Biospecimen Processing

Photograph showing test tubes with droppers

Services provided by the Biospecimen Accessioning and Processing (BAP) Core start with a consultation. Trained staff members are available to meet with the study team to consult on study-specific services. The consultation can include specimen collection, aliquoting strategy and storage, and sample requirements for downstream analysis.

Customer support

The core's customer support team works with study staff during the study build process to ensure that the study flows smoothly and that the appropriate services are performed to meet the study's goals. Having comprehensive and accurate information about the study requirements before the start ensures that the study is built quickly and efficiently.

Services include:

  • Assessing the study requirements for sample processing to determine if the BAP Core can meet study needs.
  • Coordinating the lab manual with core workflows to ensure the appropriate services are applied.
  • Coordinating clinical lab testing on research samples.

Sample accessioning

Specimens accessioned in the core laboratory are tracked with the Research Laboratory Information Management System (RLIMS), so each specimen is associated with patient data. This accessioning serves as a front door for routing of specimens for downstream services. This includes core laboratories focused on gene expression, genotyping, next-generation sequencing, proteomics and cytogenetics.

Sample processing

Blood and bodily fluids can be centrifuged and fractionated manually or by automation. Reagents can be added to the resulting fractions, which are then typically stored frozen.

Nucleic acid extraction

  • DNA purification: DNA can be purified from fresh or frozen whole blood, white blood cells, frozen tissue, paraffin-embedded tissue, cultured cells, buccal cells, and saliva collected in an Oragene kit. Cell-free DNA extraction from plasma is also available. Total and double-stranded DNA is quantified using a spectrophotometer. The concentration and volume are tracked in the RLIMS.
  • RNA purification: RNA can be purified from whole blood collected in a PAXgene Vacutainer and from frozen tissue, paraffin-embedded tissue and cultured cells. The RNA is quantified using a spectrophotometer, with the quality determined using a Bioanalyzer. The concentration, volume and RNA integrity number are tracked in the RLIMS.

Plating and sample transfer

The BAP Core provides project-based plating services depending on the number of samples in the request and the type of container the samples are aliquoted into. Projects must be submitted to the core's nucleic acid extraction plating and aliquoting team.

PBMC isolation

The core performs cryopreservation of peripheral blood mononuclear cells (PBMC) and stores them in liquid nitrogen. Samples for PBMC processing are collected in a sodium heparinized (NaHep or green top) blood tube. The study build process includes lab manual review and identification and documentation of the PBMC processing requirements in the protocol spreadsheet. Samples are routed to the PBMC processing area when accessioning is complete and processed, according to the protocol spreadsheet instructions.