Biospecimen Quality Control - STR Profiling

Many biospecimen repositories or tissue core facilities collect de-identified biospecimens such as blood or tissue from human patients for use in IRB approved research projects studying everything from factors that contribute to cancer to studying specific disorders such as Crohn's disease, diabetes, or Alzheimer's disease.

How does a biospecimen or tissue core facility use the STR profiling test?

There are many ways in which STR profiling can be utilized as an essential quality control check of human biospecimens, here are a few examples:

Comparing Normal versus Diseased Tissue

Research facilities, which are connected to hospital systems, may collect samples of normal and diseased human material from willing and informed patients with a specific disease type (e.g. lung cancer). Qualified researchers can utilize these de-identified human biospecimens in their research projects to study changes in the normal tissue that progress to cancer or other disorders. In order to properly compare the research data obtained from the normal "control" sample to the data obtained from the tumor or diseased sample, the biospecimen core facility should perform a cost effective and straightforward STR profiling quality control check to confirm that the identity of the human biospecimens match each other PRIOR to starting any experiments and before sending any biospecimens to other researchers (internal or external collaborators). If possible, the STR profiles of the normal and diseased specimens should be compared to the STR profile of the patient's reference specimen (e.g., whole blood, buccal swabs, etc) prior to starting any experiments.

Translational Studies

Databases of genomic information from willing and informed patients with specific genetic disorders or conditions are useful tools in assessing causality, new technologies and treatments. In order to ensure that all the genetic information compiled from these patients is assigned to the correct patient, a quick and easy STR profiling DNA identification test should be done on that patient's "reference" sample (e.g., buccal swab, whole blood, etc.). This ensures that all downstream applications using that DNA extract can be quickly and easily traced back to that patient's reference STR profile when needed; a quality control test essential to the validity of the downstream data.

Why STR profiling for human DNA identification?

STR profiling is the most often used method for human DNA identification – it is the same technique that is recommended for the authentication of human cell lines used for research purposes [4]. The STR profiling method is quick, cost-efficient, and the human identification results are straightforward (only identical twins have the same STR profile). Once you receive your baseline reference STR profile of your de-identified patient samples, you can use that reference STR profile as a QC tracking code for all downstream uses of those specimens (e.g., in the creation of primary and/or cancer cell lines, stem cell lines or xenografts, or in translational genomics research between the normal and tumor/diseased tissue).

Inadvertent cell line contamination has been a major problem for biomedical researchers for over 50 years [1]; by performing this essential quality control check on the biospecimens used for translational genomics research or used to create cancer cell lines, stem cell lines and xenografts, you are helping to keep research on a solid foundation.

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Advantages of STR profiling in identifying human biospecimens?

The advantages of STR profiling over other “identification” methods are, at minimum, twofold:

The STR profile does not contain medically relevant information which makes it the perfect choice for human DNA identification and,
STR profiling is a universally accepted method for human DNA identification and tracking of human biospecimens from collection all the way through the creation and use of continuous cell lines [4]. The biospecimen core facility’s obligation would be to check that the original patient sample (e.g. blood) STR profile matches the benign and tumor or diseased tissue prior to storing these specimens for downstream uses by other researchers. If you are a researcher using human biospecimens for purposes such as creating primary or cancer cell lines, stem cell lines or xenografts, you can utilize the STR profiling test for continued quality control tracking of specimens received from the core facility. If a suspected specimen mix-up occurs, you would be able to utilize the STR profile to sort out the potential contamination issue. In addition, if you also house commercially available cell lines in your research lab, there are online STR profile databases, such as the databases maintained by Cellosaurus, ATCC (American Type Culture Collection) and DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH), which are available to check the STR profile of your in-house specimens against those repository cell line samples (which may be growing alongside your in-house specimens). Without the STR profile, you would not be able to compare your cancer cell line, primary cell line, stem cell line or xenograft to samples available in commonly used repositories as most repositories utilize the STR profile for quality control tracking purposes.

In addition, the NCBI (National Center for Biotechnology Information) supported BioSample database hosts a growing collection of authenticated human cell lines in an effort to address the problem of cell line misidentification; these records include the STR profile information as well as the supporting peak data. As a creator of in-house cell lines from human biospecimens obtained from your biospecimen core facility, you would be able to submit the STR profile of your newly created cell line for inclusion in the BioSample database so that all researchers utilizing your cell line can check the authenticity of the sample in their own lab.

What are the details of the STR profiling test for quality control testing of human biospecimens?

he turnaround time for our STR profiling test for human biospecimens is as quick as 2-3 business days and it includes 15 autosomal sites plus amelogenin (gender marker) using the PowerPlex16HS kit (Promega). The test also includes a MOUSE marker for the detection of mouse DNA contamination, especially helpful for patient-derived xenograft (PDx) models and labs that utilize both human and mouse cell lines (to exclude cross-contamination). This essential quality control test is cost efficient and easy to interpret with low prices (volume discounts available). See our pricing options.

*Please note that FFPE samples or other non-standard samples (e.g., bone) will incur additional DNA extraction charges above what is charged for fresh tissue or blood DNA extractions and may take longer to process due to the condition of the non-standard biospecimen.

Please note: STR profiling is for research purposes only