Hear from two experts about how SNP-based genetic fingerprinting workflows support sample identity and quality control in biobanking.
In any biobanking or research workflow, the process of accurately labeling and keeping track of collected samples, known as sample identification, is critical for helping to ensure research integrity and reproducibility. Samples may be shared among researchers or with external collaborators and service providers – especially in complex multiphase studies – leading to a risk of mix-ups. Potential sample-handling errors are unavoidable and can occur at any point in the process: during collection, before and after when the samples enter a biobank or storage facility, or even in the lab where testing is going to take place. This means researchers might be spending time and money processing misidentified, poor-quality or even contaminated samples, compromising data integrity and leading to the incorrect interpretation of results.
DNA fingerprinting:
- Ensures sample quality – processing samples with verified DNA at a high standard avoids wasted resources
- Ensures sample identity – fingerprinting verifies that the sample matches the expected profile and confirms accurate distribution
- Establishes a baseline DNA fingerprint – this allows for issues to be identified prior to distribution and helps the biobank or biorepository distribute higher-quality samples
Standard BioTools and the Indiana University Genetics Biobank (IUGB) paired up for an ISBER webinar discussing how SNP-based genetic fingerprinting workflows support high-confidence sample identity and quality control in biobanking. Read on to learn more about why Michael Denton, Supervisor, DNA and Genetic Identity Laboratories, and Molly Walling, DNA Identity Specialist, have integrated single-nucleotide polymorphism fingerprinting workflows using Biomark™ technology at the IUGB and how molecular fingerprinting can safeguard against the mishandling of specimens, streamline QC processes and scale across large collections.
The IUGB started in the late nineties as a National Institute on Aging (NIA)-funded biorepository, predominantly focusing on Alzheimer’s disease. Since then, the biobank has expanded to include a number of additional biorepositories and biospecimens; to date, the IUGB has about 4.5 million specimens cataloged in its biorepository. It is the national centralized repository for Alzheimer’s disease, the primary biorepository for the Michael J. Fox Foundation, focusing on Parkinson’s disease, and also works with NCAA-DOD Grand Alliance CARE Consortium, looking at concussion studies. The IUGB houses a number of different biospecimens, including DNA, RNA, plasma, serum, PBMC and cerebrospinal fluid (CSF).
Between 1990–2018, the IUGB accumulated about 1.3 million samples and distributed about 330,000 samples; from 2018–2025, the biobank accumulated about 4.5 million samples and distributed about 580,000 samples. Rapid acceleration at this scale underlines the need for solid and reliable QC practices.
Enter Standard BioTools™ technology. The IUGB has what Walling calls a “fleet” of SBI microfluidics platforms – two Juno™ systems, one Biomark HD system and two Biomark X9 Systems – that since 2018 have helped the biobank successfully run 4,500 integrated fluidic circuits (IFCs), leading to 423,000 samples analyzed and 226,421 samples distributed. The fleet of SBI tools helps the IUGB perform four workflows of DNA fingerprinting:
- PROC – occurs at sample accessioning. This identifies problematic samples, such as samples with a low SNP call rate, that are contaminated or that show discordance between reported and genetic sex. Performing this process at accessioning establishes a baseline DNA fingerprint, allowing the IUGB to compare that to any subsequent runs of the sample and also check identity in longitudinally collected samples.
- DIST – occurs during sample distribution. This process protects against human error by identifying DNA quality issues, such as a low genotype calling rate or sample contamination. It also checks for sample identity, comparing genetic sex to reported sex and concordance between distribution and intake DNA fingerprints.
- HIST – used to create a baseline genotype for banked samples. Through this process, the IUGB has been able to go back through their frozen samples from 1990–2018, fingerprinting over 100,000 samples in the past year and a half alone. This has provided researchers with reportable data for specific biomarkers.
- LAB – used to troubleshoot samples through internal investigation
The IUGB used Standard BioTools IFCs for their DNA fingerprinting assay. IFC technology is ideal for versatile, fast results, providing multiplex throughput with singleplex simplicity: Samples and assays are loaded into the chip separately and automatically combined in a pairwise manner to create individual singleplex reactions, with up to 192 singleplex reactions per sample. This means users can add, remove or replace assays on demand and scale throughput without changing technologies.
In fact, the IUGB has been able to customize the DNA fingerprinting assay on an as-needed basis. In 2018, they added an APOE SNP, of interest in Alzheimer’s disease research; in 2019, they added an additional genetic sex SNP; and in 2022, they added a LRRK2 SNP, of interest in Parkinson’s disease research. “It’s been nice,” Walling says of being able to configure the SNP panel. “Researchers have asked … ‘is there any way we can implement an assay for this particular neurodegenerative disorder?’ We can come to Standard BioTools and say, ‘Hey, we have a SNP that is on the panel for a chromosome, do you think we could replace it?’ ”
The biobank’s DNA fingerprinting workflow also protects their samples, identifying errors earlier and allowing the IUGB to explore alternate DNA or biospecimen sources to help identify one-off samples. “We all know how precious these samples are,” Walling says. “We’re trying to save as many … as possible, and that allows us to expand our research.”
Because the use of genetic fingerprinting can raise questions around patient consent and data privacy, the IUGB takes deliberate steps to safeguard both. As Walling explains, fingerprinting data is stored within a secure institutional database protected through the university’s VPN, and all shared information is fully de-identified, containing only coded barcodes, not names or personal health data. “This isn’t like a consumer genetic test,” Walling says. “All fingerprinting data are used strictly for research, not diagnostics, and are completely separated from any clinical or identifying records.” This approach ensures that researchers gain valuable genetic insights while maintaining the confidentiality and privacy of donor information.
Using SBI technology to create and uphold proper sample identification has provided the IUGB with “increased confidence” in their samples. It allows for potential issues to be found earlier, saving time and money down the road. Most of all, it benefits research overall. “We can ensure we provide a quality sample and people can rely on our biobank to send them the best-quality samples from participants that we can,” Walling says. “And that can lead to higher-quality research, which downstream can help benefit science as a whole.”