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1. Evaluation of a Multi-Component Phenotype Algorithm for Systemic Lupus Erythematosus across the PCORnet, OMOP, and i2b2 Common Data Models

Author

Steven Tran, Luke Rasmussen, Jennifer Pacheco, Philip Silberman, Martin Borsje, Prasanth Nannapaneni, Daniel Schneider, Yuan Luo, Abel Kho, Rosalind Ramsey-Goldman, and Theresa Walunas

Subjects
Demography. Population. Vital events, HB848-3697
Abstract

The aim of this study was to evaluate the performance of a computable phenotype for systemic lupus erythematosus (SLE) patients when it is ported from a local data warehouse to the i2b2, OMOP, and PCORnet CDMs. We adapted the SLE phenotype to the Northwestern Medicine (NM) Enterprise Data Warehouse (EDW) and NU i2b2, OMOP, and PCORnet instances. Each of the phenotype’s 17 components were determined by a rules-based algorithm built on diagnosis, medication, lab, and procedure codes. We assessed the phenotype over 168 clinician-confirmed SLE patients and 100 healthy controls and calculated agreement between the EDW and CDMs for overall SLE classification, individual SLICC criteria membership, and individual code occurrence level aggregates - count, first and last date, lab values using Cohen’s kappa (Cκ) and intraclass correlation coefficients (ICC). For overall SLE classification, agreement of the OMOP and PCORnet datamarts with the EDW was high (Cκ 0.928, 0.802, respectively) while that of i2b2 was low (Cκ 0.328). For the panel of SLICC criteria, OMOP had high agreement for 14/17 SLICC criteria (Cκ 0.792-1.000). PCORnet had high agreement for 13/17 criteria (Cκ 0.708-1.000). i2b2 had high agreement for 10/17 criteria (Cκ 0.813-1.000) with the exception of lab-based criteria. While agreement between the EDW and CDMs at the level of individual codes was relatively poor, agreement at the levels of overall SLE classification and individual SLICC criteria were reasonably high for OMOP and PCORnet, suggesting that inconsistencies at a micro, code level become less apparent at the macro, phenotype level.

Published
2024
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2. Northwestern University resource and education development initiatives to advance collaborative artificial intelligence across the learning health system

Author

Yuan Luo, Chengsheng Mao, Lazaro N. Sanchez‐Pinto, Faraz S. Ahmad, Andrew Naidech, Luke Rasmussen, Jennifer A. Pacheco, Daniel Schneider, Leena B. Mithal, Scott Dresden, Kristi Holmes, Matthew Carson, Sanjiv J. Shah, Seema Khan, Susan Clare, Richard G. Wunderink, Huiping Liu, Theresa Walunas, Lee Cooper, Feng Yue, Firas Wehbe, Deyu Fang, David M. Liebovitz, Michael Markl, Kelly N. Michelson, Susanna A. McColley, Marianne Green, Justin Starren, Ronald T. Ackermann, Richard T. D'Aquila, James Adams, Donald Lloyd‐Jones, Rex L. Chisholm, and Abel Kho

Subjects
artificial intelligence, Collaborative AI in Healthcare, collaborative learning, health workforce, learning health system, multimodal machine learning, Medicine (General), R5-920, Public aspects of medicine, RA1-1270
Abstract

Abstract Introduction The rapid development of artificial intelligence (AI) in healthcare has exposed the unmet need for growing a multidisciplinary workforce that can collaborate effectively in the learning health systems. Maximizing the synergy among multiple teams is critical for Collaborative AI in Healthcare. Methods We have developed a series of data, tools, and educational resources for cultivating the next generation of multidisciplinary workforce for Collaborative AI in Healthcare. We built bulk‐natural language processing pipelines to extract structured information from clinical notes and stored them in common data models. We developed multimodal AI/machine learning (ML) tools and tutorials to enrich the toolbox of the multidisciplinary workforce to analyze multimodal healthcare data. We have created a fertile ground to cross‐pollinate clinicians and AI scientists and train the next generation of AI health workforce to collaborate effectively. Results Our work has democratized access to unstructured health information, AI/ML tools and resources for healthcare, and collaborative education resources. From 2017 to 2022, this has enabled studies in multiple clinical specialties resulting in 68 peer‐reviewed publications. In 2022, our cross‐discipline efforts converged and institutionalized into the Center for Collaborative AI in Healthcare. Conclusions Our Collaborative AI in Healthcare initiatives has created valuable educational and practical resources. They have enabled more clinicians, scientists, and hospital administrators to successfully apply AI methods in their daily research and practice, develop closer collaborations, and advanced the institution‐level learning health system.

