Sample Handling
Recommended Use
Sample handling is used to assess the quantity and quality of study sample DNA and prepare those samples for genotyping
Requirements
In concert with the SAIC-Frederick Extraction Lab, the Core Genotyping Facility has piloted several projects using the new "Staging Laboratory" approach. While the studies to date have been limited, we have seen success such that we feel confident in beginning to utilize the new method. Below is a summary of the process we have developed into a Staging Laboratory workflow. See Staging Lab Sample Receipt Guidelines.
For exceptions where study samples have approval to be handled at the CGF, samples must arrive at the CGF according to the CGF Sample Receipt Guidelines.
Process (at CGF)
For sample handling to occur, a small portion of each sample will be used for quantification and DNA profiling to support QC processes and the genotyping requested. During initial sample handling, the sample volume and concentration will be assessed. Sample quantitation is initially determined by the NanoDrop® micro-volume spectrophotometer. All samples must contain a minimum volume of 50 µl, or such volume will be increased to 50 µl. If the sample's concentration as determined by NanoDrop® at the CGF is less than 25 ng/µl, it will be removed from sample handling and the investigator will be notified of the sample failures.
All samples whose concentration is greater than 25 ng/µl as determined by NanoDrop® will be transferred into barcoded master sample racks and normalized to 25 ng/µl. Each sample will then be assayed with the Invitrogen™ PicoGreen® assay for DNA concentration ("QDNA") and will be profiled using the Applied Biosystems (ABI) Identifiler® assay. The resulting PicoGreen® concentration measurements will be the primary measurement used for genotyping qualification and the genotypes from the ABI Identifiler® assay will be used for Pre-Genotyping QC.
Reporting
A report of samples that did not pass sample handling and cannot be included in the genotyping project will be included in the Pre-Genotyping QC report. See Pre-Genotyping QC Reporting section for details.
