browsing isolated population data

• Published in: BMC bioinformatics 2005-12, Vol.6 Suppl 4 (S4), p.S17-S17, Article S17
• Main Authors: Mancosu, Gianmaria, Cosso, Massimiliano, Marras, Francesca, Borlino, Cesare Cappio, Ledda, Giuseppe, Manias, Teresa, Adamo, Mauro, Serra, Donatella, Melis, Paola, Pirastu, Mario
• Format: Article
• Language: English
• Subjects: Algorithms; Chromosome Mapping; Computational Biology - methods; Computer Graphics; Database Management Systems; Databases, Genetic; Female; Genetic Linkage; Genetic Markers; Genetics, Population - methods; Humans; Information Storage and Retrieval; Internet; Italy; Linkage Disequilibrium; Male; Models, Genetic; Pedigree; Population; Population Groups; Programming Languages; Software; User-Computer Interface
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-6-S4-S17

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. 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. 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.