Published
2024
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3. Natural language processing to identify lupus nephritis phenotype in electronic health records

Author

Yu Deng, Jennifer A. Pacheco, Anika Ghosh, Anh Chung, Chengsheng Mao, Joshua C. Smith, Juan Zhao, Wei-Qi Wei, April Barnado, Chad Dorn, Chunhua Weng, Cong Liu, Adam Cordon, Jingzhi Yu, Yacob Tedla, Abel Kho, Rosalind Ramsey-Goldman, Theresa Walunas, and Yuan Luo

Subjects
Natural language processing, Electronic health records, Computational phenotyping, Lupus nephritis, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data from the Northwestern Medicine Enterprise Data Warehouse (NMEDW). Methods We developed five algorithms: a rule-based algorithm using only structured data (baseline algorithm) and four algorithms using different NLP models. The first NLP model applied simple regular expression for keywords search combined with structured data. The other three NLP models were based on regularized logistic regression and used different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components (i.e. a curated list of CUIs, regular expression concepts, structured data) respectively. The baseline algorithm and the best performing NLP algorithm were externally validated on a dataset from Vanderbilt University Medical Center (VUMC). Results Our best performing NLP model incorporated features from both structured data, regular expression concepts, and mapped concept unique identifiers (CUIs) and showed improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.52 vs 0.93) datasets compared to the baseline lupus nephritis algorithm. Conclusion Our NLP MetaMap mixed model improved the F-measure greatly compared to the structured data only algorithm in both internal and external validation datasets. The NLP algorithms can serve as powerful tools to accurately identify lupus nephritis phenotype in EHR for clinical research and better targeted therapies.

Published
2024
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7. Identifying Contextual Factors and Strategies for Practice Facilitation in Primary Care Quality Improvement Using an Informatics-Driven Model: Framework Development and Mixed Methods Case Study

Author

Jiancheng Ye, Donna Woods, Jennifer Bannon, Lucy Bilaver, Gayle Kricke, Megan McHugh, Abel Kho, and Theresa Walunas

Subjects
Medical technology, R855-855.5
Abstract

BackgroundThe past decade has seen increasing opportunities and efforts to integrate quality improvement into health care. Practice facilitation is a proven strategy to support redesign and improvement in primary care practices that focuses on building organizational capacity for continuous improvement. Practice leadership, staff, and practice facilitators all play important roles in supporting quality improvement in primary care. However, little is known about their perspectives on the context, enablers, barriers, and strategies that impact quality improvement initiatives. ObjectiveThis study aimed to develop a framework to enable assessment of contextual factors, challenges, and strategies that impact practice facilitation, clinical measure performance, and the implementation of quality improvement interventions. We also illustrated the application of the framework using a real-world case study. MethodsWe developed the TITO (task, individual, technology, and organization) framework by conducting participatory stakeholder workshops and incorporating their perspectives to identify enablers and barriers to quality improvement and practice facilitation. We conducted a case study using a mixed methods approach to demonstrate the use of the framework and describe practice facilitation and factors that impact quality improvement in a primary care practice that participated in the Healthy Hearts in the Heartland study. ResultsThe proposed framework was used to organize and analyze different stakeholders’ perspectives and key factors based on framework domains. The case study showed that practice leaders, staff, and practice facilitators all influenced the success of the quality improvement program. However, these participants faced different challenges and used different strategies. The framework showed that barriers stemmed from patients’ social determinants of health, a lack of staff and time, and unsystematic facilitation resources, while enablers included practice culture, staff buy-in, implementation of effective practice facilitation strategies, practice capacity for change, and shared complementary resources from similar, ongoing programs. ConclusionsOur framework provided a useful and generalizable structure to guide and support assessment of future practice facilitation projects, quality improvement initiatives, and health care intervention implementation studies. The practice leader, staff, and practice facilitator all saw value in the quality improvement program and practice facilitation. Practice facilitators are key liaisons to help the quality improvement program; they help all stakeholders work toward a shared target and leverage tailored strategies. Taking advantage of resources from competing, yet complementary, programs as additional support may accelerate the effective achievement of quality improvement goals. Practice facilitation–supported quality improvement programs may be opportunities to assist primary care practices in achieving improved quality of care through focused and targeted efforts. The case study demonstrated how our framework can support a better understanding of contextual factors for practice facilitation, which could enable well-prepared and more successful quality improvement programs for primary care practices. Combining implementation science and informatics thinking, our TITO framework may facilitate interdisciplinary research in both fields.

