2024
- Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
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Sarah L. Stenton, Melanie C. O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W. Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O. B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G. Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M. Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-LuriaHuman Genomics, 2024. https://doi.org/10.1186/s40246-024-00604-w
- Pharmacogenomics for Prader-Willi syndrome: caregiver interest and planned utilization
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Yael Bar-Peled, Jessica J Denton, Jaimie L Richards, Donna Brown, Elizabeth Worthey, Theresa V StrongPharmacogenomics, 2024. https://doi.org/10.2217/pgs-2023-0189
- Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder
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Jennefer N. Kohler, Nicole R. Legro, Dustin Baldridge, Jimann Shin, Angela Bowman, Berrak Ugur, Madelyn M. Jackstadt, Leah P. Shriver, Gary J. Patti, Bo Zhang, Wenjia Feng, Anthony R. McAdow, Pagé Goddard, Rachel A. Ungar, Tanner Jensen, Kevin S. Smith, Laure Fresard, Raquel Alvarez, Devon Bonner, Chloe M. Reuter, Colleen McCormack, Elijah Kravets, Shruti Marwaha, James M. Holt, Undiagnosed Diseases Network, Elizabeth A. Worthey, Euan A. Ashley, Stephen B. Montgomery, Paul G. Fisher, John Postlethwait, Pietro De Camilli, Lila Solnica-Krezel, Jonathan A. Bernstein, Matthew T. WheelerGenetics in Medicine, 2024. https://doi.org/10.1016/j.gim.2024.101166
- Vitamin D status and variable responses to supplements depend in part on genetic factors in adults with cystic fibrosis
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Andrew T. Braun, HuiChuan J. Lai, Anita Laxova, Julie A. Biller, Erin K. Hubertz, Zijie Zhao, Qiongshi Lu, Sangita Murali, Donna M. Brown, Elizabeth A. Worthey, Philip M. FarrellJournal of Cystic Fibrosis, 2024. https://doi.org/10.1016/j.jcf.2024.02.005
- Molecular Characterization of Juxtaglomerular Cell Tumors: Evidence of Alterations in MAPK–RAS Pathway
-
João Lobo, Sofia Canete-Portillo, Maria Del Carmen Rodriguez Pena, Jesse K. McKenney, Manju Aron, Felipe Massicano, Brandon M. Wilk, Manavalan Gajapathy, Donna M. Brown, Dilek E. Baydar, Andres Matoso, Nathalie Rioux-Leclerq, Chin-Chen Pan, Maria S. Tretiakova, Kiril Trpkov, Sean R. Williamson, Soroush Rais-Bahrami, Alexander C. Mackinnon, Shuko Harada, Elizabeth A. Worthey, Cristina Magi-GalluzziModern Pathology, 2024. https://doi.org/10.1016/j.modpat.2024.100492
2023
- Ten simple rules for using public biological data for your research
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Vishal H. Oza, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina Uno-Antonison, Brandon Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, Brittany N. LasseignePLOS Computational Biology, 2023. https://doi.org/10.1371/journal.pcbi.1010749
- QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data
-
Manavalan Gajapathy, Brandon M Wilk, Elizabeth A WortheyJournal of Open Source Software, 2023. https://doi.org/10.21105/joss.05313
- Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project
-
Sarah L. Stenton, Melanie O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O.B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-LuriamedRxiv, 2023. https://doi.org/10.1101/2023.08.02.23293212
- Rosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling
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Angelina E Uno-Antonison, Rabab Fatima, James Scherer, Alexander Moss, Donna Brown, Aleksandra Foksinska, Manavalan Gajapathy, Elizabeth J Wilk, Brittany N Lasseigne, Elizabeth WortheyJournal of Open Source Software, 2023. https://doi.org/10.21105/joss.05443
- Impact of intrinsic and extrinsic risk factors on early‐onset lung disease in cystic fibrosis
