An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied.
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An established quality control (QC) process was applied to samples by study (Referred to as "QC Groups") to ensure that only high-quality genotypes were retained for the analytic data set. QC metrics included completion rates by sample or locus, sample heterozygosity rate and duplicate concordance rate and standard thresholds for exclusion of data generated per array were applied. The results of 198 arrays from 153 different individuals were excluded.
boolean
C0680251 (UMLS CUI [1,1])
C0796344 (UMLS CUI [1,2])
We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release.
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We also excluded individuals and loci with discordance rates greater than 1% after merging the genotypes generated from different arrays, resulting in exclusion of 5 individuals (2 ATBC, 1 CPSII and 2 PLCO). Assays from Illumina Hap1, Omni1, Omni2.5 arrays were harmonized based on the locus meta-data of 1000 Genomes June 2010 release and HapMap 3 February 2009 release. An additional 763 loci were excluded due to incompatible alleles (either matching directly or by reverse complementing) between our data and the public reference data.
boolean
C0680251 (UMLS CUI [1,1])
C3639994 (UMLS CUI [1,2])
C0017431 (UMLS CUI [1,3])