Published
2022
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9. Identification of Open Reading Frames Unique to a Select Agent: Ralstonia solanacearum Race 3 Biovar 2

Author

Dean W. Gabriel, Caitilyn Allen, Mark Schell, Timothy P. Denny, Jean T. Greenberg, Yong Ping Duan, Zomary Flores-Cruz, Qi Huang, Jennifer M. Clifford, Gernot Presting, Enid T. González, Joseph Reddy, John Elphinstone, Jill Swanson, Jian Yao, Vincent Mulholland, Li Liu, William Farmerie, Manjeera Patnaikuni, Botond Balogh, David Norman, Anne Alvarez, Jose A. Castillo, Jeffrey Jones, Gerry Saddler, Theresa Walunas, Aleksey Zhukov, and Natalia Mikhailova

Subjects
bacterial wilt, comparative genomics, Microbiology, QR1-502, Botany, QK1-989
Abstract

An 8× draft genome was obtained and annotated for Ralstonia solanacearum race 3 biovar 2 (R3B2) strain UW551, a United States Department of Agriculture Select Agent isolated from geranium. The draft UW551 genome consisted of 80,169 reads resulting in 582 contigs containing 5,925,491 base pairs, with an average 64.5% GC content. Annotation revealed a predicted 4,454 protein coding open reading frames (ORFs), 43 tRNAs, and 5 rRNAs; 2,793 (or 62%) of the ORFs had a functional assignment. The UW551 genome was compared with the published genome of R. solanacearum race 1 biovar 3 tropical tomato strain GMI1000. The two phylogenetically distinct strains were at least 71% syntenic in gene organization. Most genes encoding known pathogenicity determinants, including predicted type III secreted effectors, appeared to be common to both strains. A total of 402 unique UW551 ORFs were identified, none of which had a best hit or >45% amino acid sequence identity with any R. solanacearum predicted protein; 16 had strong (E < 10-13) best hits to ORFs found in other bacterial plant pathogens. Many of the 402 unique genes were clustered, including 5 found in the hrp region and 38 contiguous, potential prophage genes. Conservation of some UW551 unique genes among R3B2 strains was examined by polymerase chain reaction among a group of 58 strains from different races and biovars, resulting in the identification of genes that may be potentially useful for diagnostic detection and identification of R3B2 strains. One 22-kb region that appears to be present in GMI1000 as a result of horizontal gene transfer is absent from UW551 and encodes enzymes that likely are essential for utilization of the three sugar alcohols that distinguish biovars 3 and 4 from biovars 1 and 2.

Published
2006
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13. A metadata framework for computational phenotypes

Author

Matthew Spotnitz, Nripendra Acharya, James J Cimino, Shawn Murphy, Bahram Namjou, Nancy Crimmins, Theresa Walunas, Cong Liu, David Crosslin, Barbara Benoit, Elisabeth Rosenthal, Jennifer A Pacheco, Anna Ostropolets, Harry Reyes Nieva, Jason S Patterson, Lauren R Richter, Tiffany J Callahan, Ahmed Elhussein, Chao Pang, Krzysztof Kiryluk, Jordan Nestor, Atlas Khan, Sumit Mohan, Evan Minty, Wendy Chung, Wei-Qi Wei, Karthik Natarajan, and Chunhua Weng

Subjects
Health Informatics
Abstract

With the burgeoning development of computational phenotypes, it is increasingly difficult to identify the right phenotype for the right tasks. This study uses a mixed-methods approach to develop and evaluate a novel metadata framework for retrieval of and reusing computational phenotypes. Twenty active phenotyping researchers from 2 large research networks, Electronic Medical Records and Genomics and Observational Health Data Sciences and Informatics, were recruited to suggest metadata elements. Once consensus was reached on 39 metadata elements, 47 new researchers were surveyed to evaluate the utility of the metadata framework. The survey consisted of 5-Likert multiple-choice questions and open-ended questions. Two more researchers were asked to use the metadata framework to annotate 8 type-2 diabetes mellitus phenotypes. More than 90% of the survey respondents rated metadata elements regarding phenotype definition and validation methods and metrics positively with a score of 4 or 5. Both researchers completed annotation of each phenotype within 60 min. Our thematic analysis of the narrative feedback indicates that the metadata framework was effective in capturing rich and explicit descriptions and enabling the search for phenotypes, compliance with data standards, and comprehensive validation metrics. Current limitations were its complexity for data collection and the entailed human costs.

