Post-Genotyping QA/QC
Overview
To ensure error-free compliance with all laboratory processes, staff at the CGR routinely review genotyping data prior to its delivery to investigators. The senior project manager examines assay and sample completion, and checks genotype concordance among embedded laboratory and study quality control (QC) samples. Assay completion rates must meet or exceed 95%. Fluidigm Biomark assays with completion rates less than 80% will be rerun automatically using the Taqman® uniplex format. Following QC review, the genotyping data is reformatted for delivery to investigators.
The delivery consists of 4 files. The summary.pdf contains an overview of the project, including sample and assay completion and concordance rates. A short QC summary is also included with the described dbSNP and genome build.
The locus_status.txt file contains all genetic information on the assay and loci used in the genotyping project. Assay information includes a CGR alias and assay ID, validation type, reporting alleles, and completion rate. The loci information includes the dbSNP ID, current NT position, genomic systematic and protein systematic (if available).
The sample_status.txt file contains the sample information for the genotyping project including: sample ID, genotyping status and completion rate per sample. Details on the assayable feild can be found in the Sample Report Status document.
Details on the assayable field can be found in the Sample Report Status document. The validated.sdat file contains all genotyping information for the project on one tabular page, with the assay ID listed across the top horizontal axis and the sample ID across the left vertical axis.