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Leslie Huang, HuiChuan J. Lai, Jie Song, Zijie Zhao, Qiongshi Lu, Sangita G. Murali, Donna M. Brown, Elizabeth A. Worthey, Philip M. FarrellPediatric Pulmonology, 2023. https://doi.org/10.1002/ppul.26625
- Development of adaptive anoikis resistance promotes metastasis that can be overcome by CDK8/19 Mediator kinase inhibition
-
Mehri Monavarian, Emily Faith Page, Resha Rajkarnikar, Asha Kumari, Liz Quintero Macias, Felipe Massicano, Nam Y Lee, Sarthak Sahoo, Nadine Hempel, Mohit Kumar Jolly, Lara Ianov, Elizabeth Worthey, Abhyudai Singh, Eugenia V Broude, Karthikeyan MythreyebioRxiv, 2023. https://doi.org/10.1101/2023.12.04.569970
- PCa-Clf: A Classifier of Prostate Cancer Patients into Patients with Indolent and Aggressive Tumors Using Machine Learning
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Yashwanth Karthik Kumar Mamidi, Tarun Karthik Kumar Mamidi, Md Wasi Ul Kabir, Jiande Wu, Md Tamjidul Hoque, Chindo HicksMachine Learning and Knowledge Extraction, 2023. https://doi.org/10.3390/make5040066
2022
- Genetic factors help explain the variable responses of young children with cystic fibrosis to vitamin D supplements
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HuiChuan J. Lai, Jie Song, Qiongshi Lu, Sangita Murali, Manavlan Gajapathy, Brandon M. Wilk, Donna M. Brown, Elizabeth A. Worthey, Philip M. Farrell, the FIRST Study GroupClinical Nutrition ESPEN, 2022. https://doi.org/10.1016/j.clnesp.2022.07.018
- DOCKopathies: A systematic review of the clinical pathologies associated with human DOCK pathogenic variants
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Adrienne Samani, Katherine G. English, Michael A. Lopez, Camille L. Birch, Donna M. Brown, Gurpreet Kaur, Elizabeth A. Worthey, Matthew S. AlexanderHuman Mutation, 2022. https://doi.org/10.1002/humu.24398
2021
- Development of An Individualized Risk Prediction Model for COVID-19 Using Electronic Health Record Data
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Tarun Karthik Kumar Mamidi, Thi K. Tran-Nguyen, Ryan L. Melvin, Elizabeth A. WortheyFrontiers in Big Data, 2021. https://doi.org/10.3389/fdata.2021.675882
- One is the loneliest number: genotypic matchmaking using the electronic health record
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Elly Brokamp, Mary E. Koziura, John A. Phillips, Leigh Anne Tang, Joy D. Cogan, Lynette C. Rives, Amy K. Robertson, Laura Duncan, Anna Bican, Josh F. Peterson, John H. Newman, Rizwan Hamid, Lisa Bastarache, Undiagnosed Diseases Network, Mercedes E. Alejandro, Mahshid S. Azamian, Carlos A. Bacino, Ashok Balasubramanyam, Bret L. Bostwick, Lindsay C. Burrage, Hsiao-Tuan Chao, Gary D. Clark, William J. Craigen, Shweta U. Dhar, Lisa T. Emrick, Alica M. Goldman, Neil A. Hanchard, Fariha Jamal, Lefkothea Karaviti, Seema R. Lalani, Brendan H. Lee, Richard A. Lewis, Ronit Marom, Paolo M. Moretti, David R. Murdock, Sarah K. Nicholas, James P. Orengo, Jennifer E. Posey, Lorraine Potocki, Jill A. Rosenfeld, Susan L. Samson, Daryl A. Scott, Alyssa A. Tran, Tiphanie P. Vogel, Hugo J. Bellen, Michael F. Wangler, Shinya Yamamoto, Christine M. Eng, Pengfei Liu, Patricia A. Ward, David B. Goldstein, Nicholas Stong, Heidi Cope, Yong-hui Jiang, Allyn McConkie-Rosell, Kelly Schoch, Vandana Shashi, Rebecca C. Spillmann, Jennifer A. Sullivan, Queenie K.