As part of the Cancer Genomics Research Laboratory, the DNA Extraction and Staging Laboratory (DESL) located in Frederick, MD, is responsible for the preparation of samples for investigators at NCI's Division of Cancer Epidemiology and Genetics (DCEG). This laboratory extracts DNA when needed and performs a series of quality checks to stage samples at a standard concentration for automated plate creation. The assigned Project Manager and the Quality Control group work with investigators to ensure that the appropriate subjects meet quality control criteria for genotyping. Plates are then shipped to the CGR and other outside collaborators in a run-ready state, ready to enter any assay platform requested. In this way, the assay laboratory receives only the amount of material that is needed to complete the genotyping or sequencing project in a pre-plated fashion specifically designed for the platform to be used. This allows the project to begin quickly without additional sample handling, reduces the actual amounts of DNA consumed, and eliminates the need for storage of leftover DNA.
Any samples requested for downstream assays at the CGR or at collaborating institutions are extracted, quantified, fingerprinted and staged at a standard concentration. Automated plating of staged samples can occur rapidly upon request.
Incoming specimens must be accompanied by a manifest for sample acquisition into the Laboratory Information Management System (LIMS). For ease of handling in DESL's highly automated pipeline, specific vials are required for pre-extracted DNA. Should samples be arriving from outside of NCI's repositories, DESL will furnish Sample Kits with pre-barcoded tubes such that samples can immediately enter the queue without the need for error-prone sample transfers.
Following extraction (if necessary), samples enter the sample handling pipeline, during which a small portion of each sample will be used for quantifying and profiling the DNA to support QC processes and the requested genotyping. Each sample will be subjected to a volume measurement and an initial quantification via OD. As needed, samples will be normalized to fall within the standard curve and detection range of a fluorescent-based assay for dsDNA concentration and will be staged at a standard concentration in 96-well robotic racks for automated storage in the REMP Small Size Store (SSS). Once in the SSS, samples are profiled via a DNA fingerprinting assay. The resulting dsDNA concentration measurements will be the primary measurement used for genotyping and sequencing qualification along with the profiling genotypes.
A report of samples that did not pass sample handling, and therefore cannot be included in the genotyping project, will be summarized in the Pre-Genotyping QC Report. See Pre-Genotyping QC Reporting section for details..