Abstract
The concept of maximal perfect haplotype blocks is introduced as a simple pattern allowing to identify genomic regions that show signatures of natural selection. The model is formally defined and a simple algorithm is presented to find all perfect haplotype blocks in a set of phased chromosome sequences. Application to three whole chromosomes from the 1000 genomes project phase 3 data set shows the potential of the concept as an effective approach for quick detection of selection in large sets of thousands of genomes.
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Notes
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For convenience, we exclude multiallelic sites which may contain alleles coded as 2 or 3, or merge the minor alleles if they are rare and represent them as 1. These make up only a small fraction of the total SNPs in real data, and we therefore do not expect any overall effect.
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A genetic map required to do so is available for example as part of Browning et al. [2] at http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps.
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In the following, \(y_0\) is arbitrarily fixed at 0.00005, corresponding to \(\frac{1}{2N_e}\) with an effective population size \(N_e=10{,}000\).
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Cunha, L., Diekmann, Y., Kowada, L., Stoye, J. (2018). Identifying Maximal Perfect Haplotype Blocks. In: Alves, R. (eds) Advances in Bioinformatics and Computational Biology. BSB 2018. Lecture Notes in Computer Science(), vol 11228. Springer, Cham. https://doi.org/10.1007/978-3-030-01722-4_3
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DOI: https://doi.org/10.1007/978-3-030-01722-4_3
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