Selected article for: "allele frequency and quality filter"
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_7
    Snippet: For genome-wide association testing in the Phase 1 and Phase 2 data, we kept those SNPs with a minor allele frequency (MAF) > 1% and with an imputation quality score > 0.7; >9.2M variants were available in both the Phase 1 and Phase 2 after imputation and filtering (82.6% and 77.6% of SNPs in Phase 1 and Phase 2 respectively had an info score ≥ 0.9; Supplementary Table 1) . For MHC association testing, we analyzed only those variants with MAF >.....
    Document: For genome-wide association testing in the Phase 1 and Phase 2 data, we kept those SNPs with a minor allele frequency (MAF) > 1% and with an imputation quality score > 0.7; >9.2M variants were available in both the Phase 1 and Phase 2 after imputation and filtering (82.6% and 77.6% of SNPs in Phase 1 and Phase 2 respectively had an info score ≥ 0.9; Supplementary Table 1) . For MHC association testing, we analyzed only those variants with MAF > 1%. No imputation quality filter was applied to the MHC-specific imputed data; 97.7% and 96.4% of MHC variants in Phase 1 and Phase 2, respectively, had an imputation quality score > 0.9 (Supplementary Table 1) .

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