Apr 10, 2015

Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Favored Allele

BioRxiv : the Preprint Server for Biology
Roy RonenVineet Bafna

Abstract

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory — for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, a...Continue Reading

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Mentioned in this Paper

Factor XII Deficiency
F12
Genome
Pathogenic Organism
Theoretical Study
Genomics
Blood group antigen D
Subclone
Simulation
Frequency of Urination (Function)

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