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Genotype concordance checks were performed to verify sibling status and eliminate duplicate samples, monozygotic twins, and unrelated subjects.
Though the possibility of clinician misdiagnosis exists, extensive quality control measures were taken to guard against it, including concordance checks by multiple graders.
The backend database has been built on Microsoft SQL Server 2014, with custom SQL algorithms to provide, for example, live concordance checks between reviewers' double coding.
As an additional quality control check of internally imputation genotypes we performed genotype concordance checks with the Illumina HumanHap550 GWAS chip.
However, duplication and quality control concordance checks could help to minimise this risk and automation would reduce technical variations between assay plates.
We further recommend, if cost allows, to duplicate samples (which is easily performed in a multiplexed experiment) and validate computed SNPs by inter-sample concordance checks between these technical replicates.
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Similarly, Mendelian-inheritance error checking of the custoMendelian-inheritance error errors, checking with 2.38% human errofs identheied by concordance checking.
Concordance checking identifies only human errors, whereas Mendelian-inheritance error checking is capable of detection of additional errors, such as Mendelian-inheritance error
Inheritance checking of the commercial marker data identified that the results contained 0.13% human errors and 0.12% other errors (0.25% total error), whereas concordance checking found 0.16% human errors.
These data suggest that Mendelian-inheritance error checking is a worthwhile strategy for both types of genotyping data, whereas fine-Mendelian-inheritance errore from checkingnce checkisg than do studies using commercial marker data.
After pair-wise concordance check and further visual inspection, the genotype datasets from different arrays were merged.
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