Volume 49 | March 31, 2022
A program of NIH’s National Center for Advancing Translational Sciences
Two Surveys for N3C Data Enclave Users

N3C Data Enclave Tools Survey

We would like to hear about your experience using N3C Data Enclave tools! Please complete this short survey. Your feedback is very valuable to us and greatly appreciated, as it will help us to continually improve your experience in the platform, from the tooling and features to support and training materials.
We Need Just 2 Minutes of Your Time!

N3C User Satisfaction Survey

As part of the N3C program evaluation, we are collecting information about your experience with N3C, as well as your utilization of N3C resources. Your feedback is extremely valuable to understand what is working well and what can be improved. The brief survey should take only 1–2 minutes to complete.
Data Enhancements

Questions about Data Enhancements? Please post them on Slack
       New Slack: https://bit.ly/join-n3c-pasc-slack

Viral Variant Summary Data Now Available

N3C is now working with select sites to bring in viral variant data and make it available to investigators who have successfully completed the application process. The viral variant initiative is being implemented in two phases: 

  • Phase I uses PPRL to link viral variant summary data and includes a limited amount of information on the patient’s type of variant (Delta, Omicron, etc.) and the date collected.
  • In phase II, in addition to the summary data, the viral variant sequence will be available for investigators.

The viral variant summary data consists of high-level clinical information that includes at minimum the following values:

  1. specimen_id: unique identifier of specimen ID.
  2. site_n3c_patient_id: patient identifier.
  3. viral_variant_summary: this free text consists of a combination of WHO and/or PANGO lineage information.
  4. specimen_collection_date: date specimen was collected from the patient .

The initial viral variant data set includes data from six sites. The data set will eventually include 15 sites (eight CTSA sites and seven CTR sites).

Getting Access to Linked Data Sets

Viral variant summary data is considered level 3 data, as are all data sets that incorporate the privacy-preserving record linkage (PPRL) or other patient linkages. The Data Use Request (DUR) has been modified to include a set of checkboxes for all currently available PPRL datasets (see image below). In addition to all standard level 3 requirements (described below), users need to choose the datasets they would like and describe their use in the DUR rational paragraph for the Data Access Committee (DAC).

This level of access requires all investigators to submit a DUR, which in turn needs a signed institutional data use agreement (DUA), a letter of determination and attestation to the N3C Code of Conduct, IT security training, and human subject training. A new checkbox has been added to the DUR form (see image below) where investigators can request access to linked data sets like mortality and viral variant prior to submission to the NCATS’ federally staffed Data Access Committee (DAC) for review.
If you have questions about accessing the viral variant summary data, please submit an N3C Support Desk ticket.

Published works using N3C data are listed on the N3C Cohort Exploration Dashboard. The Publications tab displays titles and links to fully published articles, articles online ahead of print, and published preprints, as well as a list of accepted conference presentations and posters.

Recent N3C Articles Accepted for Journal Publication

Recent N3C Preprints

Help Us Track N3C Publications!

When you have a research product that is ready for publication or accepted for presentation, please submit it via the N3C Publication Intent Form, which will notify the Publication Committee of N3C output to be registered. (Research products include: manuscripts, posters, conference papers, blogs, press releases, podium presentations, etc.)

Per the N3C Attribution and Publication Principles, all manuscripts using N3C community resources must be reviewed by the Publication Committee. Non-manuscript products do not require review but should be submitted after they have been accepted by the conference to allow for promotion and tracking of collaborator accomplishments.

View the Publication Review web page for more details.
New Public Health Browser Makes COVID-19 Snapshot Data Accessible to All

N3C recently launched the Public Health Browser, which provides snapshots of high-value health data for policy makers, investigators, and entrepreneurs to facilitate further research questions for better health outcomes. 

With the launch of the Public Health Browser, aggregate summary data is now available for stakeholders to access sample sizes of relevant data cohorts without requesting access to the N3C Data Enclave, which can only be accessed through a secure cloud portal.
The ten dashboards that are currently available in the Public Health Browser include:

  • Summary Data: a snapshot of all COVID+ patients in the N3C Data Enclave, including demographics, comorbidities, and vaccination counts.
  • Pediatrics Summary Data: a snapshot of COVID+ patients under the age of 18 in the N3C Data Enclave, including demographics, comorbidities, and vaccination counts.
  • Medications: a list of medications of interest and counts for the COVID+ patients in the N3C Data Enclave for each of the prescribed medications. 
  • Cumulative and Average COVID+ Cases: Daily and cumulative COVID+ patient counts in the N3C Data Enclave and seven-day rolling averages. 
  • COVID+ Reinfection: infection and reinfection data for COVID+ patients in the N3C Data Enclave.
  • Regional Distribution of COVID+ Patients: incidence of COVID+ patients in the N3C Data Enclave over nine geographical regions.
  • Diabetes Mellitus: a snapshot of pediatric and adult COVID+ patients in the N3C Data Enclave with Diabetes Mellitus Type 1 and Type 2. 
  • Smoking: a snapshot of all COVID+ patients in the N3C Data Enclave, aggregated by demographics, severity, and smoking status.
  • Disease Snapshots: a snapshot of the COVID+ patients in the N3C Data Enclave with select comorbidities, including cancer, congestive heart failure, dementia, diabetes, diabetes with complications, HIV, hemophagocytic lymphohistiocytosis (HLH), liver disease (mild), liver disease (severe), metastasis, myocardial infarction, paralysis, peptic ulcer disease, peripheral vascular disease, pulmonary disease, renal disease, rheumatologic disease, and stroke. 
  • Cumulative Participant Data: provides the counts of the cumulative demographics data for all patients in the N3C Data Enclave. A downloadable spreadsheet is available.

