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The microarray data quality was confirmed by standard quality control methods (not shown) and the data was normalized using the RMA method.
However, it should be noted that many of our cases were not identified by standard quality control procedures or picked up by copy number variant algorithms, which look for local variations in signal intensities and allele frequencies.
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By standard quality-control procedures, SNPs with a minor allele frequency of at least 0.01, call rates of at least 0.95, and P values in Hardy-Weinberg disequilibrium tests of at least 5 × 10−7 in unrelated individuals with SNP call rates of at least 0.90 were analyzed in this study.
By applying standard quality control filters, only 480 individuals were retained for further analysis.
By applying standard quality control filters on the SNPs, 382 037 SNPs were retained for further analysis.
We next conducted more standard quality control measures by performing analyses on two distinct datasets: (1) including individuals that were genotyped at ∼1 million SNPs (1932 samples) and (2) including all 2490 samples.
All chips used in the analysis passed standard quality control metrics assessed by GenomeStudio (Illumina) as well as visual inspection for anomalies and artifacts.
We performed standard quality control measures.
All samples met the Illumina standard quality control checks.
At the time of the heparin incident, the oversulphated chondroitin sulphate could not be distinguished from heparin by the standard quality-control tests used.
Concentrations of the calibration standards, quality controls and unknowns were evaluated by Analyst software (version 1.5; B Sciex, Darmstadt, Germany).
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