Many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3. Evidence for selective sweeps is also found in In Chromosome 2, the most extreme signal is found in the lactase gene, which previously has been shown to be undergoing positive selection. Project and to Chromosome 2 data from the HapMap project. We considered different values of the scaled selection intensity and the time since the fixation of the positively selected allele. To illustrate the method, we apply our approach to data from the Seattle SNP We performed computer simulations to assess the ability of the various HMM methods to detect a selective sweep ( Tables 13 ). Our new test also provides estimates of the location of the selective sweep(s)Īnd the magnitude of the selection coefficient. Rates and demography (i.e., has low Type I error). XP-CLR is a site frequency spectrum (SFS)-based method that detects selective sweeps by jointly modeling the multi-locus allele frequency differentiation. Likelihood, has a high power to detect selective sweeps and is surprisingly robust to assumptions regarding recombination Using extensive simulations, we show that a new parametric test, based on composite Here, we present several new tests aimed at detecting Such a process leaves traces in genomes that can be detected in a future time point. Rates, and provide no method for correcting for ascertainment biases. The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps. Methods for detecting selective sweeps have little or no robustness to the demographic assumptions and varying recombination Detecting selective sweeps from genomic SNP data is complicated by the intricate ascertainment schemes used to discover SNPs,Īnd by the confounding influence of the underlying complex demographics and varying mutation and recombination rates.
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