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2. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H, Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B, Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N, Faro, Valeria Lo, Lopera-Maya, Esteban A, Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J, Chapman, Sinéad B, Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M, Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A, Guare, Lindsay A, Gignoux, Christopher R, Graham, Sarah E, Hornsby, Whitney E, Ingold, Nathan, Ismail, Said I, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y, Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H, Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M, Thani, Asma Al, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H, Damrauer, Scott M, Douville, Nicholas J, Finer, Sarah, Fritsche, Lars G, Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J, Guo, Yu, Hunt, Karen A, Ioannidis, Alexander, Jansonius, Nomdo M, Konuma, Takahiro, Lee, Ming Ta Michael, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E, Moatamed, Babak, Nava-Aguilar, Marco A, Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A, Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C, Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K, Franke, Lude, Gamazon, Eric R, Ganna, Andrea, Gaunt, Tom R, Ge, Tian, Huang, Hailiang, and Huffman, Jennifer

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Good Health and Well Being, Biobank of the Americas, Biobank Japan Project, BioMe, BioVU, CanPath - Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center for Personalized Medicine, deCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank of Korea, Penn Medicine BioBank, Qatar Biobank, QSkin Sun and Health Study, Taiwan Biobank, HUNT Study, UCLA ATLAS Community Health Initiative, Uganda Genome Resource, UK Biobank, GWAS, ancestry diversity, biobank, genetic association studies, meta-analysis, phenotype harmonization
Abstract

Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)-a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

Published
2022

5. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation

Author

Lo Faro, Valeria, Bhattacharya, Arjun, Zhou, Wei, Zhou, Dan, Wang, Ying, Läll, Kristi, Kanai, Masahiro, Lopera-Maya, Esteban, Straub, Peter, Pawar, Priyanka, Tao, Ran, Zhong, Xue, Namba, Shinichi, Sanna, Serena, Nolte, Ilja M., Okada, Yukinori, Ingold, Nathan, MacGregor, Stuart, Snieder, Harold, Surakka, Ida, Shortt, Jonathan, Gignoux, Chris, Rafaels, Nicholas, Crooks, Kristy, Verma, Anurag, Verma, Shefali S., Guare, Lindsay, Rader, Daniel J., Willer, Cristen, Martin, Alicia R., Brantley, Milam A., Jr., Gamazon, Eric R., Jansonius, Nomdo M., Joos, Karen, Cox, Nancy J., and Hirbo, Jibril

Published
2024
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6. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine

Author

Wiley, Laura K., Shortt, Jonathan A., Roberts, Emily R., Lowery, Jan, Kudron, Elizabeth, Lin, Meng, Mayer, David, Wilson, Melissa, Brunetti, Tonya M., Chavan, Sameer, Phang, Tzu L., Pozdeyev, Nikita, Lesny, Joseph, Wicks, Stephen J., Moore, Ethan T., Morgenstern, Joshua L., Roff, Alanna N., Shalowitz, Elise L., Stewart, Adrian, Williams, Cole, Edelmann, Michelle N., Hull, Madelyne, Patton, J. Tacker, Axell, Lisen, Ku, Lisa, Lee, Yee Ming, Jirikowic, Jean, Tanaka, Anna, Todd, Emily, White, Sarah, Peterson, Brett, Hearst, Emily, Zane, Richard, Greene, Casey S., Mathias, Rasika, Coors, Marilyn, Taylor, Matthew, Ghosh, Debashis, Kahn, Michael G., Brooks, Ian M., Aquilante, Christina L., Kao, David, Rafaels, Nicholas, Crooks, Kristy R., Hess, Steve, Barnes, Kathleen C., and Gignoux, Christopher R.

Published
2024
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8. The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors

Author

Deignan, Joshua L., Aggarwal, Vimla, Bale, Allen E., Bellissimo, Daniel B., Booker, Jessica K., Cao, Yang, Crooks, Kristy R., Deak, Kristen L., Del Gaudio, Daniela, Funke, Birgit, Hoppman, Nicole L., Horner, Vanessa, Hufnagel, Robert B., Jackson-Cook, Colleen, Koduru, Prasad, Leung, Marco L., Li, Shibo, Liu, Pengfei, Luo, Minjie, Mao, Rong, Mason-Suares, Heather, Mikhail, Fady M., Moore, Stephen R., Naeem, Rizwan C., Pollard, Laura M., Repnikova, Elena A., Shao, Lina, Shaw, Brandon M., Shetty, Shashirekha, Smolarek, Teresa A., Spiteri, Elizabeth, Van Ziffle, Jessica, Vance, Gail H., Vnencak-Jones, Cindy L., and Williams, Eli S.

Published
2024
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9. The future is now: Implementation of standard of care, preemptive pharmacogenomic testing in patients with gastrointestinal cancers.

Author

Hearst, Emily C, primary, Martin, James L, additional, Crooks, Kristy R, additional, Greene, Casey S, additional, Hess, Kaitlyn W, additional, Johnson, Natalie, additional, Kao, David P, additional, Rafaels, Nicholas, additional, Carson, Katelyn, additional, Meguid, Cheryl L, additional, Taucher, Kate, additional, Davis, S. Lindsey, additional, Lieu, Christopher Hanyoung, additional, and Aquilante, Christina L, additional

Published
2024
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10. Host methylation predicts SARS-CoV-2 infection and clinical outcome.