Published
2023
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15. Neptune: an environment for the delivery of genomic medicine

Author

Venner Eric, Victoria Yi, David Murdock, Sara E. Kalla, Tsung-Jung Wu, Aniko Sabo, Shoudong Li, Qingchang Meng, Xia Tian, Mullai Murugan, Michelle Cohen, Christie Kovar, Wei-Qi Wei, Wendy K. Chung, Chunhua Weng, Georgia L. Wiesner, Gail P. Jarvik, Donna Muzny, Richard A. Gibbs, Debra Abrams, Samuel E. Adunyah, Ladia Albertson-Junkans, Berta Almoguera, Darren C. Ames, Paul Appelbaum, Samuel Aronson, Sharon Aufox, Lawrence J. Babb, Adithya Balasubramanian, Hana Bangash, Melissa Basford, Lisa Bastarache, Samantha Baxter, Meckenzie Behr, Barbara Benoit, Elizabeth Bhoj, Suzette J. Bielinski, Sarah T. Bland, Carrie Blout, Kenneth Borthwick, Erwin P. Bottinger, Mark Bowser, Harrison Brand, Murray Brilliant, Wendy Brodeur, Pedro Caraballo, David Carrell, Andrew Carroll, Lisa Castillo, Victor Castro, Gauthami Chandanavelli, Theodore Chiang, Rex L. Chisholm, Kurt D. Christensen, Wendy Chung, Christopher G. Chute, Brittany City, Beth L. Cobb, John J. Connolly, Paul Crane, Katherine Crew, David R. Crosslin, Jyoti Dayal, Mariza De Andrade, Jessica De la Cruz, Josh C. Denny, Shawn Denson, Tim DeSmet, Ozan Dikilitas, Michael J. Dinsmore, Sheila Dodge, Phil Dunlea, Todd L. Edwards, Christine M. Eng, David Fasel, Alex Fedotov, Qiping Feng, Mark Fleharty, Andrea Foster, Robert Freimuth, Christopher Friedrich, Stephanie M. Fullerton, Birgit Funke, Stacey Gabriel, Vivian Gainer, Ali Gharavi, Andrew M. Glazer, Joseph T. Glessner, Jessica Goehringer, Adam S. Gordon, Chet Graham, Robert C. Green, Justin H. Gundelach, Heather S. Hain, Hakon Hakonarson, Maegan V. Harden, John Harley, Margaret Harr, Andrea Hartzler, M. Geoffrey Hayes, Scott Hebbring, Nora Henrikson, Andrew Hershey, Christin Hoell, Ingrid Holm, Kayla M. Howell, George Hripcsak, Jianhong Hu, Elizabeth Duffy Hynes, Joy C. Jayaseelan, Yunyun Jiang, Yoonjung Yoonie Joo, Sheethal Jose, Navya Shilpa Josyula, Anne E. Justice, Divya Kalra, Elizabeth W. Karlson, Brendan J. Keating, Melissa A. Kelly, Eimear E. Kenny, Dustin Key, Krzysztof Kiryluk, Terrie Kitchner, Barbara Klanderman, Eric Klee, David C. Kochan, Viktoriya Korchina, Leah Kottyan, Emily Kudalkar, Alanna Kulchak Rahm, Iftikhar J. Kullo, Philip Lammers, Eric B. Larson, Matthew S. Lebo, Magalie Leduc, Ming Ta (Michael) Lee, Niall J. Lennon, Kathleen A. Leppig, Nancy D. Leslie, Rongling Li, Wayne H. Liang, Chiao-Feng Lin, Jodell E. Linder, Noralane M. Lindor, Todd Lingren, James G. Linneman, Cong Liu, Wen Liu, Xiuping Liu, John Lynch, Hayley Lyon, Alyssa Macbeth, Harshad Mahadeshwar, Lisa Mahanta, Bradley Malin, Teri Manolio, Maddalena Marasa, Keith Marsolo, Michelle L. McGowan, Elizabeth McNally, Jim Meldrim, Frank Mentch, Hila Milo Rasouly, Jonathan Mosley, Shubhabrata Mukherjee, Thomas E. Mullen, Jesse Muniz, David R. Murdock, Shawn Murphy, Melanie F. Myers, Bahram Namjou, Yizhao Ni, Robert C. Onofrio, Aniwaa Owusu Obeng, Thomas N. Person, Josh F. Peterson, Lynn Petukhova, Cassandra J. Pisieczko, Siddharth Pratap, Cynthia A. Prows, Megan J. Puckelwartz, Ritika Raj, James D. Ralston, Arvind Ramaprasan, Andrea Ramirez, Luke Rasmussen, Laura Rasmussen-Torvik, Soumya Raychaudhuri, Heidi L. Rehm, Marylyn D. Ritchie, Catherine Rives, Beenish Riza, Dan M. Roden, Elisabeth A. Rosenthal, Avni Santani, Schaid Dan, Steven Scherer, Stuart Scott, Aaron Scrol, Soumitra Sengupta, Ning Shang, Himanshu Sharma, Richard R. Sharp, Rajbir Singh, Patrick M.A. Sleiman, Kara Slowik, Joshua C. Smith, Maureen E. Smith, Duane T. Smoot, Jordan W. Smoller, Sunghwan Sohn, Ian B. Stanaway, Justin Starren, Mary Stroud, Jessica Su, Casey Overby Taylor, Kasia Tolwinski, Sara L. Van Driest, Sean M. Vargas, Matthew Varugheese, David Veenstra, Eric Venner, Miguel Verbitsky, Gina Vicente, Michael Wagner, Kimberly Walker, Theresa Walunas, Liwen Wang, Qiaoyan Wang, Scott T. Weiss, Quinn S. Wells, Peter S. White, Ken L. Wiley, Janet L. Williams, Marc S. Williams, Michael W. Wilson, Leora Witkowski, Laura Allison Woods, Betty Woolf, Julia Wynn, Yaping Yang, Ge Zhang, Lan Zhang, and Hana Zouk

