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Relatedness within and between the six supercolonies was calculated using Relatedness 5.0.8 [26], including all individuals as reference population.
Three scenarios S40, S60 and S80 with respectively 40%, 60%, and 80% of the individuals as reference individuals were investigated.
The entire analysis of pooled samples in Dataset 2 was repeated (from GenomeStudio clustering, genotype determination and visual examination, and allele frequency estimation relative to genotype clusters) using two single subsets of 20 and 50 individuals as reference individuals.
The fact that parents were not systematically tested, and the use of a pool of six individuals as reference DNA probably explain why most CNVs identified on CGX-12 were classified as benign.
In a continuation of that study, presence of multiple ACPA reactivities and of HLA-SE showed the highest risk for RA compared with ACPA-negative/HLA-SE-negative individuals as reference [ 13].
In this case, a core set of individuals is fully sequenced, and the lower density genotypes of the remaining individuals will be imputed to whole-genome sequence genotypes using the sequenced individuals as reference [ 5- 8].
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Another approach which uses a third individual as reference when assigning a dyad to a relatedness category seems to perform better than a purely dyadic approach (Wang 2007) and could change the number of required loci for an RCA presented here.
Exome variants of these individuals served as reference variant sets in our work.
The two decision curves for the extreme strategies to treat none or all individuals serve as reference lines to judge whether a prediction model has any additional benefit.
In the scenario with HF individuals both as reference population and selection candidates, the deterministic accuracies (Equations 19 and 24) were calculated for a single HF individual using a reference population consisting of all remaining HF individuals.
The present study has also shown that all-cause mortality is significantly higher in obese insulin-resistant subjects but not obese insulin-sensitive subjects, when compared with nonobese insulin-sensitive individuals (considered as reference group).
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