Author

Konigsberg, Iain R, Barnes, Bret, Campbell, Monica, Davidson, Elizabeth, Zhen, Yingfei, Pallisard, Olivia, Boorgula, Meher Preethi, Cox, Corey, Nandy, Debmalya, Seal, Souvik, Crooks, Kristy, Sticca, Evan, Harrison, Genelle F, Hopkinson, Andrew, Vest, Alexis, Arnold, Cosby G, Kahn, Michael G, Kao, David P, Peterson, Brett R, Wicks, Stephen J, Ghosh, Debashis, Horvath, Steve, Zhou, Wanding, Mathias, Rasika A, Norman, Paul J, Porecha, Rishi, Yang, Ivana V, Gignoux, Christopher R, Monte, Andrew A, Taye, Alem, and Barnes, Kathleen C

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Emerging Infectious Diseases, Prevention, Lung, Vaccine Related, Biodefense, Clinical Research, Infectious Diseases, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Infection, Good Health and Well Being, Pneumonia & Influenza, Predictive markers, Viral infection
Abstract

BackgroundSince the onset of the SARS-CoV-2 pandemic, most clinical testing has focused on RT-PCR1. Host epigenome manipulation post coronavirus infection2-4 suggests that DNA methylation signatures may differentiate patients with SARS-CoV-2 infection from uninfected individuals, and help predict COVID-19 disease severity, even at initial presentation.MethodsWe customized Illumina's Infinium MethylationEPIC array to enhance immune response detection and profiled peripheral blood samples from 164 COVID-19 patients with longitudinal measurements of disease severity and 296 patient controls.ResultsEpigenome-wide association analysis revealed 13,033 genome-wide significant methylation sites for case-vs-control status. Genes and pathways involved in interferon signaling and viral response were significantly enriched among differentially methylated sites. We observe highly significant associations at genes previously reported in genetic association studies (e.g. IRF7, OAS1). Using machine learning techniques, models built using sparse regression yielded highly predictive findings: cross-validated best fit AUC was 93.6% for case-vs-control status, and 79.1%, 80.8%, and 84.4% for hospitalization, ICU admission, and progression to death, respectively.ConclusionsIn summary, the strong COVID-19-specific epigenetic signature in peripheral blood driven by key immune-related pathways related to infection status, disease severity, and clinical deterioration provides insights useful for diagnosis and prognosis of patients with viral infections.

Published
2021

12. Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures

Author

Popejoy, Alice B, Crooks, Kristy R, Fullerton, Stephanie M, Hindorff, Lucia A, Hooker, Gillian W, Koenig, Barbara A, Pino, Natalie, Ramos, Erin M, Ritter, Deborah I, Wand, Hannah, Wright, Matt W, Yudell, Michael, Zou, James Y, Plon, Sharon E, Bustamante, Carlos D, Ormond, Kelly E, and Group, Clinical Genome Resource Ancestry and Diversity Working

Subjects
Health Services and Systems, Health Sciences, Genetics, Biological Sciences, Precision Medicine, Human Genome, Good Health and Well Being, Adult, Child, Data Collection, Ethnicity, Female, Genetic Testing, Genetic Variation, Genomics, Humans, Male, Prohibitins, Surveys and Questionnaires, Clinical Genome Resource (ClinGen) Ancestry and Diversity Working Group, CSER, ClinGen, ancestry, clinical genetics, diversity, ethnicity, precision medicine, race, survey, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.

Published
2020

13. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie-Julie, Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Mutaamba, Maasha, Partanen, Juulia J., Brumpton, Ben M., Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Palta, Priit, Pandit, Anita, Preuss, Michael H., Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Zawistowski, Matthew, Zhong, Xue, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H., Douville, Nicholas J., Finer, Sarah, Fritsche, Lars G., Griffiths, Christopher J., Guo, Yu, Hunt, Karen A., Konuma, Takahiro, Marioni, Riccardo E., Nomdo, Jansonius, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Shortt, Jonathan A., Straub, Peter, Tao, Ran, Vanderwerff, Brett, Barnes, Kathleen C., Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K., Franke, Lude, Gamazon, Eric R., Ganna, Andrea, Gaunt, Tom R., Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Koskela, Jukka T., Lajonchere, Clara, Law, Matthew H., Li, Liming, Lindgren, Cecilia M., Loos, Ruth J.F., MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M., Porteous, David J., Shavit, Jordan A., Snieder, Harold, Trembath, Richard C., Vonk, Judith M., Whiteman, David, Wicks, Stephen J., Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Cox, Nancy J., Geschwind, Daniel H., Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E., Lin, Yen-Feng, Mägi, Reedik, Martin, Hilary C., Medland, Sarah E., Okada, Yukinori, Palotie, Aarno V., Pasaniuc, Bogdan, Sanna, Serena, Smoller, Jordan W., Stefansson, Kari, van Heel, David A., Walters, Robin G., Zöllner, Sebastian, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., Lopera, Esteban, Kerminen, Sini, Wu, Kuan-Han, Bhatta, Laxmi, Brumpton, Ben, Deelen, Patrick, Murakami, Yoshinori, Willer, Cristen, and Hirbo, Jibril

Published
2023
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14. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J., Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M., Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A., Guare, Lindsay A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Ismail, Said I., Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H., Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M., Al Thani, Asma, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H., Damrauer, Scott M., Douville, Nicholas J., Finer, Sarah, Fritsche, Lars G., Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J., Guo, Yu, Hunt, Karen A., Ioannidis, Alexander, Jansonius, Nomdo M., Konuma, Takahiro, Michael Lee, Ming Ta, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E., Moatamed, Babak, Nava-Aguilar, Marco A., Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A., Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C., Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K., Franke, Lude, Gamazon, Eric R., Ganna, Andrea, Gaunt, Tom R., Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Katsanis, Nicholas, Koskela, Jukka T., Lajonchere, Clara, Law, Matthew H., Li, Liming, Lindgren, Cecilia M., Loos, Ruth J.F., MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M., Porteous, David J., Shavit, Jordan A., Snieder, Harold, Takano, Tomohiro, Trembath, Richard C., Vonk, Judith M., Whiteman, David C., Wicks, Stephen J., Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Bustamante, Carlos D., Cox, Nancy J., Fatumo, Segun, Geschwind, Daniel H., Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E., Lee, Seunggeun, Lin, Yen-Feng, Mbarek, Hamdi, Mägi, Reedik, Martin, Hilary C., Medland, Sarah E., Okada, Yukinori, Palotie, Aarno V., Pasaniuc, Bogdan, Rader, Daniel J., Ritchie, Marylyn D., Sanna, Serena, Smoller, Jordan W., Stefansson, Kari, van Heel, David A., Walters, Robin G., Zöllner, Sebastian, Biobank of the Americas, Biobank Japan Project, BioMe, BioVU, CanPath - Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center for Personalized Medicine, deCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank of Korea, Penn Medicine BioBank, Qatar Biobank, The Qskin Sun and Health Study, Taiwan Biobank, The Hunt Study, Ucla Atlas Community Health Initiative, Uganda Genome Resource, Uk Biobank, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., and Elzur, Roy

Published
2022
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15. A polygenic risk score for the QT interval is an independent predictor of drug-induced QT prolongation.