Subjects
Computer science, business.industry, Process (engineering), MEDLINE, High-Throughput Nucleotide Sequencing, Genomics, Data science, Article, Personalization, Variety (cybernetics), Workflow, Neptune, Pharmacogenomics, Health care, Electronic Health Records, Humans, business, Software, Genetics (clinical)
Abstract

Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .

Published
2021
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18. Returning integrated genomic risk and clinical recommendations: the eMERGE study

Author

Jodell E. Linder, Aimee Allworth, Sarah T. Bland, Pedro J. Caraballo, Rex L. Chisholm, Ellen Wright Clayton, David R. Crosslin, Ozan Dikilitas, Alanna DiVietro, Edward D. Esplin, Sophie Forman, Robert R. Freimuth, Adam S. Gordon, Richard Green, Maegan V. Harden, Ingrid A. Holm, Gail P. Jarvik, Elizabeth W. Karlson, Sofia Labrecque, Niall J. Lennon, Nita A. Limdi, Kathleen F. Mittendorf, Shawn N. Murphy, Lori Orlando, Cynthia A. Prows, Luke V. Rasmussen, Laura Rasmussen-Torvik, Robb Rowley, Konrad Teodor Sawicki, Tara Schmidlen, Shannon Terek, David Veenstra, Digna R. Velez Edwards, Devin Absher, Noura S. Abul-Husn, Jorge Alsip, Hana Bangash, Mark Beasley, Jennifer E. Below, Eta S. Berner, James Booth, Wendy K. Chung, James J. Cimino, John Connolly, Patrick Davis, Beth Devine, Stephanie M. Fullerton, Candace Guiducci, Melissa L. Habrat, Heather Hain, Hakon Hakonarson, Margaret Harr, Eden Haverfield, Valentina Hernandez, Christin Hoell, Martha Horike-Pyne, George Hripcsak, Marguerite R. Irvin, Christopher Kachulis, Dean Karavite, Eimear E. Kenny, Atlas Khan, Krzysztof Kiryluk, Bruce Korf, Leah Kottyan, Iftikhar J. Kullo, Katie Larkin, Cong Liu, Edyta Malolepsza, Teri A. Manolio, Thomas May, Elizabeth M. McNally, Frank Mentch, Alexandra Miller, Sean D. Mooney, Priyanka Murali, Brenda Mutai, Naveen Muthu, Bahram Namjou, Emma F. Perez, Megan J. Puckelwartz, Tejinder Rakhra-Burris, Dan M. Roden, Elisabeth A. Rosenthal, Seyedmohammad Saadatagah, Maya Sabatello, Dan J. Schaid, Baergen Schultz, Lynn Seabolt, Gabriel Q. Shaibi, Richard R. Sharp, Brian Shirts, Maureen E. Smith, Jordan W. Smoller, Rene Sterling, Sabrina A. Suckiel, Jeritt Thayer, Hemant K. Tiwari, Susan B. Trinidad, Theresa Walunas, Wei-Qi Wei, Quinn S. Wells, Chunhua Weng, Georgia L. Wiesner, Ken Wiley, Josh F. Peterson, Adam Gordon, Agboade Sobowale, Akshar Patel, Alanna Strong, Alborz Sherafati, Alborz Sherfati, Alex Bick, Alka Chandel, Alyssa Rosenthal, Amit Khera, Amy Kontorovich, Andrew Beck, Andy Beck, Angelica Espinoza, Anna Lewis, Anya Prince, Ayuko Iverson, Bahram Namjou Khales, Barbara Benoit, Becca Hernan, Ben Kallman, Ben Kerman, Ben Shoemaker, Benjamin Satterfield, Bethany Etheridge, Blake Goff, Bob Freimuth, Bob Grundmeier, Brenae Collier, Brett Harnett, Brian Chang, Brian Piening, Brittney Davis, Candace Patterson, Carmen Demetriou, Casey Ta, Catherine Hammack, Catrina Nelson, Caytie Gascoigne, Chad Dorn, Chad Moretz, Chris Kachulis, Christie Hoell, Christine Cowles, Christoph Lange, Cindy Prows, Cole Brokamp, Courtney Scherr, Crystal Gonzalez, Cynthia Ramirez, Daichi Shimbo, Dan Roden, Daniel Schaid, Dave Kaufman, David Crosslin, David