-G. Tan, Nicole M. Walley, Pankaj Agrawal, Alan H. Beggs, Gerard T. Berry, Lauren C. Briere, Cynthia M. Cooper, Laurel A. Cobban, Elizabeth L. Fieg, Frances High, Ingrid A. Holm, Susan Korrick, Joel B. Krier, Sharyn A. Lincoln, Joseph Loscalzo, Richard L. Maas, Calum A. MacRae, J. Carl Pallais, Lance H. Rodan, Edwin K. Silverman, Joan M. Stoler, David A. Sweetser, Melissa Walker, Chris A. Walsh, Cecilia Esteves, Emily G. Kelley, Isaac S. Kohane, Kimberly LeBlanc, Alexa T. McCray, Matthew Might, David P. Bick, Camille L. Birch, Braden E. Boone, Donna M. Brown, Daniel C. Dorset, Angela L. Jones, Jozef Lazar, Shawn E. Levy, Thomas May, J. Scott Newberry, Elizabeth A. Worthey, Ian R. Lanza, Devin Oglesbee, Eva Morava-Kozicz, Brendan C. Lanpher, Surendra Dasari, Guney Bademci, Deborah Barbouth, Stephanie Bivona, Olveen Carrasquillo, Ta Chen Peter Chang, Irman Forghani, Alana Grajewski, Rosario Isasi, Byron Lam, Roy Levitt, Xue Zhong Liu, Jacob McCauley, Ralph Sacco, Mario Saporta, Judy Schaechter, Mustafa Tekin, Fred Telischi, Willa Thorson, Stephan Zuchner, Gabriel F. Batzli, Heather A. Colley, Jyoti G. Dayal, David J. Eckstein, Donna M. Krasnewich, Laura A. Mamounas, Teri A. Manolio, John J. Mulvihill, Robb K. Rowley, Catherine H. Sillari, Cecelia P. Tamburro, Tiina K. Urv, Anastasia L. Wise, Maria T. Acosta, Carsten Bonnenmann, Elizabeth A. Burke, Precilla D’Souza, Mariska Davids, David D. Draper, Tyra Estwick, Carlos Ferreira, Rena A. Godfrey, Catherine A. Groden, Jean M. Johnston, C. Christopher Lau, Ellen F. Macnamara, Valerie V. Maduro, Thomas C. Markello, Marie Morimoto, Avi Nath, Donna Novacic, Barbara N. Pusey, Prashant Sharma, Camilo Toro, Colleen E. Wahl, Guoyun Yu, Andrea L. Gropman, Eva Baker, David R. Adams, William A. Gahl, May Christine V. Malicdan, Cynthia J. Tifft, Lynne A. Wolfe, John Yang, Matthew Brush, Jean-Philippe F. Gourdine, Melissa Haendel, David M. Koeller, Jennifer E. Kyle, Thomas O. Metz, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, Euan A. Ashley, Jonathan A. Bernstein, Devon Bonner, Terra R. Coakley, Liliana Fernandez, Paul G. Fisher, Jason Hom, Yong Huang, Jennefer N. Kohler, Marta M. Majcherska, Shruti Marwaha, Colleen E. McCormack, Chloe M. Reuter, Jacinda B. Sampson, Kevin S. Smith, Matthew T. Wheeler, Diane B. Zastrow, Chunli Zhao, Maura Ruzhnikov, Laure Fresard, Holly K. Tabor, Archana N. Raja, Gill Bejerano, Beth A. Martin, Shirley Sutton, Patrick Allard, Manish J. Butte, Esteban C. Dell’Angelica, Naghmeh Dorrani, Emilie D. Douine, Brent L. Fogel, Alden Huang, Deborah Krakow, Hane Lee, Sandra K. Loo, Martin G. Martin, Julian A. Martínez-Agosto, Stanley F. Nelson, Christina G.S. Palmer, Jeanette C. Papp, Neil H. Parker, Genecee Renteria, Rebecca H. Signer, Janet S. Sinsheimer, Jijun Wan, Lee-kai Wang, Jeremy D. Woods, Amanda J. Yoon, Lorenzo Botto, Ashley Andrews, Nicola Longo, John Carey, John Bohnsack, Dave Viskochil, Moretti Paolo, Pace Laura, Justin Alvey, Jim Bale, Gabor Marth, Matt Velinder, Aaron Quinlan, Rong Mao, Pinar Bayrak-Toydemir, John H. Postlethwait, Monte Westerfield, Lisa Shakachite, F. Sessions Cole, Nichole Hayes, Dana Kiley, Kathleen Shields, Kathy Sisco, Jennifer Wambach, Daniel Wegner, Dustin Baldridge, Timothy Schedl, Lilianna Solnica-Krezel, Stephen Pak, Jimann ShinGenetics in Medicine, 2021. https://doi.org/10.1038/s41436-021-01179-w
- A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases
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Jennifer E Kyle, Kelly G Stratton, Erika M Zink, Young-Mo Kim, Kent J Bloodsworth, Matthew E Monroe, Undiagnosed Diseases Network, Carlos A Bacino, Neil A Hanchard, Richard A Lewis, Jill A Rosenfeld, Daryl A Scott, Alyssa A Tran, Patricia A Ward, Lindsay C Burrage, Gary D Clark, Mercedes E Alejandro, Jennifer E Posey, Michael F Wangler, Brendan H Lee, William J Craigen, Hugo J Bellen, Sarah K Nicholas, Bret L Bostwick, Susan L Samson, Alica M Goldman, Paolo M Moretti, Christine M Eng, Donna M Muzny, James P Orengo, Tiphanie P Vogel, Seema R Lalani, David R Murdock, Mahshid S Azamian, Jordan S Orange, Lisa T Emrick, Shweta U Dhar, Ashok Balasubramanyam, Lorraine Potocki, Shinya Yamamoto, Yaping Yang, Shan Chen, Fariha Jamal, Lefkothea Karaviti, Ronit Marom, Sharyn A Lincoln, Chris A Walsh, Alan H Beggs, Lance H Rodan, Joan M Stoler, Gerard T Berry, Laurel A Cobban, Calum A MacRae, Joel B Krier, Edwin K Silverman, Elizabeth L Fieg, Richard L Maas, Joseph Loscalzo, Aaron Aday, Susan Korrick, David B Goldstein, Nicholas Stong, Jennifer A Sullivan, Rebecca C Spillmann, Loren D M Pena, Queenie K -G Tan, Nicole M Walley, Yong-hui Jiang, Allyn McConkie-Rosell, Kelly Schoch, Vandana Shashi, Heidi Cope, Ingrid A Holm, Isaac S Kohane, Alexa T McCray, Cecilia Esteves, Kimberly LeBlanc, Matthew Might, Emily Kelley, Elizabeth A Worthey, Camille L Birch, Donna M Brown, Katrina M. Waters, Bobbie-Jo M. Webb-Robertson, David M Koeller, Thomas O MetzScientific Data, 2021. https://doi.org/10.1038/s41597-021-00894-y