There will be two to three dashboards added in the near future that will include snapshots of long COVID/post-acute sequelae of SARS-CoV-2 (PASC), mortality, and possibly a reinfection time series. N3C will continue to add new dashboards to the Public Health Browser as new data sets become available.

Explore N3C’s Public Health Browser to learn more, or email cd2h@ohsu.edu with questions or comments.
Domain Team Updates/Announcements

New Monthly Domain Team Leads Meeting

We have a new monthly Domain Team Leads Meeting!

The next Domain Team Leads Meeting will take place April 14, 2022 at 3:00 p.m. EST. The meeting will be co-led by Dr. Scott Chapman (University of Minnesota) and Dr. George Sokos (West Virginia University), who are also N3C Team Leads for the Cardiovascular Disease Domain Team. 

The Domain Team Leads Meeting occurs on the second Thursday of each month. Please contact Sharon Patrick (patricks@hsc.wvu.edu) for a meeting invite.
Dr. Scott Chapman, University of Minnesota
Dr. George Sokos, West Virginia University
Note: This meeting replaces the Biweekly Clinical Scenario meeting.

New GIS and Spatial Epidemiology Domain Team

The mission of the GIS and Spatial Epidemiology (GSE) Domain Team is to facilitate the technical implementation of basic and advanced GIS and spatial statistical methods within the National COVID Cohort Collaborative database. This group also provides expertise to other domain teams interested in applying spatial statistical or epidemiological methods within the scope of their work. 
The GSE Domain Team is led by Dr. Brian Hendricks, Phd, MS, an epidemiologist with expertise in applying spatial statistics to study geographic context of risk and access to care for drug misuse and infectious diseases. He is director for the WVU Spatial Epidemiology and Statistics Lab and spatial epidemiologist for the WV Clinical and Translational Sciences Institute where he provides expertise in spatial statistics for the Biostatistics, Epidemiology, and Research Design (BERD)
The GSE Domain Team meets bi-weekly. Please contact Sharon Patrick (patricks@hsc.wvu.edu) for a meeting invite.
N3C at AMIA 2022 Informatics Summit!
Thank you to everyone who represented N3C at the American Medical Informatics Association (AMIA) 2022 Informatics Summit in Chicago last week! It was great to see many of the CD2H and N3C team members in person — some for the first time, others for the first time in more than two years!

Understanding, Applying and Sustaining Maturity in Biomedical Informatics 
Speakers: Adam Wilcox, Boyd Knosp, Jodyn Platt, Nicholas Anderson, Genevieve Melton-Meaux, William Barnett, Justin Starren
Panel - How Distributed Clinical Observations Become Big-data COVID Research Publications Using the N3C 
Speakers: Christopher Chute, Anita Walden, Emily Pfaff, Davera Gabriel, Charisse Madlock-Brown
Oral Presentation - COVID: Health Disparities, Patient Portals, Children and More! 
Speakers: Laura Wiley (session chair), Jennifer Pacheco, Elise Lang, Lily Cook, Jimmy Phuong, Hanieh Razzaghi, Alexandra Rizaldi

Variability in EHR Data About Race and Ethnicity as Observed in the National COVID Cohort Collaborative Data Enclave
Speaker: Lily Cook

Advancing Interoperability of Patient-level Social Determinants of Health Data to Support COVID-19 Research
Speakers: Jimmy Phuong, Stephanie Hong
Panel - Lessons Learned from a National Data to Health Coordinating Center 
Speakers: Adam Wilcox, Anita Walden, Christopher Chute, Randi Foraker, Alexis Graves
Panel - Machine Learning, Data, Algorithms, and Equity in Biomedicine and Healthcare 
Speakers: Anthony Solomonides, Dina Paltoo, Charisse Madlock-Brown, Jimmy Phuong, Arash Shaban-Nejad, Vignesh Subbian, Naoko Muramatsu
Panel - De-Identified Record Linkage: the power of combining PPRL and an Honest Linkage Broker 
Speakers: Umberto Tachinardi, Abel Kho, Kenneth Gersing, Jasmin Phua

Poster: Using N3C Enclave for Drug-Drug Interaction studies: the case of DOAC-Dexamethasone Interaction and the risk of Thrombosis
Speaker: Olga Kravchenko

N3Community Forum

Presentations take place on select Mondays from 5–6 p.m. ET/2–3 p.m. PT. To attend these and future N3Community Forum presentations, please register here.