Kochan, Davinder Singh, Debbie Abrams, Digna Velez Edwards, Eduardo Morales, Edward Esplin, Ehsan Alipour, Eimear Kenny, Elisabeth Rosenthal, Eliza Duvall, Elizabeth McNally, Elizabeth Bhoj, Elizabeth Cohn, Elizabeth Hibler, Elizabeth Karlson, Ellen Clayton, Emily Chesnut, Emily DeFranco, Emily Gallagher, Emily Soper, Emma Perez, Erin Cash, Eta Berner, Fei Wang, Firas Wehbe, Francisco Ricci, Gabriel Shaibi, Gail Jarvik, George Hahn, Georgia Wiesner, Gillian Belbin, Gio Davogustto, Girish Nadkarni, Haijun Qiu, Hannah Beasley, Hao Liu, Heide Aungst, Hemant Tiwari, Hillary Duckham, Hope Thomas, Iftikhar Kullo, Ingrid Holm, Isabelle Allen, Iuliana Ionita-Laza, Jacklyn Hellwege, Jacob Petrzelka, Jacqueline Odgis, Jahnavi Narula, Jake Petrzelka, Jalpa Patel, James Cimino, James Meigs, James Snyder, Janet Olson, Janet Zahner, Jeff Pennington, Jen Pacheco, Jennifer Allen Pacheco, Jennifer Morse, Jeremy Corsmo, Jim Cimino, Jingheng Chen, Jocelyn Fournier, Jodell Jackson, Joe Glessner, Joel Pacyna, Johanna Smith, John Lynch, John Shelley, Jonathan Mosley, Jordan Nestor, Jordan Smoller, Joseph Kannry, Joseph Sutton, Josh Peterson, Joshua Smith, Julia Galasso, Julia Smith, Julia Wynn, Justin Gundelach, Justin Starren, Karmel Choi, Kate Mittendorf, Katherine Anderson, Katherine Bonini, Kathleen Leppig, Kathleen Muenzen, Kelsey Stuttgen, Kenny Nguyen, Kevin Dufendach, Kiley Atkins, Konrad Sawicki, Kristjan Norland, Laura Beskow, Li Hsu, Lifeng Tian, Lisa Mahanta, Lisa Martin, Lisa Wang, Lizbeth Gomez, Lorenzo Thompson, Lucas Richter, Luke Rasmussen, Lynn Petukhova, Madison O’Brien, Maegan Harden, Malia Fullerton, Marta Guindo, Martha Horike, Marwah Abdalla, Marwan Hamed, Mary Beth Terry, Mary Maradik, Matt Wyatt, Matthew Davis, Matthew Lebo, Maureen Smith, Maya del Rosario, Meckenzie Behr, Meg Roy-Puckelwartz, Mel Habrat, Melanie Myers, Meliha Yetisgen, Merve Iris, Michael DaSilva, Michael Preuss, Michelle McGowan, Mingjian Shi, Minoli Perera, Minta Thomas, Mitch Elkind, Mohammad Abbass, Mohammad Saadatagah, Molly Hess, Molly Maradik, Nataraja 'RJ' Vaitinadin, Nataraja Vaitinadin, Neil Netherly, Niall Lennon, Ning Shang, Nita Limdi, Noah Forrest, Noheli Romero, Nora Robinson, Noura Abul-Husn, Omar Elsekaily, Patricia Kovatch, Paul Appelbaum, Paul Francaviglia, Paul O’Reilly, Paulette Chandler, Pedro Caraballo, Peter Tarczy-Hornoch, Pierre Shum, Priya Marathe, Qiping Feng, Quinn Wells, Rachel Atchley, Radhika Narla, Rene Barton, Rex Chisholm, Richard Sharp, Riki Peters, Rita Kukafka, Robert Freimuth, Robert Green, Robert Winter, Roger Mueller, Ruth Loos, Ryan Irvin, Sabrina Suckiel, Sajjad Hussain, Samer Sharba, Sandy Aronson, Sarah Jones, Sarah Knerr, Scott Nigbur, Scott Weiss, Sean Mooney, Sharon Aufox, Sharon Nirenberg, Shawn Murphy, Sheila O’Byrne, Shing Wang (Sam) Choi, Sienna Aguilar, S.T. Bland, Stefanie Rodrigues, Stephanie Ledbetter, Stephanie Rutledge, Stuart James Booth, Su Xian, Susan Brown Trinidad, Suzanne Bakken, Teri Manolio, Tesfaye Mersha, Thevaa Chandereng, Tian Ge, Todd Edwards, Tom Kaszemacher, Valerie Willis, Vemi Desai, Vimi Desai, Virginia Lorenzi, Vivian Gainer, Wendy Chung, Wu-Chen Su, Xiao Chang, Yiqing Zhao, Yuan Luo, and Yufeng Shen