Author

Simon, Steven T., Lin, Meng, Trinkley, Katy E., Aleong, Ryan, Rafaels, Nicholas, Crooks, Kristy R., Reiter, Michael J., Gignoux, Christopher R., and Rosenberg, Michael A.

Subjects
GENETIC risk score, DRUG side effects, ELECTRONIC health records, ODDS ratio, STANDARD deviations, DECISION making
Abstract

Drug-induced QT prolongation (diLQTS), and subsequent risk of torsade de pointes, is a major concern with use of many medications, including for non-cardiac conditions. The possibility that genetic risk, in the form of polygenic risk scores (PGS), could be integrated into prediction of risk of diLQTS has great potential, although it is unknown how genetic risk is related to clinical risk factors as might be applied in clinical decision-making. In this study, we examined the PGS for QT interval in 2500 subjects exposed to a known QT-prolonging drug on prolongation of the QT interval over 500ms on subsequent ECG using electronic health record data. We found that the normalized QT PGS was higher in cases than controls (0.212±0.954 vs. -0.0270±1.003, P = 0.0002), with an unadjusted odds ratio of 1.34 (95%CI 1.17–1.53, P<0.001) for association with diLQTS. When included with age and clinical predictors of QT prolongation, we found that the PGS for QT interval provided independent risk prediction for diLQTS, in which the interaction for high-risk diagnosis or with certain high-risk medications (amiodarone, sotalol, and dofetilide) was not significant, indicating that genetic risk did not modify the effect of other risk factors on risk of diLQTS. We found that a high-risk cutoff (QT PGS ≥ 2 standard deviations above mean), but not a low-risk cutoff, was associated with risk of diLQTS after adjustment for clinical factors, and provided one method of integration based on the decision-tree framework. In conclusion, we found that PGS for QT interval is an independent predictor of diLQTS, but that in contrast to existing theories about repolarization reserve as a mechanism of increasing risk, the effect is independent of other clinical risk factors. More work is needed for external validation in clinical decision-making, as well as defining the mechanism through which genes that increase QT interval are associated with risk of diLQTS. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Characterizing substructure via mixture modeling of genetic similarity in large-scale summary statistics

Author

Stoneman, Hayley R, primary, Price, Adelle, additional, Trout, Nikole Scribner, additional, Lamont, Riley, additional, Tifour, Souha, additional, Pozdeyev, Nikita, additional, Crooks, Kristy, additional, Lin, Meng, additional, Rafaels, Nicholas, additional, Marker, Katie M, additional, Gignoux, Christopher R, additional, and Henrdicks, Audrey E, additional

Published
2024
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17. Implementation of clopidogrel pharmacogenetic clinical decision support for a preemptive return of results program

Author

Aquilante, Christina L, primary, Trinkley, Katy E, additional, Lee, Yee Ming, additional, Crooks, Kristy R, additional, Hearst, Emily C, additional, Heckman, Simeon M, additional, Hess, Kaitlyn W, additional, Kudron, Elizabeth L, additional, Martin, James L, additional, Swartz, Carolyn T, additional, and Kao, David P, additional

Published
2024
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20. OR32-02 Thyroid Cancer Polygenic Risk Score Improves Risk Stratification Of Thyroid Nodules When Added To Ultrasound Imaging

Author

Pozdeyev, Nikita, primary, Dighe, Manjiri, additional, Barrio, Martin, additional, Raeburn, Christopher, additional, Smith, Harry A, additional, Fisher, Matthew, additional, Chavan, Sameer, additional, Rafaels, Nicholas, additional, Shortt, Jonathan, additional, Leu, Michael, additional, Clark, Toshimasa, additional, Marshall, Carrie, additional, Haugen, Bryan R, additional, Subramanian, Devika, additional, Crooks, Kristy, additional, Gignoux, Christopher, additional, and Cohen, Trevor A, additional

Published
2023
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21. Thyroid Cancer Polygenic Risk Score Improves Classification of Thyroid Nodules as Benign or Malignant

Author

Pozdeyev, Nikita, primary, Dighe, Manjiri, additional, Barrio, Martin, additional, Raeburn, Christopher, additional, Smith, Harry, additional, Fisher, Matthew, additional, Chavan, Sameer, additional, Rafaels, Nicholas, additional, Shortt, Jonathan A, additional, Lin, Meng, additional, Leu, Michael G, additional, Clark, Toshimasa, additional, Marshall, Carrie, additional, Haugen, Bryan R, additional, Subramanian, Devika, additional, Crooks, Kristy, additional, Gignoux, Christopher, additional, and Cohen, Trevor, additional

Published
2023
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23. Actionable exomic incidental findings in 6503 participants: challenges of variant classification