- Functional and structural analysis of cytokine-selective IL6ST defects that cause recessive hyper-IgE syndrome
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Yin-Huai Chen, Diane B. Zastrow, Riley D. Metcalfe, Lisa Gartner, Freia Krause, Craig J. Morton, Shruti Marwaha, Laure Fresard, Yong Huang, Chunli Zhao, Colleen McCormack, David Bick, Elizabeth A. Worthey, Christine M. Eng, Jessica Gold, Undiagnosed Diseases Network, Stephen B. Montgomery, Paul G. Fisher, Euan A. Ashley, Matthew T. Wheeler, Michael W. Parker, Veerabahu Shanmugasundaram, Tracy L. Putoczki, Dirk Schmidt-Arras, Arian Laurence, Jonathan A. Bernstein, Michael D.W. Griffin, Holm H. UhligJournal of Allergy and Clinical Immunology, 2021. https://doi.org/10.1016/j.jaci.2021.02.044
2020
- Applying whole-genome sequencing in relation to phenotype and outcomes in siblings with cystic fibrosis.
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Melissa A. Wilk, Andrew T. Braun, Philip M. Farrell, Anita Laxova, Donna M. Brown, James M. Holt, Camille L. Birch, Nadiya Sosonkina, Brandon M. Wilk, Elizabeth A. WortheyCold Spring Harbor molecular case studies, 2020. https://doi.org/10.1101/mcs.a004531
- Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease
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Christian R. Marshall, Shimul Chowdhury, Ryan J. Taft, Mathew S. Lebo, Jillian G. Buchan, Steven M. Harrison, Ross Rowsey, Eric W. Klee, Pengfei Liu, Elizabeth A. Worthey, Vaidehi Jobanputra, David Dimmock, Hutton M. Kearney, David Bick, Shashikant Kulkarni, Stacie L. Taylor, John W. Belmont, Dimitri J. Stavropoulos, Niall J. Lennon, Medical Genome Initiativenpj Genomic Medicine, 2020. https://doi.org/10.1038/s41525-020-00154-9
- Exome Sequencing Identifies Abnormalities in Glycosylation and ANKRD36C in Patients with Immune-Mediated Thrombotic Thrombocytopenic Purpura
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Malay Basu, Felipe Massicano, Lijia Yu, Konstantine Halkidis, Vikram Pillai, Wenjing Cao, Liang Zheng, X. ZhengThrombosis and Haemostasis, 2020. https://doi.org/10.1055/s-0040-1719030
- Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex
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Donna M. Werling, Sirisha Pochareddy, Jinmyung Choi, Joon-Yong An, Brooke Sheppard, Minshi Peng, Zhen Li, Claudia Dastmalchi, Gabriel Santpere, André M.M. Sousa, Andrew T.N. Tebbenkamp, Navjot Kaur, Forrest O. Gulden, Michael S. Breen, Lindsay Liang, Michael C. Gilson, Xuefang Zhao, Shan Dong, Lambertus Klei, A. Ercument Cicek, Joseph D. Buxbaum, Homa Adle-Biassette, Jean-Leon Thomas, Kimberly A. Aldinger, Diana R. O’Day, Ian A. Glass, Noah A. Zaitlen, Michael E. Talkowski, Kathryn Roeder, Matthew W. State, Bernie Devlin, Stephan J. Sanders, Nenad SestanCell Reports, 2020. https://doi.org/10.1016/j.celrep.2020.03.053
- The Undiagnosed Diseases Network as a Tool for Graduate Medical Education
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Aaron W. Aday, Joel B. Krier, J. Carl Pallais, Elizabeth L. Fieg, Calum A. MacRae, Joseph Loscalzo, Members of the UDNThe American Journal of Medicine, 2020. https://doi.org/10.1016/j.amjmed.2019.06.034
- Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling
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Brett V. Johnson, Raman Kumar, Sabrina Oishi, Suzy Alexander, Maria Kasherman, Michelle Sanchez Vega, Atma Ivancevic, Alison Gardner, Deepti Domingo, Mark Corbett, Euan Parnell, Sehyoun Yoon, Tracey Oh, Matthew Lines, Henrietta Lefroy, Usha Kini, Margot Van Allen, Sabine Grønborg, Sandra Mercier, Sébastien Küry, Stéphane Bézieau, Laurent Pasquier, Martine Raynaud, Alexandra Afenjar, Thierry Billette de Villemeur, Boris Keren, Julie Désir, Lionel Van Maldergem, Martina Marangoni, Nicola Dikow, David A. Koolen, Peter M. VanHasselt, Marjan Weiss, Petra Zwijnenburg, Joaquim Sa, Claudia Falcao Reis, Carlos López-Otín, Olaya Santiago-Fernández, Alberto Fernández-Jaén, Anita Rauch, Katharina Steindl, Pascal Joset, Amy Goldstein, Suneeta Madan-Khetarpal, Elena Infante, Elaine Zackai, Carey Mcdougal, Vinodh Narayanan, Keri Ramsey, Saadet Mercimek-Andrews, Loren Pena, Vandana Shashi, Undiagnosed Diseases Network, Kelly Schoch, Jennifer A. Sullivan, Filippo Pinto e Vairo, , Pavel N. Pichurin, Sarah A. Ewing, Sarah S. Barnett, Eric W. Klee, M. Scott Perry, Mary Kay Koenig, Catherine E. Keegan, Jane L. Schuette, Stephanie Asher, Yezmin Perilla-Young, Laurie D. Smith, Jill A. Rosenfeld, Elizabeth Bhoj, Paige Kaplan, Dong Li, Renske Oegema, Ellen van Binsbergen, Bert van der Zwaag, Marie Falkenberg Smeland, Ioana Cutcutache, Matthew Page, Martin Armstrong, Angela E. Lin, Marcie A. Steeves, Nicolette den Hollander, Mariëtte J.V. Hoffer, Margot R.F. Reijnders, Serwet Demirdas, Daniel C. Koboldt, Dennis Bartholomew, Theresa Mihalic Mosher, Scott E. Hickey, Christine Shieh, Pedro A. Sanchez-Lara, John M. Graham, Jr., Kamer Tezcan, G.B. Schaefer, Noelle R. Danylchuk, Alexander Asamoah, Kelly E. Jackson, Naomi Yachelevich, Margaret Au, Luis A. Pérez-Jurado, Tjitske Kleefstra, Peter Penzes, Stephen A. Wood, Thomas Burne, Tyler Mark Pierson, Michael Piper, Jozef Gécz, Lachlan A. JollyBiological Psychiatry, 2020. https://doi.org/10.1016/j.biopsych.2019.05.028
2019
- Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy
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A. Bhatia, B. C. Mobley, J. Cogan, M. E. Koziura, E. Brokamp, J. Phillips, J. Newman, S. A. Moore, R. HamidClin Imaging, 2019. https://doi.org/10.1016/j.clinimag.2019.06.010
- VarSight: prioritizing clinically reported variants with binary classification algorithms
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James M. Holt, Brandon Wilk, Camille L. Birch, Donna M. Brown, Manavalan Gajapathy, Alexander C. Moss, Nadiya Sosonkina, Melissa A. Wilk, Julie A. Anderson, Jeremy M. Harris, Jacob M. Kelly, Fariba Shaterferdosian, Angelina E. Uno-Antonison, Arthur Weborg, Undiagnosed Diseases Network, Elizabeth A. WortheyBMC Bioinformatics, 2019. https://doi.org/10.1186/s12859-019-3026-8
- Identification of Pathogenic Structural Variants in Rare Disease Patients through Genome Sequencing
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James M Holt, Camille L Birch, Donna M Brown, Manavalan Gajapathy, Nadiya Sosonkina, Brandon Wilk, Melissa A Wilk, Rebecca C Spillmann, Nicholas Stong, Hane Lee, Alden Y Huang, Devon Bonner, Jennefer N Kohler, Ellen F Macnamara, Undiagnosed Diseases Network, Stanley F Nelson, Vandana Shashi, Elizabeth A WortheybioRxiv, 2019. https://doi.org/10.1101/627661
- Recurrent mosaic MTOR c.5930C > T (p.Thr1977Ile) variant causing megalencephaly, asymmetric polymicrogyria, and cutaneous pigmentary mosaicism: Case report and review of the literature
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Maureen Handoko, Lisa T. Emrick, Jill A. Rosenfeld, Xia Wang, Alyssa A. Tran, Alicia Turner, John W. Belmont, Undiagnosed Diseases Network, Brendan H. Lee, Carlos A. Bacino, Hsiao‐Tuan ChaoAmerican Journal of Medical Genetics Part A, 2019. https://doi.org/10.1002/ajmg.a.61007
- Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay
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Keren Machol, Justine Rousseau, Sophie Ehresmann, Thomas Garcia, Thi Tuyet Mai Nguyen, Rebecca C. Spillmann, Jennifer A. Sullivan, Vandana Shashi, Yong-hui Jiang, Nicholas Stong, Elise Fiala, Marcia Willing, Rolph Pfundt, Tjitske Kleefstra, Megan T. Cho, Heather McLaughlin, Monica Rosello Piera, Carmen Orellana, Francisco Martínez, Alfonso Caro-Llopis, Sandra Monfort, Tony Roscioli, Cheng Yee Nixon, Michael F. Buckley, Anne Turner, Wendy D. Jones, Peter M. van Hasselt, Floris C. Hofstede, Koen L.I. van Gassen, Alice S. Brooks, Marjon A. van Slegtenhorst, Katherine Lachlan, , Jessica Sebastian, Suneeta Madan-Khetarpal, Desai Sonal, Naidu Sakkubai, Julien Thevenon, Laurence Faivre, Alice Maurel, Slavé Petrovski, Ian D. Krantz, Jennifer M. Tarpinian, Jill A. Rosenfeld, Brendan H. Lee, Undiagnosed Diseases Network, Philippe M. CampeauThe American Journal of Human Genetics, 2019. https://doi.org/10.1016/j.ajhg.2018.11.007
2018
- The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development
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Andrew T.N. Tebbenkamp, Luis Varela, Jinmyung Choi, Miguel I. Paredes, Alice M. Giani, Jae Eun Song, Matija Sestan-Pesa, Daniel Franjic, André M.M. Sousa, Zhong-Wu Liu, Mingfeng Li, Candace Bichsel, Marco Koch, Klara Szigeti-Buck, Fuchen Liu, Zhuo Li, Yuka I. Kawasawa, Constantinos D. Paspalas, Yann S. Mineur, Paolo Prontera, Giuseppe Merla, Marina R. Picciotto, Amy F.T. Arnsten, Tamas L. Horvath, Nenad SestanCell, 2018. https://doi.org/10.1016/j.cell.2018.09.014
- Whole Genome Transcriptome Analysis of the Association between Obesity and Triple-Negative Breast Cancer in Caucasian Women
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Tarun K. K. Mamidi, Jiande Wu, Paul B. Tchounwou, Lucio Miele, Chindo HicksInternational Journal of Environmental Research and Public Health, 2018. https://doi.org/10.3390/ijerph15112338
- Autosomal recessive Noonan syndrome associated with biallelic LZTR1 variants
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Jennifer J. Johnston, Jasper J. van der Smagt, Jill A. Rosenfeld, Alistair T. Pagnamenta, Abdulrahman Alswaid, Eva H. Baker, Edward Blair, Guntram Borck, Julia Brinkmann, William Craigen, Vu Chi Dung, Lisa Emrick, David B. Everman, Koen L. van Gassen, Suleyman Gulsuner, Margaret H. Harr, Mahim Jain, Alma Kuechler, Kathleen A. Leppig, Donna M. McDonald-McGinn, Ngoc Thi Bich Can, Amir Peleg, Elizabeth R. Roeder, R.Curtis Rogers, Lena Sagi-Dain, Julie C. Sapp, Alejandro A. Schäffer, Denny Schanze, Helen Stewart, Jenny C. Taylor, Nienke E. Verbeek, Magdalena A. Walkiewicz, Elaine H. Zackai, Christiane Zweier, Members of the Undiagnosed Diseases Network, Martin Zenker, Brendan Lee, Leslie G. BieseckerGenetics in Medicine, 2018. https://doi.org/10.1038/gim.2017.249
- Further evidence for the involvement of EFL1 in a Shwachman–Diamond-like syndrome and expansion of the phenotypic features
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Queenie K.-G. Tan, Heidi Cope, Rebecca C. Spillmann, Nicholas Stong, Yong-Hui Jiang, Marie T. McDonald, Jennifer A. Rothman, Megan W. Butler, Donald P. Frush, Ralph S. Lachman, Brendan Lee, Carlos A. Bacino, Melanie J. Bonner, Chad M. McCall, Avani A. Pendse, Nicole Walley, Undiagnosed Diseases Network, Vandana Shashi, Loren D.M. PenaMolecular Case Studies, 2018. https://doi.org/10.1101/mcs.a003046
2017
- Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic
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David Bick, Pamela C. Fraser, Michael F. Gutzeit, Jeremy M. Harris, Tina M. Hambuch, Daniel C. Helbling, Howard J. Jacob, Juliet N. Kersten, Steven R. Leuthner, Thomas May, Paula E. North, Sasha Z. Prisco, Bryce A. Schuler, Mary Shimoyama, Kimberly A. Strong, Scott K. Van Why, Regan Veith, James Verbsky, Arthur M. Weborg Jr., Brandon M. Wilk, Rodney E. Willoughby Jr., Elizabeth A. Worthey, David P. DimmockJ Pediatr Genet, 2017. https://doi.org/10.1055/s-0036-1593968
2016
