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This even holds true for the imputation of samples with ancestry other than those present in the population-specific reference sets, which provides further motivation for international efforts towards large and integrated reference sets.
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Additionally, contacts in the countries for which out-of-sample imputation was undertaken suggested that the imputed values had face validity.
The OTU table was used as the input file for metagenome imputation of individual sediment samples.
It was, however, interesting to observe that the imputation of the Italian samples was improved more by this combined reference panel, leading us to speculate that populations that are poorly represented in the reference panel benefit more from a large and diverse reference set.
To maximize the quality of imputation, the samples were not prephased.
To maximize the quality of imputation, the samples were not pre-phased.
> -wrap-foot> > -wrap-foot> > -wrap-foot> > -wrap-foot> The accuracy of imputation of rs681524 in all samples but from TwinsUK could be assessed in two samples from the G-EAR consortium (Carlantino and Friuli Venezia Giulia), subsets of which had whole-genome sequencing data available in addition to the original imputation (Table 6).
We performed genotype imputation analysis for each set of samples by utilizing a Hidden Markov model as programmed in MACH version 1.0 (http://www.sph.umich.edu/csg/abecasis/mach/index.html).html
The new associations are probably due to the larger number of samples and imputation of SNPs not present on previously used genotyping arrays, using data from the 1000 Genomes project.
The nCounter® platform is of great utility to the malaria community, as it is amenable to many different types of samples, and imputation allows researchers to measure a small number of genes and gain an understanding of global expression patterns.
Additionally, to assess the effect of the reference panel sample size on imputation performance, we varied the number of samples from 300 to 848, by increments of 200, to examine the performance of imputation strategies.
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