Author

Amendola, Laura M, Dorschner, Michael O, Robertson, Peggy D, Salama, Joseph S, Hart, Ragan, Shirts, Brian H, Murray, Mitzi L, Tokita, Mari J, Gallego, Carlos J, Kim, Daniel Seung, Bennett, James T, Crosslin, David R, Ranchalis, Jane, Jones, Kelly L, Rosenthal, Elisabeth A, Jarvik, Ella R, Itsara, Andy, Turner, Emily H, Herman, Daniel S, Schleit, Jennifer, Burt, Amber, Jamal, Seema M, Abrudan, Jenica L, Johnson, Andrew D, Conlin, Laura K, Dulik, Matthew C, Santani, Avni, Metterville, Danielle R, Kelly, Melissa, Foreman, Ann Katherine M, Lee, Kristy, Taylor, Kent D, Guo, Xiuqing, Crooks, Kristy, Kiedrowski, Lesli A, Raffel, Leslie J, Gordon, Ora, Machini, Kalotina, Desnick, Robert J, Biesecker, Leslie G, Lubitz, Steven A, Mulchandani, Surabhi, Cooper, Greg M, Joffe, Steven, Richards, C Sue, Yang, Yaoping, Rotter, Jerome I, Rich, Stephen S, O’Donnell, Christopher J, Berg, Jonathan S, Spinner, Nancy B, Evans, James P, Fullerton, Stephanie M, Leppig, Kathleen A, Bennett, Robin L, Bird, Thomas, Sybert, Virginia P, Grady, William M, Tabor, Holly K, Kim, Jerry H, Bamshad, Michael J, Wilfond, Benjamin, Motulsky, Arno G, Scott, C Ronald, Pritchard, Colin C, Walsh, Tom D, Burke, Wylie, Raskind, Wendy H, Byers, Peter, Hisama, Fuki M, Rehm, Heidi, Nickerson, Debbie A, and Jarvik, Gail P

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, Clinical Research, Good Health and Well Being, Adult, Black People, Exome, Female, Gene Frequency, Genes, Dominant, Genetic Association Studies, Genetic Testing, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Incidental Findings, Male, Phenotype, Polymorphism, Single Nucleotide, White People, Medical and Health Sciences, Bioinformatics
Abstract

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.

Published
2015

25. Thyroid Cancer Polygenic Risk Score Improves Classification of Thyroid Nodules as Benign or Malignant.

Author

Pozdeyev, Nikita, Dighe, Manjiri, Barrio, Martin, Raeburn, Christopher, Smith, Harry, Fisher, Matthew, Chavan, Sameer, Rafaels, Nicholas, Shortt, Jonathan A, Lin, Meng, Leu, Michael G, Clark, Toshimasa, Marshall, Carrie, Haugen, Bryan R, Subramanian, Devika, Crooks, Kristy, Gignoux, Christopher, and Cohen, Trevor

Subjects
THYROID nodules, THYROID cancer, GENOME-wide association studies
Abstract

Context Thyroid nodule ultrasound-based risk stratification schemas rely on the presence of high-risk sonographic features. However, some malignant thyroid nodules have benign appearance on thyroid ultrasound. New methods for thyroid nodule risk assessment are needed. Objective We investigated polygenic risk score (PRS) accounting for inherited thyroid cancer risk combined with ultrasound-based analysis for improved thyroid nodule risk assessment. Methods The convolutional neural network classifier was trained on thyroid ultrasound still images and cine clips from 621 thyroid nodules. Phenome-wide association study (PheWAS) and PRS PheWAS were used to optimize PRS for distinguishing benign and malignant nodules. PRS was evaluated in 73 346 participants in the Colorado Center for Personalized Medicine Biobank. Results When the deep learning model output was combined with thyroid cancer PRS and genetic ancestry estimates, the area under the receiver operating characteristic curve (AUROC) of the benign vs malignant thyroid nodule classifier increased from 0.83 to 0.89 (DeLong, P value =.007). The combined deep learning and genetic classifier achieved a clinically relevant sensitivity of 0.95, 95% CI [0.88-0.99], specificity of 0.63 [0.55-0.70], and positive and negative predictive values of 0.47 [0.41-0.58] and 0.97 [0.92-0.99], respectively. AUROC improvement was consistent in European ancestry-stratified analysis (0.83 and 0.87 for deep learning and deep learning combined with PRS classifiers, respectively). Elevated PRS was associated with a greater risk of thyroid cancer structural disease recurrence (ordinal logistic regression, P value =.002). Conclusion Augmenting ultrasound-based risk assessment with PRS improves diagnostic accuracy. [ABSTRACT FROM AUTHOR]

Published
2024
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27. Pathology, Biomarkers, and Molecular Diagnostics

Author

Franklin, Wilbur A., primary, Aisner, Dara L., additional, Davies, Kurtis D., additional, Crooks, Kristy, additional, Post, Miriam D., additional, Kleinschmidt-DeMasters, Bette K., additional, Ashwood, Edward, additional, Bunn, Paul A., additional, and Varella-Garcia, Marileila, additional

Published
2020
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28. Contributors

