Human sample identification is an essential element of many research projects employing human cells, tissues, or mixtures. Identification may be required to track and confirm sample provenance for databasing, biobanking, or research purposes. For example, archival tumor/normal specimen pairs may be tested to confirm they are derived from the same individual. Human identification may also be used as verification of twin zygosity or parentage in research studies to improve reliability of familial information. In its most sensitive application, human identification may be used to detect mixtures in human research samples—to rule out external contamination in samples, to identify contamination due to histological procedures, to track chimerism, or to study xenografts, among other things.
DNA genotyping using short tandem repeat (STR) markers is currently the gold-standard for human sample identification. STR markers consist of short, repetitive sequence elements 3–7bp in length. Distributed widely throughout the human genome, STR markers are highly polymorphic genetic markers which may be used for both forensic and non-forensic human identification. Genotyping at STR markers can be performed using PCR with dye-labeled primers. The number of repeats for each allele in a given individual can be determined, based on the size of the amplified fragments, following electrophoretic separation on a capillary electrophoresis instrument.
There are fluorescent PCR multiplex STR kits optimized for human sample identification in research labs. These kits include several highly polymorphic STR markers plus two sex-linked markers. Lab workflows can be streamlined when all markers can be amplified in a single PCR reaction. A high number of markers allows for better discrimination between human samples, including related individuals. Used in detection of human mixtures, this system also increases the likelihood of informative alleles, unique to both contributors, that can be used to estimate their relative contributions to the sample.
While many researchers have relied on forensic chemistries that are often intended for samples with very low DNA concentration, kits that have been optimized for 2.5–5ng DNA input specifically for the research community are desirable. The increased DNA input can improve robust detection of minor genetic contributors by reducing stochastic effects on PCR.
The availability of benchtop capillary electrophoresis instruments paired with multiplex STR kits brings the capability of human sample identification to individual labs. The small footprint and low-to medium throughput of these instruments means that research labs can now perform their own testing without waiting for sample batching or core lab turnaround. Researchers can control the entire workflow, from amplification and electrophoresis conditions, to data analysis, with a potential for faster turnaround to support key research projects.
Human sample identification and mixed sample analysis with STR genotyping can confirm sample provenance and identify sample contamination or chimerism in many research areas, even the most sensitive applications. To learn more about DNA genotyping using STR markers with the Spectrum Compact CE System for detection of low-level human contributors in mixed samples, download the application note: Human Sample Identification and Mixed Sample Analysis Using the GenePrint® 24 System