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Following quality control, 958 markers were genotyped in both datasets.
Following quality control, CCR5 SNP genotypes and placental expression was available for 196 mother-infant pairs.
Following quality control analyses, the genome-wide association analysis with 331,060 SNP genotypes was conducted on 336 iron deficient cases and 343 normal controls.
Following quality control filters using thresholds defined by simulation, a total of 11321 CNV calls were made across 575 cases and 621 controls.
Following quality control filtering of the sequences we used RDP-Classifier [25] to assign taxonomic classifications to the sequences for ecological analysis.
Following quality control as outlined in the ANZgene GWAS [28], this dataset consisted of 1618 MS cases of European ancestry from Australia and New Zealand, and 3413 healthy controls of European ancestry from Australia, the UK and the US.
Following quality control checks, 846 of the 54,001markers were excluded because of low (<95%) call rate, 6511 markers were excluded because of low minor allele frequency (MAF) <0.002 and 294 markers were excluded because they were out of Hardy-Weinberg equilibrium in controls at a false discovery rate (FDR <0.2).
Following quality control was performed.
Following quality control, 70 SNPs were accepted for association analysis.
Following quality control, SNP data were analyzed by Armitage's trend test.
Following quality control processing (described below), 37 MC and 26 MBOT remained.
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