Author

Abbruzzese, James L., primary, Abdel-Wahab, Omar, additional, Abou-Alfa, Ghassan K., additional, Abrahm, Janet L., additional, Abrams, Jeffrey S., additional, Abramson, Jeremy S., additional, Aisner, Dara L., additional, Alonso-Basanta, Michelle, additional, Anampa, Jesus, additional, Anderson, Megan E., additional, Antonarakis, Emmanuel S., additional, Aplenc, Richard, additional, Appelbaum, Frederick R., additional, Araujo, Luiz H., additional, Asban, Ammar, additional, Ashwood, Edward, additional, Awan, Farrukh T., additional, Aylward, Juliet L., additional, Balar, Arjun V., additional, Balentine, Courtney J., additional, Barta, Stefan K., additional, Bartlett, Nancy, additional, Basen-Engquist, Karen, additional, Beaupin, Lynda Kwon, additional, Berkowitz, Ross S., additional, Berry, Donald A., additional, Bevers, Therese, additional, Boggess, John F., additional, Brahmer, Julie R., additional, Brown, Janet, additional, Brown, Karen, additional, Brown, Powel, additional, Browner, Ilene, additional, Bunn, Paul A., additional, Burns, William R., additional, Byrd, John C., additional, Cadoo, Karen, additional, Carbone, David P., additional, Carter, H. Ballentine, additional, Castillo, Jorge J., additional, Chang, Alfred E., additional, Chang, Eric, additional, Chanock, Stephen J., additional, Chapuy, Claudia I., additional, Chauhan, Vikash P., additional, Chen, Herbert, additional, Chen, Ronald C., additional, Cheung, Nai-Kong V., additional, Choe, Jennifer H., additional, Christian, Michaele C., additional, Cinciripini, Paul M., additional, Clarke, Michael F., additional, Coleman, Robert E., additional, Coleman, Robert L., additional, Coletta, Adriana M., additional, Collins, Jerry M., additional, Connors, Jean M., additional, Cools, Michael, additional, Coombes, Kevin R., additional, Cortes, Jorge, additional, Costa, Mauro W., additional, Covey, Anne, additional, Cowan, Kenneth H., additional, Crane, Christopher H., additional, Crawford, Jeffrey, additional, Crooks, Kristy, additional, Culkin, Daniel J., additional, Czito, Brian G., additional, Dalerba, Piero, additional, Dalmau, Josep, additional, Dang, Mai, additional, D'Angelica, Michael, additional, Davies, Kurtis D., additional, Davis, Myrtle, additional, Dea, Nicolas, additional, De Jesus-Acosta, Ana, additional, DeMarzo, Angelo M., additional, DeWeese, Theodore L., additional, Diehn, Maximilian, additional, Digumarthy, Subba R., additional, Dispenzieri, Angela, additional, Do, Khanh T., additional, Dobrenkov, Konstantin, additional, Dome, Jeffrey S., additional, Doroshow, James H., additional, Dorsey, Jay F., additional, Dubard-Gault, Marianne, additional, DuBois, Steven G., additional, Duda, Dan G., additional, Dunlop, Malcolm, additional, Duska, Linda R., additional, Duvic, Madeleine, additional, El Dika, Imane, additional, El-Serag, Hashem, additional, Engelmann, Jeffrey M., additional, Ettinger, David S., additional, Fashoyin-Aje, Lola A., additional, Fearon, Eric R., additional, Ford, James M., additional, Franklin, Wilbur A., additional, Freer, Phoebe E., additional, Freidlin, Boris, additional, Freifeld, Alison G., additional, Friedlander, Terence W., additional, Friedman, Debra L., additional, Fuller, Arian F., additional, Galluzzi, Lorenzo, additional, Gebhardt, Mark C., additional, George, Daniel J., additional, Geyer, Mark B., additional, Giaccia, Amato J., additional, Gilbert, Mark R., additional, Goldner, Whitney, additional, Goldstein, Donald P., additional, Goodman, Annekathryn, additional, Goodman, Karyn A., additional, Gordon, Kathleen, additional, Graeff-Armas, Laura, additional, Greenstein, Alexander J., additional, Grossman, Stuart A., additional, Grupp, Stephan, additional, Gupta, Arjun, additional, Haider, Irfanullah, additional, Haigentz, Missak, additional, Hainsworth, John D., additional, Haithcock, Benjamin E., additional, Hallemeier, Christopher L., additional, Hanash, Samir, additional, Hanrahan, Aphrothiti J., additional, Harding, James, additional, Harrison, Michael R., additional, Hasham, Muneer G., additional, Hawk, Ernest, additional, Hayman, Jonathan, additional, Heinlen, Jonathan E., additional, Henry, N. Lynn, additional, Herman, Joseph, additional, Hobbs, Brian P., additional, Holen, Ingunn, additional, Horn, Leora, additional, Horowitz, Neil S., additional, Horwitz, Steven M., additional, Houghton, Odette, additional, Howard, Scott C., additional, Hudis, Clifford A., additional, Hunger, Stephen P., additional, Hurria, Arti, additional, Ilson, David H., additional, Im, Annie, additional, Iyer, Gopa, additional, Jaffee, Elizabeth M., additional, Jagsi, Reshma, additional, Jain, Rakesh K., additional, Jarnagin, William, additional, Jatoi, Aminah, additional, Jhingran, Anuja, additional, Johnson, David H., additional, Johnston, Brian, additional, Johnston, Patrick G., additional, Judy, Kevin D., additional, Kachnic, Lisa A., additional, Kaidar-Person, Orit, additional, Kalva, Sanjeeva, additional, Kamin, Deborah Y., additional, Kantarjian, Hagop, additional, Karakousis, Giorgos, additional, Karam-Hage, Maher, additional, Kaskas, Nadine M., additional, Kastan, Michael B., additional, Katabi, Nora, additional, Kaul, Daniel R., additional, Kelley, Scott R., additional, Kemeny, Nancy, additional, Kent, Erin E., additional, Kepp, Oliver, additional, Khagi, Simon, additional, Kilgore, Joshua E., additional, Kim, D. Nathan, additional, Kleinschmidt-DeMasters, Bette K., additional, Korn, Edward L., additional, Kroemer, Guido, additional, Ku, Geoffrey Y., additional, Kummar, Shivaani, additional, Ky, Bonnie, additional, Laheru, Daniel A., additional, Lambert, Paul F., additional, Lawler, Mark, additional, Le-Rademacher, Jennifer G., additional, Lee, John Y.K., additional, Lee, Nancy Y., additional, Lee, Susanna L., additional, Leeman, Jonathan E., additional, Linkermann, Andreas, additional, Liu, Jinsong, additional, Lo, Simon, additional, Locasale, Jason W., additional, Loprinzi, Charles L., additional, Lowery, Maeve, additional, Ludwig, Emmy, additional, Lunning, Matthew A., additional, Lustig, Robert A., additional, Machtay, Mitchell, additional, Mackall, Crystal, additional, Mahvi, David A., additional, Mahvi, David M., additional, Maity, Amit, additional, Majithia, Neil, additional, Malumbres, Marcos, additional, Maresso, Karen Colbert, additional, Martin, John D., additional, Matsuo, Koji, additional, Matthews, Natalie H., additional, Mauro, Lauren, additional, Mayer, R. Samuel, additional, McCaskill-Stevens, Worta, additional, McNamara, Megan A., additional, Mehta-Shah, Neha, additional, Merritt, Robert E., additional, Milowsky, Matthew I., additional, Minasian, Lori M., additional, Mitchell, Tara C., additional, Mitsis, Demytra, additional, Mollica, Michelle, additional, Mooney, Margaret, additional, Moustafa, Farah, additional, Nabati, Lida, additional, Naidoo, Jarushka, additional, Narang, Amol, additional, Nelson, Heidi, additional, Nelson, William G., additional, Nesbit, Suzanne, additional, Niglas, Mark, additional, O'Connor, Tracey, additional, Offit, Kenneth, additional, Onciu, Mihaela, additional, O’Reilly, Eileen M., additional, Ostrander, Elaine A., additional, Pappas-Taffer, Lisa, additional, Pardoll, Drew, additional, Park, Jae H., additional, Patel, Anery, additional, Patel, Anish J., additional, Patierno, Steven R., additional, Pavletic, Steven Z., additional, Phillips, Peter C., additional, Post, Miriam D., additional, Pruitt, Amy A., additional, Querfeld, Christiane, additional, Rabius, Vance A., additional, Rajkumar, S. Vincent, additional, Ramadan, Mohammad O., additional, Rankin, Erinn B., additional, Reddy, Sushanth, additional, Reid, Michael A., additional, Reznik, Scott, additional, Rizack, Tina, additional, Robinson, Jason D., additional, Robinson-Bostom, Leslie, additional, Rodriguez-Galindo, Carlos, additional, Romesser, Paul B., additional, Rosen, Steven T., additional, Rosenfeld, Myrna R., additional, Rosenthal, Nadia, additional, Ross, Meredith, additional, Rowland, Julia H., additional, Russell, Anthony H., additional, Sabel, Michael S., additional, Sahgal, Arjun, additional, Salinas, Ryan D., additional, Salo-Mullen, Erin E., additional, Salto-Tellez, Manuel, additional, Sanderson, Sydney M., additional, Sandlund, John T., additional, Santana, Victor M., additional, Savage, Michelle, additional, Schreiber, Eric C., additional, Schuchter, Lynn, additional, Schultz, Liora, additional, Seiden, Michael V., additional, Sellers, Morgan M., additional, Shah, Payal D., additional, Shia, Jinru, additional, Shilo, Konstantin, additional, Small, Eric, additional, Smith, Angela B., additional, Snow, Stephen N., additional, Solit, David B., additional, Sood, Anil K., additional, Soto-Perez-de-Celis, Enrique, additional, Sparano, Joseph A., additional, Spiegelman, Vladimir S., additional, Spunt, Sheri L., additional, Stadler, Zsofia K., additional, Steensma, David P., additional, Stone, Richard M., additional, Stranne, Steven Kent, additional, Stratton, Kelly, additional, Sugden, Bill, additional, Swanson, Andrew M., additional, Tallman, Martin S., additional, Talmadge, James E., additional, Teachey, David T., additional, Teba, Catalina V., additional, Tefferi, Ayalew, additional, Teh, Bin Tean, additional, Teng, Joyce M.C., additional, Tepper, Joel E., additional, Thaker, Premal H., additional, Thrift, Aaron P., additional, Tran, Arthur-Quan, additional, Triska, Grace, additional, Trump, Donald, additional, Tsai, Kenneth, additional, Tseng, Chia-Lin, additional, Tseng, Diane, additional, Van Schaeybroeck, Sandra, additional, Van Tine, Brian A., additional, Vanness, Erin R., additional, Varadhachary, Gauri, additional, Varella-Garcia, Marileila, additional, Wahl, Richard L., additional, Walsh, Michael F., additional, Wang, Thomas, additional, Weiss, Jared, additional, Weissman, Irving L., additional, Westin, Shannon N., additional, White, Jeffrey D., additional, Wilson, Richard, additional, Wong, Richard J., additional, Wood, Gary S., additional, Xu, Yaohui G., additional, Xu-Welliver, Meng, additional, Yust-Katz, Shlomit, additional, Zagar, Timothy, additional, Zeman, Elaine M., additional, Zhang, Tian, additional, and Zwiebel, James A., additional

