Case Study: Enabling High-Throughput Biobanking Operations with OpenSpecimen in Dubai

Biospecimen Management

The health system deployed OpenSpecimen to support high-throughput biospecimen collection under its Women’s Health Repository, driving research across four core conditions: Polycystic Ovary Syndrome (PCOS), Endometriosis, Endometrial Cancer, and Pre-eclampsia. Through OpenSpecimen, the team tracks a diverse set of biological materials, including whole blood (EDTA and serum), PAXgene tubes, serum, plasma, frozen tissue, and downstream derivatives such as DNA, RNA, and PBMCs. By standardizing on 2D pre-barcoded tubes across collection workflows, the biobank established scan-based tracking from the point of collection, eliminating manual data entry errors.

To safeguard specimen viability, OpenSpecimen is configured to capture granular pre-analytical parameters directly within daily workflows. This includes tracking single- or double-centrifugation protocols (such as spinning EDTA and serum tubes at 1500 × g for 15 minutes at room temperature or 4°C), snap-freezing timelines, and nucleic acid quantification metrics. Additionally, Krishagni has automated downstream operations by connecting OpenSpecimen directly with Tecan liquid-handling robotics for automated sample preparation and an Azenta BioStore (via Azenta Strata software) for automated sample storage and retrieval.

Collecting Clinical Data and Online Surveys

The biobank leveraged OpenSpecimen’s integrated survey and form modules to capture comprehensive clinical data and participant-reported questionnaires directly at the point of care and online. For study cohorts under the Women’s Health Repository—including endometriosis, polycystic ovary syndrome (PCOS), pre-eclampsia, and endometrial cancer—the team configured customized data structures to standardize collection across key health and lifestyle domains:

• Patient Demographics & Identification: Captures participant identity, medical record number (MRN), date of birth, nationality, and ethnicity.
• Clinical Presentation & History: Tracks primary diagnoses, ICD-10 coding, surgical histories, active medications, allergies, and familial disease patterns.
• Obstetrics & Gynecology History: Records detailed reproductive health metrics, including last menstrual period (LMP), pregnancy status, fetal parameters, IVF treatment history, contraceptive usage, and Pap smear records.
• Physical Examination & Diagnostic Criteria: Standardizes clinical measurements—such as height, weight, and blood pressure—alongside clinical phenotyping, including Rotterdam criteria for PCOS and FIGO staging for endometrial cancer.
• Nutrition & Lifestyle Questionnaires: Collects dietary habits across primary food groups, weight fluctuation history, specific diet regimens, nutritional supplements, and alternative medicine usage.

Integrations: Enterprise EHR and LIS via HL7

The biobank integrated OpenSpecimen with its electronic health record (EHR) system (Epic) and laboratory information system (LIS) (SunQuest) using HL7 messaging interfaces to automate participant enrollment and specimen tracking.

• Participant Registration & Consent (EHR): The EHR handles patient registration and biobanking consent, sending an automated HL7 ADT message to OpenSpecimen to create the participant record when consent is obtained.
• Specimen Collection & Pathology Orders (LIS): The LIS manages pathology orders and transmits specimen collection details back to OpenSpecimen once samples are drawn.
• Flexible Protocol Handling: The HL7 processor accommodates real-world clinical collection variations. For example, if a protocol specifies one 10 mL EDTA tube but staff collects two 6 mL tubes, OpenSpecimen records the actual physical collection rather than forcing the workflow to match the predefined protocol template.

Laboratory staff can then initiate downstream biobanking workflows by simply scanning the collected tubes.

Integration: Tecan Liquid-Handling

In the next phase of implementation, the biobank will integrate OpenSpecimen with Tecan liquid-handling robotics to automate high-throughput laboratory workflows. Once fully deployed, this integration will allow laboratory staff to generate aliquots and assign storage locations in bulk via a single CSV file upload, significantly reducing manual data entry and accelerating specimen processing times.

Integration: Azenta BioStore Automated Sample Storage

The institution established a bidirectional integration between OpenSpecimen and the Azenta BioStore automated storage platform via the Azenta Strata management software. This integration lets OpenSpecimen communicate directly with the physical storage environment, automatically synchronizing specimen placements, retrievals, and precise rack/position assignments to ensure real-time alignment between physical biobank inventory and digital records.