ACTRI Facilities and Resources

The Altman Clinical and Translational Research Institute (ACTRI), partially funded through a Clinical and Translational Science Award from the National Center for Advancing Translational Science, provides funding, training, staffing, consultation, space and equipment to investigators at UC San Diego and ACTRI partner institutions. The Institute includes six divisions: the Center for Clinical Research (inpatient and outpatient Clinics and staff; Design, Biostatistics, Ethics, and Regulatory units); Biomedical Informatics; Translational Research Technology (TRT); Community Engagement; Education, Training and Career Development; and Translational Research Alliance.

Staffing

Directors of each ACTRI division are available to investigators and staff for advice and consultation. Investigators can also request assistance from the ACTRI research navigator to determine appropriate services. Clinical staffing includes RNs, LVNs, phlebotomists, dietitian, DEXA tech, Cardiac Ultrasound tech, allied health personnel, unit clerks, Pharmacists and Pharmacy Technicians, clinical trials coordinators and project managers. Research associates and staff scientists staff the biomarker laboratory. Programmers and database managers support IT as well as the clinical trial management software platform and REDCap. Masters and PhD level biostatisticians are on staff in the biostatistics unit. A program representative is available for community consults. Project scientists and faculty provide consultation on genomic analysis in the Center for Computational Biology and Bioinformatics. Faculty is available for regulatory and ethics consultations. Assistance with regulatory submissions for human subjects’ protocols is provided by dedicated regulatory analysts. Administrative staff is available to help with budgeting for clinical trials.

Administration

Resources: The ACTRI administration currently occupies the second floor of the new Altman Clinical and Translational Research Institute (ACTRI). ACTRI is located adjacent to the Jacobs Medical Center in La Jolla, Calif., and is geographically co-located with UC San Diego’s top-tier research and clinical patient care facilities. ACTRI serves as the hub of UC San Diego’s intensely collaborative clinical and translational research environment, allowing investigators to exchange resources and ideas that improve collaboration on related research projects inside and outside the facility. The second floor is approximately 22,000 square feet and includes offices and cubicles, conference rooms and huddle rooms. The building is a 360,000-square-foot translational research facility totaling seven floors, which includes wet and dry research labs, laboratory support space, clinical space for translational research participants, research offices, a large scale auditorium (144 seats) for presentations on clinical research and a café for building occupants, visitors and the campus community. In addition to the ACTRI staff, the Office of Clinical Trials Administration, Office of Coverage Analysis, and the Human Research Protections Program occupy offices on the second floor of ACTRI. All employees have networked computers and hardline phones. Some have additional portable devices to respond to service requests and inquiries after normal working hours.

The ultimate goal of the Altman ACTRI is to create a working space where medical treatment and clinical research are co-located in close geographic proximity while providing state-of-the-art translational research laboratories and research participant space. The building creates a unique, multidisciplinary environment that brings together laboratory scientists and clinical investigators to understand disease, develop new methods of treatment and translate clinical research results into clinical practice.

Clinical Facilities

Resources: The Center for Clinical Research currently supports adult and pediatric clinical research at two sites. Located on the first floor in the new ACTRI building, the outpatient Clinic is approximately 18,000 square feet that is dedicated solely to clinical research and includes a phase I clinical trials unit, infusion center, exercise physiology unit, sleep study unit and a metabolic kitchen for studies on translational metabolomics. A new translational research magnetic resonance imager (MRI) for human imaging will be located downstairs. A 1,000-square-foot investigational pharmacy with temperature-controlled space for storage and compounding areas, and a lab for sample acquisition and processing, are available. Inpatient beds, located on the tenth floor of the Hillcrest Medical Center, accommodate subjects needing stays of 24 or more hours. There is also a 251- square-foot processing laboratory on the tenth floor.

Equipment: Major equipment used in our clinical research facilities includes ECG machines; a Hologic DEXA scanner; exercise equipment including ergometer and treadmill systems with full cardio-respiratory measurement capabilities; Philips ultrasound equipment for echocardiography and vascular imaging; pharmacy equipment including a Pyxis machine, a refrigerator, a freezer and a glove box for handling sterile material; and refrigerated centrifuges for sample processing with dedicated refrigerators and a freezer for short-term sample storage.