Published
2020
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29. Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Author

Wiggs, Janey L, Yaspan, Brian L, Hauser, Michael A, Kang, Jae H, Allingham, R Rand, Olson, Lana M, Abdrabou, Wael, Fan, Bao J, Wang, Dan Y, Brodeur, Wendy, Budenz, Donald L, Caprioli, Joseph, Crenshaw, Andrew, Crooks, Kristy, DelBono, Elizabeth, Doheny, Kimberly F, Friedman, David S, Gaasterland, Douglas, Gaasterland, Terry, Laurie, Cathy, Lee, Richard K, Lichter, Paul R, Loomis, Stephanie, Liu, Yutao, Medeiros, Felipe A, McCarty, Cathy, Mirel, Daniel, Moroi, Sayoko E, Musch, David C, Realini, Anthony, Rozsa, Frank W, Schuman, Joel S, Scott, Kathleen, Singh, Kuldev, Stein, Joshua D, Trager, Edward H, VanVeldhuisen, Paul, Vollrath, Douglas, Wollstein, Gadi, Yoneyama, Sachiko, Zhang, Kang, Weinreb, Robert N, Ernst, Jason, Kellis, Manolis, Masuda, Tomohiro, Zack, Don, Richards, Julia E, Pericak-Vance, Margaret, Pasquale, Louis R, and Haines, Jonathan L

Subjects
Biological Sciences, Genetics, Clinical Research, Neurosciences, Eye Disease and Disorders of Vision, Neurodegenerative, Aging, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Eye, Alleles, Chromosomes, Human, Pair 8, Chromosomes, Human, Pair 9, Exfoliation Syndrome, Genome-Wide Association Study, Glaucoma, Open-Angle, Homeodomain Proteins, Humans, Nerve Degeneration, Optic Nerve, Polymorphism, Single Nucleotide, RNA, Long Noncoding, RNA, Untranslated, Transforming Growth Factor beta, Developmental Biology
Abstract

Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.

