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1. 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

2. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system

Author

Batsal Devkota, Michal Kouril, Joseph W. St. Geme, Alba Gutierrez, Simone Temporal, Keith Marsolo, Peter White, Joseph A. Majzoub, Alan Yen, Jaspreet Khanna, Julie Wijesooriya, Mike Furgason, Florence T. Bourgeois, Christopher Geehan, Adda Grimberg, Arnold W. Strauss, Becca Harper, Kristen Safier, Aleksandr Nikitin, Andrew Wooten, Vidhu V Thaker, Deanne Taylor, Ingo Helbig, Darlene Barkman, Anil Kumar Degala, Gelvina Stevenson, Eric D. Marsh, Colin P. Hawkes, Andrew Dauber, Jason Stedman, In-Hee Lee, Andrew M. Rupert, Gary R. Fleisher, Ramkrishna Chakrabarty, Piotr Sliz, Alyssa Ellis, Barbara Hallinan, Kenneth D. Mandl, Susan Kornetsky, Bryan A. Wolf, Philip Dexheimer, Alan H. Beggs, Yu Zhang, Erin M. Borglund, Joel N. Hirschhorn, Andrew Joseph Guidetti, Amy Schwarzhoff, Anna Poduri, Gabor Korodi, Louis J. Muglia, Prakash Velayutham, Christopher P. Kirby, Mike Pistone, Allison Heath, Parth Divekar, Judson Kilbourn, Ranjay Kumar, Guillaume Labilloy, Alka Chandel, Ian D. Krantz, Thomas N DeSain, Kristen L. Sund, Lisa J. Martin, James Morgan, Jeremy Nix, Sawona Biswas, Tracy A. Glauser, Paul Avillach, Sek Won Kong, Niloofar Jalali, Jeremy J. Corsmo, Anna Bartels, Amy Kratchman, and Bria Morgan

Subjects
0301 basic medicine, education.field_of_study, Computer science, business.industry, Interoperability, Population, Information technology, Genomics, 030105 genetics & heredity, Institutional review board, Biobank, Data science, Article, 03 medical and health sciences, genomic medicine, electronic health records, biobanking, 030104 developmental biology, Open source, information technology, education, business, Genetics (clinical), Material transfer, federated networks
Abstract

Purpose Clinicians and researchers must contextualize a patient’s genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. Methods Three of the nation’s leading children’s hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. Results Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype–phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. Conclusions The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

Published
2020

3. Correction: The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system

Author

Kenneth D. Mandl, Tracy Glauser, Ian D. Krantz, Paul Avillach, Anna Bartels, Alan H. Beggs, Sawona Biswas, Florence T. Bourgeois, Jeremy Corsmo, Andrew Dauber, Batsal Devkota, Gary R. Fleisher, Allison P. Heath, Ingo Helbig, Joel N. Hirschhorn, Judson Kilbourn, Sek Won Kong, Susan Kornetsky, Joseph A. Majzoub, Keith Marsolo, Lisa J. Martin, Jeremy Nix, Amy Schwarzhoff, Jason Stedman, Arnold Strauss, Kristen L. Sund, Deanne M. Taylor, Peter S. White, Eric Marsh, Adda Grimberg, Colin Hawkes, Darlene Barkman, Erin M. Borglund, Ramkrishna Chakrabarty, Alka Chandel, Anil Kumar Degala, Thomas DeSain, Philip Dexheimer, Parth Divekar, Alyssa Ellis, Mike Furgason, Christopher Geehan, Andrew Joseph Guidetti, Alba Gutierrez, Barbara Hallinan, Becca Harper, Niloofar Jalali, Jaspreet Khanna, Christopher Kirby, Gabor Korodi, Michal Kouril, Amy Kratchman, Ranjay Kumar, Guillaume Labilloy, In-Hee Lee, Bria Morgan, James Morgan, Louis J Muglia, Aleksandr Nikitin, Mike Pistone, Anna Poduri, Andrew Rupert, Kristen Safier, Piotr Sliz, Gelvina Stevenson, Joseph St. Geme, Vidhu Thaker, Simone Temporal, Prakash Velayutham, Julie Wijesooriya, Bryan Wolf, Andrew Wooten, Alan Yen, and Yu Zhang

Subjects
Electronic Data Processing, Biomedical Research, Databases, Factual, Information Dissemination, Correction, Information Storage and Retrieval, Genomics, Research Personnel, Databases, Genetic, Humans, Genetics (clinical), Biological Specimen Banks, Data Management, Ethics Committees, Research
Abstract

Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model.Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications.The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

Published
2020

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