- The NIH Undiagnosed Diseases Program and Network: Applications to modern medicine
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W. A. Gahl, J. J. Mulvihill, C. Toro, T. C. Markello, A. L. Wise, R. B. Ramoni, D. R. Adams, C. J. Tifft, UdnMol Genet Metab, 2016. https://doi.org/10.1016/j.ymgme.2016.01.007
- Isomorphic semantic mapping of variant call format (VCF2RDF)
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Emanuel Diego S Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhães de Oliveira, Jonas S AlmeidaBioinformatics, 2016. https://doi.org/10.1093/bioinformatics/btw652
- Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation
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Jinmyung Choi, Parisa Shooshtari, Kaitlin E. Samocha, Mark J. Daly, Chris CotsapasPLoS Genetics, 2016. https://doi.org/10.1371/journal.pgen.1006121
- De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype
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Vandana Shashi, Loren D.M. Pena, Katherine Kim, Barbara Burton, Maja Hempel, Kelly Schoch, Magdalena Walkiewicz, Heather M. McLaughlin, Megan Cho, Nicholas Stong, Scott E. Hickey, Christine M. Shuss, Undiagnosed Diseases Network, Michael S. Freemark, Jane S. Bellet, Martha Ann Keels, Melanie J. Bonner, Maysantoine El-Dairi, Megan Butler, Peter G. Kranz, Constance T.R.M. Stumpel, Sylvia Klinkenberg, Karin Oberndorff, Malik Alawi, Rene Santer, Slavé Petrovski, Outi Kuismin, Satu Korpi-Heikkilä, Olli Pietilainen, Palotie Aarno, Mitja I. Kurki, Alexander Hoischen, Anna C. Need, David B. Goldstein, Fanny KortümThe American Journal of Human Genetics, 2016. https://doi.org/10.1016/j.ajhg.2016.08.017
- A recurrent p.Arg92Trp variant in steroidogenic factor-1 (NR5A1) can act as a molecular switch in human sex development
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Anu Bashamboo, Patricia A. Donohoue, Eric Vilain, Sandra Rojo, Pierre Calvel, Sumudu N. Seneviratne, Federica Buonocore, Hayk Barseghyan, Nathan Bingham, Jill A. Rosenfeld, Surya Narayan Mulukutla, Mahim Jain, Lindsay Burrage, Shweta Dhar, Ashok Balasubramanyam, Brendan Lee, Members of UDN, Marie-Charlotte Dumargne, Caroline Eozenou, Jenifer P. Suntharalingham, KSH de Silva, Lin Lin, Joelle Bignon-Topalovic, Francis Poulat, Carlos F. Lagos, Ken McElreavey, John C. AchermannHuman Molecular Genetics, 2016. https://doi.org/10.1093/hmg/ddw186
Grants
R01-HD111399 (Yoder)
09/06/2024 – 07/31/2029
NICHD
Mechanisms of ciliopathy associated structural birth defects
The outcomes from this project will uncover novel cilia protein interactions and subcomplexes involved in cilia formation and maintenance, cilia protein transport, and cilia sensory and signaling activities.
RC2-TR004766 (Korf)
05/01/2024 – 04/30/2029
NIH/NCATS
Rare Disease Discovery Ecosystem
Learn from the community about barriers in the Rare Disease Discovery Cycle (RDDC) and develop solutions to overcome these obstacles, optimize the system for complex rare disease diagnosis, making it more accessible to patients from diverse communities, decreasing the time from referral to evaluation, and increasing the diagnostic yield for patients with rare genetic disorders and develop a Precision Medicine Acceleration Platform (PMAP) as a module in the CCTS Data2Discovery Gateway (D2DG) that brings together and integrates extensions to both the precision medicine case management system Rosalution and the bioinformatics ecosystem U-BRITE.
U01-NS139216 (Korf)
08/01/2024 – 07/31/2028
NIH
Increasing Diversity, Diagnostic Yield, and Efficiency in Clinical Evaluations of Rare Disorders
The UAB UDP seeks to continue the affiliation, working within the UDN to provide services to groups in the Southeast and beyond who historically have not benefited from modern diagnostic investigations. The UAB UDP provides diagnostic evaluations for children and adults with chronic, undiagnosed diseases.