Missed an N3Community Forum or want to revisit a past Forum? You can find all the videos on our YouTube page.

April 4, 2022

Topic: Data quality considerations for evaluating COVID-19 treatments using N3C
Presenters: Hythem Sidky

Topic: Principles for accommodating missingness, and their role in analytic-decision frameworks for EHR-based studies
Presenters: Ken Wilkins and Harold Lehman

Topic: MLP Team Update: PASC Clustering Pipeline and GAP Insights
Presenters: Peter Robinson and Justin Reese

April 11, 2022

Topic: Rare Diseases and ORDR / RDRCN 
Presenters: Melissa Haendel and Bryan Laraway

Topic: The New N3C Public Health Dashboard Demo
Presenters: Leonie Misquitta and Dave Eichmann

April 18, 2022

Topic: Semantic Clustering
Presenters: Charisse Madlock, Justin Reese, and Hythem Sidky

Topic: Monthly RECOVER Long COVID project team updates
Presenters: Melissa Haendel and Emily Pfaff

May 2, 2022

Topic: Practical Machine Learning for COVID-19 Using EHR Data: A Case Study Using N3C
Presenters: Brad Price and Maryam Khodaverdi
Welcome New Team Members
N3C In the News

Among patients hospitalized with moderate COVID-19, those who received aspirin on the first day of hospitalization had a significantly lower risk for 28-day mortality than those who did not, according to a recent observational cohort study.

Poor glycemic control was found to be associated with increased risk for COVID-19 hospitalization and mortality, according to the results of a retrospective study published in Diabetes Care.

MedPage Today: It's Not Over for Aspirin in Moderate COVID-19 (March 24, 2022)
People with moderate COVID-19 illness tended to have better clinical outcomes if they took aspirin their first day in the hospital, according to data from the NIH's National COVID Cohort Collaborative.

Sen. Tim Kaine, D-Va., introduced the CARE for Long COVID Act. The bill seeks to encourage more research and provide resources for those suffering from lingering COVID-19 symptoms and other post-viral illnesses. In a press release, Kaine acknowledged that he is enduring mild long COVID symptoms himself.

Receiving an additional COVID-19 vaccine dose provided more protection for people with compromised immunity, according to research presented at the Conference on Retroviruses and Opportunistic Infections 2022 (CROI 2022). While the study did not analyze booster effectiveness based on the specific type of immune dysfunction, it does offer reassurance that this population can benefit from keeping up to date on vaccination.

The development of safe and effective vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Both clinical trials and real-world evidence have demonstrated that current COVID-19 vaccines are extremely effective, particularly in reducing the risk of severe disease.

Contemporary Pediatrics: What factors are linked to severe COVID-19 in children? (February 23, 2022)
Since the start of the COVID-19 pandemic, the general understanding of how the disease affects children has shifted, from being seen as a disease with little to no impact on children to children being a significant proportion of patients contracting the virus. However, a lack of large cohort studies has made it difficult to build a robust knowledge base. A recent report sheds some much needed light.
N3C Domain Teams

N3C Domain Teams enable researchers with shared interests to analyze data within the N3C Data Enclave and collaborate more efficiently in a team science environment. They include multidisciplinary Clinical Domains composed of subject matter experts, statisticians, informaticists, and machine learning specialists who focus on clinical questions surrounding COVID-19's impact on health. Cross-Cutting Domains have a varied focus that applies to multiple domains. These teams provide an opportunity to collect pilot data for grant submissions, train algorithms on larger datasets, inform clinical trial design, learn how to use tools for large-scale COVID-19 data, and validate results. N3C encourages researchers of all levels to join a Domain Team that represents their interests, or to suggest new clinical areas to explore.

Reporting Concerns

In the event that you come across activities that pose misalignment with the principles outlined in the Community Guiding Principles for the National COVID Cohort Collaborative (N3C), you can privately notify us using the Report Conduct Concerns form located on the N3C website under the SUPPORT menu. Your feedback is important and we will take prompt and confidential action to address your concerns. All data management incidents should also be reported to NCATS. Thank you for your contribution!
The National COVID Cohort Collaborative (N3C) is a complementary and synergistic partnership among the Clinical and Translational Science Awards (CTSA) Program hubs, the National Center for Data to Health (CD2H), distributed clinical data networks (PCORnet, OHDSI, ACT, TriNetX), and other partner organizations, with overall stewardship by NIH’s National Center for Advancing Translational Sciences (NCATS). The N3C aims to improve the efficiency and accessibility of analyses using a very large row-level (patient-level) COVID-19 clinical dataset, demonstrate a novel approach for collaborative pandemic data sharing, and speed understanding of and treatments for COVID-19.
CD2H is supported by the National Center for Advancing Translational Sciences (NCATS) 
at the National Institutes of Health
(Grant U24TR002306).