Selected article for: "minor allele frequency and Supplementary table"
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_40
    Snippet: Before performing imputation, we ran sample-level and SNP-level data quality control, following standard genome-wide association quality control steps. All steps, thresholds, and number of removed samples and SNPs are summarized in Supplementary Table 7 . Briefly, we used PLINK 1.9 31 to first check sample-level missingness across all samples and removed all samples with missingness >5%. Next, for the remainder of sample-level quality control, we.....
    Document: Before performing imputation, we ran sample-level and SNP-level data quality control, following standard genome-wide association quality control steps. All steps, thresholds, and number of removed samples and SNPs are summarized in Supplementary Table 7 . Briefly, we used PLINK 1.9 31 to first check sample-level missingness across all samples and removed all samples with missingness >5%. Next, for the remainder of sample-level quality control, we reduced the dataset to only high-quality SNPs: SNPs with minor allele frequency (MAF) > 10%; SNPs outside the MHC (chromosome 6), lactase locus (chromosome 2), and the inversions on chromosomes 8 and 17; SNPs with missingness < 0.1%; and SNPs linkage disequilibrium (LD) pruned at an LD (r 2 ) threshold of 0.2.

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