Published
2012

31. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H, Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B, Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N, Lo Faro, Valeria, Lopera-Maya, Esteban A, Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J, Chapman, Sinéad B, Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M, Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A, Guare, Lindsay A, Gignoux, Christopher R, Graham, Sarah E, Hornsby, Whitney E, Ingold, Nathan, Ismail, Said I, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y, Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H, Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M, Al Thani, Asma, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, De Bock, Geertruida H, Damrauer, Scott M, Douville, Nicholas J, Finer, Sarah, Fritsche, Lars G, Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J, Guo, Yu, Hunt, Karen A, Ioannidis, Alexander, Jansonius, Nomdo M, Konuma, Takahiro, Lee, Ming Ta Michael, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E, Moatamed, Babak, Nava-Aguilar, Marco A, Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A, Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C, Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K, Franke, Lude, Gamazon, Eric R, Ganna, Andrea, Gaunt, Tom R, Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Katsanis, Nicholas, Koskela, Jukka T, Lajonchere, Clara, Law, Matthew H, Li, Liming, Lindgren, Cecilia M, Loos, Ruth JF, MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M, Porteous, David J, Shavit, Jordan A, Snieder, Harold, Takano, Tomohiro, Trembath, Richard C, Vonk, Judith M, Whiteman, David C, Wicks, Stephen J, Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Bustamante, Carlos D, Cox, Nancy J, Fatumo, Segun, Geschwind, Daniel H, Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E, Lee, Seunggeun, Lin, Yen-Feng, Mbarek, Hamdi, Mägi, Reedik, Martin, Hilary C, Medland, Sarah E, Okada, Yukinori, Palotie, Aarno V, Pasaniuc, Bogdan, Rader, Daniel J, Ritchie, Marylyn D, Sanna, Serena, Smoller, Jordan W, Stefansson, Kari, Van Heel, David A, Walters, Robin G, Zöllner, Sebastian, Biobank Of The Americas, Biobank Japan Project, BioMe, BioVU, CanPath-Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center For Personalized Medicine, DeCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank Of Korea, Penn Medicine BioBank, Qatar Biobank, QSkin Sun And Health Study, Taiwan Biobank, HUNT Study, UCLA ATLAS Community Health Initiative, Uganda Genome Resource, UK Biobank, Martin, Alicia R, Willer, Cristen J, Daly, Mark J, Neale, Benjamin M, Namba, Shinichi [0000-0002-7486-3146], Guare, Lindsay A [0000-0001-6988-5319], Palta, Priit [0000-0001-9320-7008], de Bock, Geertruida H [0000-0003-3104-4471], Finer, Sarah [0000-0002-2684-4653], Jansonius, Nomdo M [0000-0002-6495-6568], Rojas-Muñoz, Agustin [0000-0001-7594-0599], Gamazon, Eric R [0000-0003-4204-8734], Ganna, Andrea [0000-0002-8147-240X], Koskela, Jukka T [0000-0002-0154-7222], MacGregor, Stuart [0000-0001-6731-8142], Palotie, Aarno V [0000-0002-2527-5874], and Apollo - University of Cambridge Repository

Subjects
biobank, meta-analysis, genetic association studies, GWAS, ancestry diversity, phenotype harmonization
Abstract

Funder: Biogen, Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)-a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

Published
2023
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32. Epidemiology of Group A Streptococcal bacteraemia in Hunter New England Local Health District, 2008 to 2019

Author

Williamson, Kirsten M, primary, Varadhan, Hemalatha, additional, Taylor, Kylie, additional, Crooks, Kristy, additional, Brett, Katie, additional, Law, Charlee, additional, Butler, Michelle, additional, Butler, Trent, additional, Green, Emily, additional, Davis, Joshua S, additional, Wilson, Paul, additional, Housen, Tambri, additional, Merritt, Tony, additional, and Durrheim, David N, additional

Published
2023
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33. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Author