Subjects
Genetics (clinical)
Abstract

Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk.To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores (PRS), monogenic risks, family history, and clinical risk assessments via a Genome Informed Risk Assessment (GIRA) report and will assess uptake of care recommendations after return of results.GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022.Return of a novel report for communicating monogenic, polygenic, and family history based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.

Published
2022

21. The ERGOTM genome analysis and discovery system.

Author

Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, and Nikos Kyrpides

Published
2003
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22. Identifying Contextual Factors and Strategies for Practice Facilitation in Primary Care Quality Improvement Using an Informatics-Driven Model: Framework Development and Mixed Methods Case Study (Preprint)

Author

Jiancheng Ye, Donna Woods, Jennifer Bannon, Lucy Bilaver, Gayle Kricke, Megan McHugh, Abel Kho, and Theresa Walunas

Abstract

BACKGROUND The past decade has seen increasing opportunities and efforts to integrate quality improvement into health care. Practice facilitation is a proven strategy to support redesign and improvement in primary care practices that focuses on building organizational capacity for continuous improvement. Practice leadership, staff, and practice facilitators all play important roles in supporting quality improvement in primary care. However, little is known about their perspectives on the context, enablers, barriers, and strategies that impact quality improvement initiatives. OBJECTIVE This study aimed to develop a framework to enable assessment of contextual factors, challenges, and strategies that impact practice facilitation, clinical measure performance, and the implementation of quality improvement interventions. We also illustrated the application of the framework using a real-world case study. METHODS We developed the TITO (task, individual, technology, and organization) framework by conducting participatory stakeholder workshops and incorporating their perspectives to identify enablers and barriers to quality improvement and practice facilitation. We conducted a case study using a mixed methods approach to demonstrate the use of the framework and describe practice facilitation and factors that impact quality improvement in a primary care practice that participated in the Healthy Hearts in the Heartland study. RESULTS The proposed framework was used to organize and analyze different stakeholders’ perspectives and key factors based on framework domains. The case study showed that practice leaders, staff, and practice facilitators all influenced the success of the quality improvement program. However, these participants faced different challenges and used different strategies. The framework showed that barriers stemmed from patients’ social determinants of health, a lack of staff and time, and unsystematic facilitation resources, while enablers included practice culture, staff buy-in, implementation of effective practice facilitation strategies, practice capacity for change, and shared complementary resources from similar, ongoing programs. CONCLUSIONS Our framework provided a useful and generalizable structure to guide and support assessment of future practice facilitation projects, quality improvement initiatives, and health care intervention implementation studies. The practice leader, staff, and practice facilitator all saw value in the quality improvement program and practice facilitation. Practice facilitators are key liaisons to help the quality improvement program; they help all stakeholders work toward a shared target and leverage tailored strategies. Taking advantage of resources from competing, yet complementary, programs as additional support may accelerate the effective achievement of quality improvement goals. Practice facilitation–supported quality improvement programs may be opportunities to assist primary care practices in achieving improved quality of care through focused and targeted efforts. The case study demonstrated how our framework can support a better understanding of contextual factors for practice facilitation, which could enable well-prepared and more successful quality improvement programs for primary care practices. Combining implementation science and informatics thinking, our TITO framework may facilitate interdisciplinary research in both fields.

