Selected article for: "component analysis and principal component"
Author: A.J.W. Haasnoot; M.W. Schilham; S.S.M. Kamphuis; P.C.E. Hissink Muller; A. Heiligenhaus; D. Foell; R.A. Ophoff; T.R.D.J. Radstake; A.I. Den Hollander; T.H.C.M. Reinards; S. Hiddingh; N. Schalij-Delfos; E.P.A.H. Hoppenreijs; M.A.J. van Rossum; C. Wouters; R.K. Saurenmann; N. Wulffraat; R. ten Cate; J.H. de Boer; S.L. Pulit; J.J.W. Kuiper
Title: An amino acid motif in HLA-DRß1 distinguishes patients with uveitis in juvenile idiopathic arthritis
  • Document date: 2017_5_22
    • ID: 4it5c9n2_41
    Snippet: With this high-quality set of SNPs, we performed principal component analysis (PCA) using EIGENSTRAT. 75 We defined samples to be of European ancestry if their principal component (PC) 1 and PC 2 values were within 6 standard deviations of the European-ancestry populations included in the HapMap 3 dataset (the CEU population, samples of Northern and Western European ancestry living in Utah; and the TSI population, Toscans living in Italy). In add.....
    Document: With this high-quality set of SNPs, we performed principal component analysis (PCA) using EIGENSTRAT. 75 We defined samples to be of European ancestry if their principal component (PC) 1 and PC 2 values were within 6 standard deviations of the European-ancestry populations included in the HapMap 3 dataset (the CEU population, samples of Northern and Western European ancestry living in Utah; and the TSI population, Toscans living in Italy). In addition, we calculated inbreeding coefficients for all samples and removed samples further than 3 standard deviations from the distribution. Related samples (pi-hat > 0.125) were also removed. Finally, using all SNPs available on chromosome X, we performed a sex check to identify samples with mismatching genotypic and phenotypic sex; samples with mismatching genotype and phenotype information were removed from the analysis.

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