What quality control measures are in place at CIDR?
All genotyping will be done blind with respect to phenotype and family relationship. The key to break the code correlating CIDR’s sample IDs with those of the investigator is available only to the Center’s statistical genetics staff members. CIDR runs four CEPH controls, four blind duplicates provided by the investigator, and two blank PCR controls along with 86 experimental samples on each 96-well plate. The blind duplicate samples are assigned “dummy” CIDR IDs before being put into production. The error rate per genotype for each project is calculated from the blind duplicate samples. Potentially problematic calls identified using internal QC measures are reviewed manually. All genotyping data is binned and is checked for consistency with Mendelian inheritance patterns where pedigree structure allows. Also, the pedigree structure file is checked against relationships inferred by genome scan data.