Published
2021
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23. Regulation of CTLA-4 expression during T cell activation

Author

Perkins, D., Wang, Z., Donovan, C., He, H., Mark, D., Guan, G., Wang, Y., Theresa Walunas, Bluestone, J., Listman, J., and Finn, P. W.

Subjects
Immunology, Immunology and Allergy
Abstract

T cell activation requires at least two distinct signals, including signaling via the Ag-specific TCR and a costimulatory pathway. The best characterized costimulatory pathway involves the CD28 molecule, which is expressed constitutively on T cells and binds the family of B7 counter-receptors on APCs. Inhibition of this costimulatory pathway prevents T cell activation and can lead to long-term T cell unresponsiveness or anergy. In contrast, CTLA4, which is homologous to CD28, has been shown to be a negative regulator of T cell activation. The CTLA4 molecule is not expressed on resting T cells, but is induced after the initial steps of T cell activation. To address the regulation of CTLA4 expression, we have analyzed CTLA4 at the level of cell surface expression, mRNA, rate of transcription, and rate of decay of message. Nuclear runoff results show an increase in the rate of transcription following T cell activation. Our analyses of non-T cells, including B cells, mastocytoma, and fibroblasts, by Northern blot analysis detect only T cell expression of CTLA4. Reporter gene analysis indicates that 335 bp of upstream CTLA4 sequence are sufficient to control inducibility. We have identified important regulatory regions that control inducible and cell-specific CTLA4 expression. These results also suggest that both positive and negative response elements modulate the transcriptional regulation of CTLA4 gene expression. Understanding the regulation of CTLA4 should provide insight into the regulation of T cell activation at the molecular level.

Published
1996
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24. CD28 expression is not essential for positive and negative selection of thymocytes or peripheral T cell tolerance

Author

Theresa Walunas, Sperling, A. I., Khattri, R., Thompson, C. B., and Bluestone, J. A.

Subjects
Immunology, Immunology and Allergy
Abstract

Thymocyte development requires positive selection of clones that can recognize Ag presented by MHC molecules and negative selection of clones that are self-reactive. However, the costimulatory signals required for negative selection and cell death, or positive selection and the transition to the peripheral lymphoid system, are not well understood. Many molecular interactions that are important for T cell activation have also been found to play a role in thymocyte development. The importance of the CD28/B7 interaction in the activation of mature T cells and recent observations that CD28 may play a role negative selection of developing CD4+CD8+ thymocytes suggest that CD28 may also be involved in development and maintenance of T cell tolerance. CD28-deficient mice were crossed to alpha beta and gamma delta TCR transgenic as well as H-2k Mlsc-bearing animals and were used to address the role of CD28 in positive and negative selection of developing T cells. The CD28-deficient animals demonstrated no obvious deficiency in either positive or negative selection of developing thymocytes. However, when mixed bone marrow chimeras were created with cells derived from both CD28-deficient and wild-type mice, the CD28+ T cells had a selective advantage over the CD28-deficient T cells. Therefore, it appears that CD28, although not essential for the selection of T cells during development, may allow for additional signals that increase the efficiency of selection and/or expansion of peripheral T cell populations.

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