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Our method is shown to detect ethnic outliers not identified by WTCCC application of PC-MDS (12) or by the PLINK allele-sharing Z-score (13); and we also show that our visualization of mosaicism in ethnically admixed chromosomes gives results similar to those of a fundamentally different visualization method (SABER) but with much less computational time and burden.
Pathways showing z-score above two (z-score ≥2.0) were identified.
Table 1 Exposure to limited English students and average test scores Share of limited English Share of Latino peers Math z-score Reading z-scorea Mean (Std. Dev).
To explore the biological significance of the transcriptome response shared by the two cell lines, z-score reports containing the most significant GO terms were generated from the commonly upregulated (Table 1) and downregulated (Table 2) genes.
A second approach evaluates allele sharing between pairs of genotyped subjects at all GWA SNPs and identifies ethnic outliers by very low allele sharing with most other subjects as quantified by a Z-score statistic implemented in PLINK (13).
This method calculates genome-wide identity-by-state (IBS) allele sharing between each subject and its "nearest neighbor" in the data set (the subject with whom it shares the highest proportion of alleles); and this enables derivation of a Z-score distribution in which outliers are identified by an extremely negative Z-score produced by low allele sharing with their nearest neighbor.
The group-based approach tries to generate several groups or classes that share overall patterns of changes in BMI [ 12], BMI z-score [ 13], or risk of high BMI [ 11] across childhood, using methods such as latent growth mixture modeling.
Z-score analysis was used for intergroup evaluation.
As a result, it was divided by position when converting it to a z-score.
Z-scores were calculated as z-score = (x-mean)/sd.
Analyses were subsequently adjusted for other confounders, as defined below: smoking status, total cholesterol z-score, HDL z-score, creatinine z-score and BMI z-score (model 2).
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