Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)

TitleHistorical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
Publication TypeJournal Article
Year of Publication2014
AuthorsShem-Tov, D., & Halperin E.
Published inPLoS Computational Biology
Volume10
Issue6
Other Numbers3797
Abstract

Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited accuracy and assume unrealistic assumptions of monogamy and synchronized generations. In order to address these issues, we develop a new method for pedigree reconstruction, PREPARE, which is based on formulations of the pedigree reconstruction problem as variants of graph coloring. The new formulation allows us to consider features that were overlooked by previous methods, resulting in a reconstruction of up to 5 generations back in time, with an order of magnitude improvement of false-negatives rates over the state of the art, while keeping a lower level of false positive rates. We demonstrate the accuracy of PREPARE compared to previous approaches using simulation studies over a range of population sizes, including inbred and outbred populations, monogamous and polygamous mating patterns, as well as synchronous and asynchronous mating.

Bibliographic Notes

PLoS Computational Biology, Vol. 10, No. 6, e1003610

Abbreviated Authors

D. Shem-Tov and E. Halperin

ICSI Research Group

Research Initiatives

ICSI Publication Type

Article in journal or magazine