Wang, Ying, primary, Namba, Shinichi, additional, Lopera, Esteban, additional, Kerminen, Sini, additional, Tsuo, Kristin, additional, Läll, Kristi, additional, Kanai, Masahiro, additional, Zhou, Wei, additional, Wu, Kuan-Han, additional, Favé, Marie-Julie, additional, Bhatta, Laxmi, additional, Awadalla, Philip, additional, Brumpton, Ben, additional, Deelen, Patrick, additional, Hveem, Kristian, additional, Lo Faro, Valeria, additional, Mägi, Reedik, additional, Murakami, Yoshinori, additional, Sanna, Serena, additional, Smoller, Jordan W., additional, Uzunovic, Jasmina, additional, Wolford, Brooke N., additional, Willer, Cristen, additional, Gamazon, Eric R., additional, Cox, Nancy J., additional, Surakka, Ida, additional, Okada, Yukinori, additional, Martin, Alicia R., additional, Hirbo, Jibril, additional, Wu, Kuan-Han H., additional, Rasheed, Humaira, additional, Hirbo, Jibril B., additional, Wang, Ying, additional, Bhattacharya, Arjun, additional, Zhao, Huiling, additional, Lopera-Maya, Esteban A., additional, Chapman, Sinéad B., additional, Karjalainen, Juha, additional, Kurki, Mitja, additional, Mutaamba, Maasha, additional, Partanen, Juulia J., additional, Brumpton, Ben M., additional, Chavan, Sameer, additional, Chen, Tzu-Ting, additional, Daya, Michelle, additional, Ding, Yi, additional, Feng, Yen-Chen A., additional, Gignoux, Christopher R., additional, Graham, Sarah E., additional, Hornsby, Whitney E., additional, Ingold, Nathan, additional, Johnson, Ruth, additional, Laisk, Triin, additional, Lin, Kuang, additional, Lv, Jun, additional, Millwood, Iona Y., additional, Palta, Priit, additional, Pandit, Anita, additional, Preuss, Michael H., additional, Thorsteinsdottir, Unnur, additional, Zawistowski, Matthew, additional, Zhong, Xue, additional, Campbell, Archie, additional, Crooks, Kristy, additional, de Bock, Geertruida H., additional, Douville, Nicholas J., additional, Finer, Sarah, additional, Fritsche, Lars G., additional, Griffiths, Christopher J., additional, Guo, Yu, additional, Hunt, Karen A., additional, Konuma, Takahiro, additional, Marioni, Riccardo E., additional, Nomdo, Jansonius, additional, Patil, Snehal, additional, Rafaels, Nicholas, additional, Richmond, Anne, additional, Shortt, Jonathan A., additional, Straub, Peter, additional, Tao, Ran, additional, Vanderwerff, Brett, additional, Barnes, Kathleen C., additional, Boezen, Marike, additional, Chen, Zhengming, additional, Chen, Chia-Yen, additional, Cho, Judy, additional, Smith, George Davey, additional, Finucane, Hilary K., additional, Franke, Lude, additional, Ganna, Andrea, additional, Gaunt, Tom R., additional, Ge, Tian, additional, Huang, Hailiang, additional, Huffman, Jennifer, additional, Koskela, Jukka T., additional, Lajonchere, Clara, additional, Law, Matthew H., additional, Li, Liming, additional, Lindgren, Cecilia M., additional, Loos, Ruth J.F., additional, MacGregor, Stuart, additional, Matsuda, Koichi, additional, Olsen, Catherine M., additional, Porteous, David J., additional, Shavit, Jordan A., additional, Snieder, Harold, additional, Trembath, Richard C., additional, Vonk, Judith M., additional, Whiteman, David, additional, Wicks, Stephen J., additional, Wijmenga, Cisca, additional, Wright, John, additional, Zheng, Jie, additional, Zhou, Xiang, additional, Boehnke, Michael, additional, Geschwind, Daniel H., additional, Hayward, Caroline, additional, Kenny, Eimear E., additional, Lin, Yen-Feng, additional, Martin, Hilary C., additional, Medland, Sarah E., additional, Palotie, Aarno V., additional, Pasaniuc, Bogdan, additional, Stefansson, Kari, additional, van Heel, David A., additional, Walters, Robin G., additional, Zöllner, Sebastian, additional, Willer, Cristen J., additional, Daly, Mark J., additional, and Neale, Benjamin M., additional

Published
2023
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34. Additional file 4 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 4: Supplementary Table 2. Prevalence ratios of antenatal vaccine coverage among diverse population groups in the Links2HealthierBubs cohort, 2012-2017

Published
2023
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35. Additional file 3 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 3: Supplementary Table 1. Indigeneity, ethnicity, remoteness and socio-economic advantage on antenatal vaccine coverage in Links2HealthierBubs cohort, 2012-2017

Published
2023
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36. Additional file 2 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 2: Supplementary box 2. Country of birth, Indigeneity and ethnicity of individual participants

Published
2023
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37. Additional file 6 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 6: Supplementary figure 2. Vaccination status in pregnancy by Indigenous status and remoteness by jurisdiction

Published
2023
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38. Additional file 1 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 1: Supplementary box 1. Vaccination sources by jurisdiction and year

Published
2023
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39. Additional file 5 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 5: Supplementary figure 1. Vaccination status in pregnancy by Indigenous status and remoteness

Published
2023
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40. Additional file 7 of Inequity of antenatal influenza and pertussis vaccine coverage in Australia: the Links2HealthierBubs record linkage cohort study, 2012–2017

Author

McHugh, Lisa, Regan, Annette K, Sarna, Mohinder, Moore, Hannah C, Van Buynder, Paul, Pereira, Gavin, Blyth, Christopher C, Lust, Karin, Andrews, Ross M, Crooks, Kristy, Massey, Peter, and Binks, Michael J

Abstract

Additional file 7: Supplementary Figure 3. a Antenatal vaccination by Indigenous status, ethnicity, and socio-economic variation in NT. b Antenatal vaccination by Indigenous status, ethnicity, and socio-economic variation in Qld. c Antenatal vaccination by Indigenous status, ethnicity, and socio-economic variation in WA

Published
2023
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41. Diagnostic utility of exome sequencing in the evaluation of neuromuscular disorders

Author

Haskell, Gloria T., Adams, Michael C., Fan, Zheng, Amin, Krunal, Guzman Badillo, Roberto J., Zhou, Linran, Bizon, Christopher, Chahin, Nizar, Greenwood, Robert S., Milko, Laura V., Shiloh-Malawsky, Yael, Crooks, Kristy R., Strande, Natasha, Tennison, Michael, Tilley, Christian R., Brandt, Alicia, Wilhelmsen, Kirk C., Weck, Karen, Evans, James P., and Berg, Jonathan S.

Published
2018
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44. Inequity of antenatal influenza and pertussis vaccine coverage in Australia: The Links2HealthierBubs record linkage cohort study, 2012-2017

Author

McHugh, Lisa, primary, Regan, Annette K, additional, Sarna, Mohinder, additional, Moore, Hannah C, additional, Buynder, Paul, additional, Pereira, Gavin, additional, Blyth, Christopher C, additional, Lust, Karin, additional, Andrews, Ross M, additional, Crooks, Kristy, additional, Massey, Peter, additional, and Binks, Michael J, additional

Published
2022
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45. Phylodynamics of a regional SARS-CoV-2 rapid spreading event in Colorado in late 2020

Author

Wade, Kristen J., primary, Tisa, Samantha, additional, Barrington, Chloe, additional, Henriksen, Jesslyn C., additional, Crooks, Kristy R., additional, