Pre-Genotyping QA/QC
Overview
Formal QA and QC processes have been instituted in order to ensure delivery of data that meets CGF defined criteria and customer expectations. Current QA activities include SOP documentation, training program, and equipment maintenance. Current QC activities include preparation and use of sample handling and genotyping controls, trending analysis and process optimization. Data analysis QC includes review of samples prior to the start of genotyping (pre-genotyping QC) and review of genotyping results before report delivery (post-genotyping QC). Future goals of the CGF QA/QC group include institution of a more robust inventory system and institution of a deviation/CAPA program.
Recommended Use
All projects submitted to CGF will go through a data review/QC process prior to the start of genotyping. This allows the CGF QA/QC group to review sample eligibility/availability before commencing actual genotyping work. Pre-genotyping QC results in a reduction of expenses by excluding contaminated, mislabeled or uninformative samples and reduces potential for post-genotyping analysis errors. Additionally, variability is minimized by including all required study samples within a single genotyping project.
Process
At a minimum, we will review the following as part of our pre-genotyping QC process:
- Concordance of defined QC pairs or groups with ABI Identifiler™ data, ensuring that QC samples received are genetically identical before moving into the genotyping queue.
- Concordance between reported gender and the amelogenin marker.
- Presence of unexpected duplicates or redundant, nonQC samples within set.
- If applicable, study matching design (i.e. we may not genotype a single member if their partner has failed initial qualification).
- Potential effects on study power and bias due to non-random exclusion of cases or controls.
Requirements
The CGF requires the submission of phenotype information in a standardized format to eliminate the need for manual manipulation of this data. Manual edits could result in errors of inclusion/exclusion decisions and delay the pace of research. For this reason, we cannot use your data to move forward with our QC processes and genotyping work unless it is in the standardized CGF subject manifest format. Please see the CGF Phenotype Manifest for additional information. It is understood that the study information that is provided is of an extremely sensitive nature. This data will only be used by trained CGF analysts and senior management; storage of data will be in folders and databases to which laboratory staff has no access privileges.
Reporting
PI's will be contacted based on the results of this pre-genotyping QC analysis, and may review the planned exclusions prior to any genotyping actually taking place. Details on this report may be found in the PGQC Report Description document.
