Selected article for: "european ancestry and reference panel"
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_48
    Snippet: Following the prephasing, we imputed all samples using the imputation reference panel constructed through whole-genome sequencing of 2,504 samples in 1000 Genomes Project (Phase 3). 28 Briefly, the 1000 Genomes Project Phase 3 data is comprised of samples collected from the Americas, Africa, East Asia, Europe and South Asia. Samples were wholegenome sequenced at ~80x coverage across the exome and at ~4x coverage in non-exome regions. We imputed t.....
    Document: Following the prephasing, we imputed all samples using the imputation reference panel constructed through whole-genome sequencing of 2,504 samples in 1000 Genomes Project (Phase 3). 28 Briefly, the 1000 Genomes Project Phase 3 data is comprised of samples collected from the Americas, Africa, East Asia, Europe and South Asia. Samples were wholegenome sequenced at ~80x coverage across the exome and at ~4x coverage in non-exome regions. We imputed the prephased haplotypes using IMPUTE2 24, 76 ; the data were phased in windows 5 megabases long, with a buffer region of 250kb. We set the effective sample size (Ne) to 20,000, per IMPUTE2 recommendations, and set k_hap to 1,000, as our sample was of European ancestry and the 1000 Genomes Phase 3 imputation reference panel contains ~1,000 haplotypes from European-ancestry individuals.

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