Computer/Information Technology

Resources: The Biomedical Informatics Division supports data acquisition, storage, and analysis. It provides clinical trials management software, including VELOS and REDCap; the Clinical Data Warehouse for Research (CDWR), which allows mining of the electronic health record at UC San Diego to obtain estimates of numbers of subjects that match a specified profile for a contemplated clinical study; UC ReX Data Explorer, which expands the CDWR capabilities by searching for possible subjects with specific demographics, diagnosis and/or procedures across the five UC medical centers; and the Center for BioInformatic Analysis, which provides consultation and analysis for genomic data.

Equipment: ACTRI, in collaboration with the UC San Diego School of Medicine Department of Biomedical Informatics (DBMI), has developed a HIPAA compliant HPC cloud. The cloud is comprised of 1024 CPU cores, over 12 TB of RAM and 1.1 Petabytes of tiered storage. It is architected for data security, data archival, data integrity, high availability and redundancy. The equipment is housed in state-of-the-art data centers at UCSD - San Diego Super Computer (SDSC) and the UCSD Medical Center Kearny Mesa Data Center (KMDC). The cloud currently houses an instance of the Research Electronic Data Capture program (REDCap); the Clinical Data Warehouse for Research (CDWR); the UC ReX Data Explorer and its current expansion through the Accruals to Clinical Trials (ACT) project; and a diverse set of development platforms enabling research and the development of new Biomedical Informatics tools and applications.

Center for Computational Biology and Bioinformatics Facility

Resources: The Center for Computational Biology and Bioinformatics (C2B2) is a centralized bioinformatics core group on the UC San Diego main campus occupying 1,800-square-feet of office space. The C2B2 has 10 offices and 3 conference rooms that can accommodate 20 people, in the Leichtag Building on the UC San Diego School of Medicine La Jolla campus.

Equipment: Computers are available to all staff in the C2B2. All personnel are equipped with at least one laptop, external monitor and other peripherals. All high-performance computing and storage (active and archival) is performed on third-party cloud computing platforms including Amazon Web Services, Google Cloud, and Microsoft Azure. UC San Diego has signed a HIPAA Business Associates Agreement (BAA) with all three vendors at this time. Additional storage in the UC San Diego HIPAA-compliant cloud (iDASH) at the SDSC will be utilized for phase I Center for Accelerating Drug Development studies using protected health information. The C2B2 has six different analysis pipelines on the cloud platforms at this time covering the sequencing of DNA, RNA, small RNA, methylation, chIP, and array datasets. High-throughput 10-gigabit ethernet is linked to the C2B2 for fast data transfer to-and-from the cloud providers.

Major Equipment

Clinical: Major equipment used in our clinical research facilities includes ECG machines, a Hologic DEXA scanner, exercise equipment including ergometer and treadmill systems with full cardio-respiratory measurement capabilities, ultrasound equipment for echocardiography and vascular imaging, a Pyxis machine and a pharmacy refrigerator and freezer. The IT service supports HIPAA compliant subject data on NetApp devices accessed through IBM blade servers located in the UC Health Kearny Mesa Data Center.

Laboratory: Molecular Devices SpectraMax 340PC384 equipped with SoftMax Pro 4.8; Molecular Devices SpectraMax M5 Reader equipped with SoftMax Pro 5.2 software for data reduction; Meso Scale Diagnostics (MSD) Sector Imager 2400; Luminex machine; Bio-Rad VersaDoc MP4000 imaging system; Leica 2400 automatic cryostat; Nikon Eclipse E800 microscope with epi-fluorescence; Nikon Diaphot inverted microscope; Olympus MicroFire digital camera; fTitertek’s Auto Gamma Counter 10/600 with AGC 2.11 software; Perkin Elmer GeneAmp 7700 Thermal Cycler; Corbett Life Sciences: CAS 1820-Xtractor Gene Robot equipped with Version 4.9.2 software; -80 ˚C Sanyo freezers; and -180 ˚C MVE TEC 3000 freezers for samples frozen with liquid nitrogen.

Translational Research Technology (TRT)

TRT provides a virtual laboratory for ACTRI researchers including specialized equipment, unique biomarker assays and biorepositories containing normal and disease specific samples. They can assist with collection, processing, and storage of samples, as well as providing previously collected samples relevant to specific projects. To ensure sample safety, the TRT Biorepository uses remote monitoring and an emergency power source. Samples are cataloged by staff using a laboratory inventory management system based on Excel macros and developed by Mongoose Coding.

TRT offers consultation for all of these services, plus facilitated access to its Affiliated Biorepositories and Affiliated Laboratories.