Efficiently calculating inbreeding on large pedigrees databases
Information Systems
Using compact encodings for path-based computations on pedigree graphs
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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We consider pedigree data structured in the form of a directed acyclic graph, and use an encoding scheme, called NodeCodes, for expediting the evaluation of queries on pedigree graph structures. Inbreeding is the quantitative measure of the genetic relationship between two individuals. The inbreeding coefficient is related to the probability that both copies of any given gene are received from the same ancestor. In this paper we discuss the evaluation of the inbreeding coefficient of a given individual using NodeCodes. We implemented and tested our approach with both synthetic and real pedigree data. Experimental results show that the use of NodeCodes provides a good alternative for queries involving the inbreeding coefficient, with significant improvements over the traditional iterative evaluation methods.