Efficient computation of the kinship coefficients
| Autor: | Brent Kirkpatrick, Shufei Ge, Liangliang Wang |
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| Rok vydání: | 2018 |
| Předmět: |
Statistics and Probability
Source code media_common.quotation_subject Pedigree chart Breeding Biochemistry Set (abstract data type) 03 medical and health sciences Statistics Kinship Animals Inbreeding Molecular Biology 030304 developmental biology media_common Mathematics 0303 health sciences Genetic diversity Models Genetic 030302 biochemistry & molecular biology Approximation algorithm social sciences humanities Pedigree Computer Science Applications Computational Mathematics Exact algorithm Computational Theory and Mathematics Algorithms Software |
| Zdroj: | Bioinformatics. 35:1002-1008 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/bty725 |
| Popis: | Motivation For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations. Historically, computations of the inbreeding coefficient were used to prohibit inbred marriages and prohibit breeding of some pairs of pedigree animals. Such prohibitions foster genetic diversity and help prevent recessive Mendelian disease at a population level. Results This paper gives the fastest known algorithms for computing the kinship coefficient of a set of individuals with a known pedigree, especially for large pedigrees. These algorithms outperform existing methods. In addition, the algorithms given here consider the possibility that the founders of the known pedigree may themselves be inbred and compute the appropriate inbreeding-adjusted kinship coefficients, which has not been addressed in literature. The exact kinship algorithm has running-time O(n2) for an n-individual pedigree. The recursive-cut exact kinship algorithm has running time O(s2m) where s is the number of individuals in the largest segment of the pedigree and m is the number of cuts. The approximate algorithm has running-time O(nd) for an n-individual pedigree on which to estimate the kinship coefficients of n individuals of interest from n founder kinship coefficients and d is the number of samples. Availability and implementation The above polynomial-time exact algorithm and the linear-time approximation algorithms are implemented as PedKin in C++ and are available under the GNU GPL v2.0 open source license. The PedKin source code is available at: http://www.intrepidnetcomputing.com/research/code/. |
| Databáze: | OpenAIRE |
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