Post-Genotyping QA/QC
Overview
In an effort to make sure all laboratory processes have occurred without error, the CGF employs a Post-Genotyping QC pipeline. This pipeline includes checking investigator duplicates for concordant genotypes and also checking internal assay controls and embedded QC samples. This process also includes the generation of final data reports in various formats.
Recommended Use
All genotyping at the CGF is followed with QA/QC checks to ensure integrity of all laboratory processes.
Process
Upon conclusion of genotyping projects, results are reviewed for assay completion and duplicate check. Completion rate of assays are anticipated at 95% or better. Expected duplicates as indicated from the investigator and derived from ABI Identifiler® assay, as well as laboratory assay controls, are examined for concordance.
Once all QC checks have been made, the final report formats are generated.
Requirements
Genotyping must be complete prior to Post-Genotyping QC.
Reporting
With the completion of each genotyping project, the QC and Analysis groups at the CGF will review the genotyping data for quality assurance and issue a genotyping report. The genotyping report will consist of four files. Each file contains a distinct set of information on the genotyping project for independent analysis. Descriptions of the contents of each report file follows.
The summary.pdf file contains an overview of the project including sample and assay completion and concordance rates in a PDF format. If only one assay is in a genotyping project, the summary.pdf is replaced by a QC Report.txt file.
The locus_status.txt file contains all genetic information on the assay and loci used in the genotyping project. This file can be opened using any text file viewer or Microsoft Excel. Assay information includes CGF alias and assay ID, validation type, reporting alleles, and completion rates. The loci information includes dbSNP ID, current NT position, genomic systematic and protein systematic (if available).
The sample_status.txt file contains all sample information for the genotyping project including: Sample ID, genotyping status, and completion rates per sample. This file can be opened using any text file viewer or Microsoft Excel. Details on the assayable field can be found in the Sample Report Status document.
The validated.sdat file contains all genotype 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. This file can be opened using any text file viewer.
