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Table 2 Principal components analysis with rare and common WGS variants

From: Estimating relationships between phenotypes and subjects drawn from admixed families

 

PCA-Seq

EIGENSTRAT

 

PCs

MAF

CEU

AMR

YRI

CEU

AMR

YRI

R2 for rare variants

10

<0.01

0.18

0.16

0.33

0.17

0.15

0.33

<0.05

0.79

0.80

0.55

0.78

0.79

0.54

20

<0.01

0.42

0.42

0.43

0.42

0.42

0.42

<0.05

0.83

0.84

0.66

0.82

0.83

0.65

R2 for common variants

10

<0.01

0.95

0.95

0.13

0.95

0.95

0.17

<0.05

0.95

0.95

0.13

0.95

0.95

0.11

20

<0.01

0.97

0.97

0.22

0.97

0.97

0.41

<0.05

0.97

0.97

0.22

0.97

0.97

0.23

R2 for all variants

10

—

0.95

0.96

0.18

0.96

0.96

0.22

20

—

0.97

0.97

0.41

0.97

0.97

0.49

  1. MAF minor allele frequency, R2, the coefficient of determination from a linear regression model with 10 PCs included as predictors and the proportion of CEU, AMR, and YRI ancestry proportions from ADMIXTURE analysis as the response