Biobank Biospecimen Sample Quality Control

Sample quality is of the utmost importance in research, and biobanks are vital in providing the high-quality samples required. But as the collection, processing, and storage of samples can all have an impact on integrity, there is a need for reliable and objective QC measures to ensure sample quality is maintained.

Understanding the right parameters to measure, however, can be challenging. There is a wide range of parameters available, with QC techniques ranging from morphological validation, biomarker measurement, or pathological and clinical data. Critical to remember though, is that the QC measures implemented should depend on the biospecimen type of interest, and to fully assess sample quality multiple parameters should be monitored. Furthermore, the timing of QC is vital, and determining sample quality both at the point of extraction and regularly throughout its storage, is key to ensure that an accurate and current representation of sample quality is obtained.

QC considerations

Nuclei acid biospecimens

The importance of nucleic acids in research means that effective nucleic acid QC is crucial. Understanding nucleic acid quality can not only aid in the selection of the best research samples, but also inform subsequent workflows; giving valuable concentration input information or indicating the number of PCR amplification cycles required.

For nucleic acids, “the most important parameters are size, quantity, integrity, and purity,” states Steve Siembieda, Product Marketing Director, Biomolecular Analysis Division, Agilent Technologies. Parameters such as DNA integrity number (DIN), genomic quality number (GQN), RNA integrity number (RIN) and RIN equivalent (RINe), and RNA quality number (RQN) provide objective and reliable metrics to assess sample quality. “Agilent automated electrophoresis instruments are specifically designed for measuring nucleic acids,” explains Siembieda, “the TapeStation, Fragment Analyzer, and Femto Pulse are each capable of determining the size, quantity, and integrity of various nucleic acid extracts including genomic DNA, total RNA, cfDNA, FFPE DNA and FFPE RNA, and small/micro-RNA.” Purity can then be measured by UV, with instruments capable of showing the number of contaminants that may be present—such as proteins or sugars.

Fluid biospecimens

Fluid biospecimens include serum and plasma, urine, and cerebrospinal fluid. The QC of fluid samples relies on the detection of known molecular biomarkers to assess specific pre-analytical variables. In order to give the most complete assessment of quality, the measurement of multiple analytes is essential—but luckily for us, there is a wide range of parameters available for each biospecimen type.

For serum and plasma, numerous useful biomarkers have been reported—a selection of which is shown below. In addition to such general parameters, molecular markers tailored to the end-use analysis and genes of interest have also been reported.

Table. Parameters Used to Assess Sample Quality of Serum and Plasma

QC of urine samples focuses on measuring a few key parameters. Creatinine, as measured by ELISA, is commonly used to normalize urine content, while sodium is frequently used as a marker of urine volume. Alkaline phosphatase activity by means of an enzymatic assay can be used to demonstrate impact of long-term storage, and pH is another simple parameter that can be easily and cheaply measured.

For cerebrospinal fluid specimens, cystatin C truncation (by means of MALDI-TOF mass spectroscopy and ELISA) and hemoglobin levels (ELISA) are useful QC measures to assess post-centrifugation conditions and hemolysis respectively.

Solid tissue biospecimens

For solid biospecimens, the QC of tissue can include both microscopic examination and the molecular characterization of nucleic acids and proteins. Reported characterization has included assessing paraffin-embedded tissue quality by RT-PCR of hypoxanthine-guanine phosphoribosyltransferase (HPRT) expression, and measuring DUSP1, Hspa1, and Jun gene expression among others to assess the effect of cold ischemia and thawing.

If the tissue biospecimen is for pathological research and was removed from a patient with a known diagnosis, confirmation of the disease state and the percentage of disease should also be recorded.

Cell specimens and microorganisms

QC of cell specimens and microorganisms can include the authentication of type, assessment of purity and viability, and contamination testing. DNA fingerprinting and phenotypic characterization are useful for cell identification—particularly if your cell type is well established. For microorganisms, phenotypic characterization is also useful, and more detailed taxonomic identification can be obtained through genotyping, ribotyping, or serotyping methods. Both purity and viability are commonly assessed by flow cytometry, and to ensure cells are contamination-free; methods of pH monitoring and visual inspection (to identify bacteria), light microscopy (for yeast and mold), electron microscopy, immunostaining, ELISA assays, or PCR (viruses) and direct microbial culture or PCR-based kits, DNA fluorochrome staining, ELISA, or specialized test kits (mycoplasma) can be used.

Conclusion

Successful research depends on high-quality samples and thorough sample QC is central to this. Ensuring a complete picture of quality is obtained relies on measuring multiple parameters and assessing quality throughout the lifecycle of the sample. But while there is a wide range of QC parameters available for each biospecimen type, measuring parameters comes at a time and cost implication, and QC can only be performed in a targeted manner if the specific measures of interest in downstream research are known. Defining and standardizing the most appropriate parameters to assess biospecimen quality therefore remains to be answered.