Enabling Biomedical Data Driven Research
Bringing you common infrastructure, and consultation services
Research IT is responsible for several of Stanford's centralized biomedical infrastructure like Stanford's Clinical Data Warehouse (aka STARR, fka STRIDE) and research data management platform like REDCap. Our team designs, develops and maintains these systems. Our centralized infrasructure efforts are subsidized and hence governed by SoM administrative leadership.
Aside from infrastructure components, Research IT offers a confidential consultion service to Stanford University biomedical researchers on topics related to technology integration, research data capture, compliance and management, data privacy & security issues. Consulting services often lead to longer term partnership. These partnerships can result in custom solutions or reusable infrastucture. Several of Stanford infrastructure components have been fully funded by faculty projects (e.g. CHOIR).
To common tools, and infrastructure services
2018 Research IT news
Enabling Stanford mission
A new way to access STAnford medicine Research data Repository (STARR)
On Stanford Center of Population Health Science Data Center portal
With Stanford Center for Population Health Science
Under a new DASHER initiative, Research IT has made de-identified STARR structured data available on PHS Data Center portal. This allows for new way of exploring STARR data that did not exist before. In particular, you can quickly navigate through the metadata and table descriptions, and visualize the distribution of data associated with the variables.
Stanford Center for Population Health Science (PHS), under the direction of Mark Cullen, Senior Associate Dean for Research, focuses on study of health determinants and outcomes in large populations. It sits at the intersection of medicine and public health, spanning basic and social sciences, enabling integrated research that encompasses virtually every domain of life and society.
The Data Center at PHS hosts a diverse collection of high-value “marquee” data sets like Truven Marketscan and partners with several data owners around the world like Born in Bradford. Via a PHI compliant data platform called Redivis running on Google Cloud Platform, the Data Center offers researchers:
- Access to a library of data assets to facilitate transdisciplinary PHS projects.
- Ability to explore the data in BigQuery via SQL queries (GUI coming).
- While data access from PHS portal needs to meet several "Data Use Agreement" criteria like HIPAA training, the process is systematic and users can keep track of the requirements on the portal.
A gold standard for sleep analytics
Alliance Sleep Questionnaire expanded for Stanford Technology Analytics and Genomics in Sleep Program
With Stanford Technology Analytics and Genomics in Sleep (STAGES) Program
Alliance Sleep Questionnaire (ASQ) Stanford Technology Analytics and Genomics in Sleep (STAGES) enrolled their first patient at Stanford Sleep Clinic in April 2018. Remaining 10 sites will go live soon. This is a significant expansion to the existing ASQ program. ASQ has been engineered by Sanjay Malunjkar at Research IT in collaboration with Eileen Leary, Sr. Manager for Clinical Research at the Sleep Clinic. ASQ first went live in Stanford Sleep Clinic in 2011 and has since enrolled 8,000 patients. The STAGES program will expand ASQ to 30,000 patients.
Here are some additional details on the STAGES research program from Eileen. The STAGES study is funded by the Klarman Family Foundation and will collect multi-modal data on 30,000 patients across 11 different sleep clinic sites (across USA and Canada). Sleep disorders and sleep dysregulation impact over 100 million Americans, causing enormous medical consequences including cardiovascular (arrhythmia, hypertension, stroke), metabolic (diabetes, obesity) and psychiatric (depression, irritability, addictive behaviors), to name only a few. Sleepiness costs millions due to workforce errors and accidents. Although the global market for just hypnotic products will reach $76.7 billion by 2019, our fundamental understanding of sleep remains a biological “black box”. This curtails our ability to identify etiologies and thus treat sleep disorders effectively. To address this unmet need, STAGES team proposes to conduct large-scale genomics studies, sleep phenotyping and automated PSG data analysis. The information will be crucial for our understanding of the genetic architecture of sleep and to improve detection, treatment and prevention of sleep disorders. To maximize research potential, all tools and data will be made available to the research community. Specifically, Stanford is responsible for collecting data for 30,000 individuals from multiple sites:
- On-line sleep/medical history questionnaire (the ASQ, a branching logic questionnaire developed by Harvard University, University of Pennsylvania, University of Wisconsin-Madison, St Luke's Hospital, and Stanford University)
- In lab nocturnal Polysomnography data (one night PSG)
- Computerized Neurocognitive Battery (U Penn CNB)
- Actigraphy over 2-4 weeks (Amazfit Arc)
- 3-D craniofacial images.
- Stored biological samples (DNA, plasma, serum) for future biomarker research
- Genome Wide Association Study (GWAS) data
This study will be a landmark that will constitute a gold standard for the analytics of sleep. In collaboration with Prometheus Research, the STAGES program has built a comprehensive data platform to allow for easy data collection and management.
Point of care clinical trials
Patient-centered opioid tapering with active behavioral treatment
With CHOIR Learning Healthcare Platform
Collaborative Health Outcomes Information Registry (CHOIR) team (Garrick Olson, Teresa Pacht, David Tom, and ex-team member Randy Strauss), working in close collaboration with Prof Sean Mackey, MD, PhD, Chief of the Division of Pain Medicine, delivered the point-of-care clinical trial feature on the CHOIR platform. This method was developed by Stanford University biostatistician Philip Lavori, PhD, and researchers from VA Boston Healthcare System in 2011 as an alternative to expensive, lengthy, double-blind, placebo-controlled clinical trials to compare drugs and procedures that are already in regular use. A layperson summary of the method can be found here and the publication is here.
Research IT is supporting a prestigious new $8.8M PCORI grant, led by Beth Darnall, PhD Clinical Professor of Anesthesiology, that will use a point-of-care clinical trial in patient-centered opioid tapering with active behavioral treatment. The study will include ~1000 participants from Stanford Pain Clinic, Stanford Primary Care, Intermountain Health Primary Care, Stieg Pain Clinic and Phoenix VA Primary Care.