ARPA-H BDFT (Might, Haendel, Dumontier, and Worthey)
08/01/2024 – 07/31/2026
ARPA-H
CHARM: An end-to-end toolchain for Collecting, Harmonizing, Reasoning about and Manipulating Biomedical Data
The ARPA-H Biomedical Data Fabric (BDF) Toolbox seeks to make it easier to connect biomedical research data from thousands of sources and overcome barriers caused by incompatible data dialects.
UG1-HD107688(Hill, Gower)
10/12/2021 – 11/30/2026
NICHD
UAB Precision Nutrition Clinical Center
The field of “precision nutrition” holds great promise for elucidating these interactions to eventually predict the optimal diet for an individual or groups of individuals. UAB is a clinical site for conducting diet interventions as a member of the Nutrition for Precision Health Consortium.
DUCAS (Kohane)
04/19/2023 – 03/31/2028
NIH
Diagnosing the Unknown for Care and Advancing Science (DUCAS)
As the Data Management Core for the next phase of the Network, we aim to enable at least an order of magnitude increase in the scale of the operations of the Network.
P30CA013148-50 (Sleckman)
04/01/2022 – 03/31/2027
NIH
Comprehensive Cancer Center Core Support Grant
The UAB O’Neal Comprehensive Cancer Center serves as a major source for effective approaches to cancer prevention, diagnosis, treatment, survivorship and as source for delivery of these discoveries, public and professional education, and ultimately as a resource for the local, regional, and national community.
1R35-CA220502 (Bhatia)
09/01/2018 – 08/31/2025
NIH
Mitigating long-term treatment related morbidity in Childhood Cancer survivors
Whole exome based secondary and tertiary analysis and interpretation of Dr. Smita Bhatia’s pediatric cancer long term survival cohort to identify common and rare molecular variation associated with treatment related morbidity.
1U54-OD030167 (Yoder)
09/10/2020 – 08/31/2025
NIH
UAB pilot center for precision animal modelling (C-PAM) – Bioinformatics section
The goal of the UAB Center for Precision Animal Modeling (C-PAM) is efficient analysis and modeling of variants identified as part of rare disease programs to provide a definitive diagnosis, evaluate specific variant impact, and support therapeutic target identification.
FPWR (Worthey)
01/01/2020 – 12/31/2025
The Foundation for Prader-Willi Research
Whole Genome Sequence Analysis in Prader-Willi Syndrome
Whole genome sequencing and interpretation to identify causal and polygenic variation outside of the PWS region on chromosome 15 capable of influencing personal risk in individuals with PWS.
R01-PA-18-003 (Bhatia)
09/01/2018 – 08/30/2023
NIH
Predicting Risk of Anthracycline-related Cardiotoxicity in Childhood Cancer Survivors
Whole exome based secondary and tertiary analysis and interpretation of Dr. Smita Bhatia’s pediatric cancer long term survival cohort to identify common and rare molecular variation associated cardiotoxicity.
CFF 19A0 2019 (Worthey)
09/01/2019 – 08/30/2023
CF foundation
Finding and Integrating Pharma and Nutrition Linked Genomic Variation in CF
Whole genome sequencing and analysis and polygenic risk analysis to identify molecular variation associated with growth, vitamin D status and EFA status in a cohort of CF patients.
11000.050.01 (Farrell)
10/13/2017 – 10/13/2020
The Legacy of Angels Foundation
Assessing the Added value of Whole Genome Sequencing in Cystic Fibrosis Newborn Screening
Whole genome sequencing, analysis, and interpretation to identified variants associated with non responder status and altered outcomes in a pediatric CF patient cohort.
UW-Madison (Greenspan)
01/01/2020 – 06/31/2020
UW-Madison Research Foundation
Identification of causal variants in a family with Ehlers-Danlos Syndrome type 3.
Whole exome based secondary and tertiary analysis and interpretation to identify causal variants in a family with Ehlers-Danlos Syndrome.
NIH OT2 (Byrd and Might)
01/24/2020-05/31/2020
NCATS
Doc Sherlock: An autonomous relay agent for discovering the unknown knowns in precision medicine
Consultation on molecular data use and interpretation for precision medicine applications.
Ramsay Award (Worthey)
09/17/2019 – 08/16/2020
Solve ME/CFS Foundation
Whole genome sequencing and analysis of ME/CFS
WGS and RNA sequencing and analysis of myalgic encephalomyelitis/chronic fatigue syndrome cases and controls to identify causal molecular variants and genetic risk factors.1R35-CA220502
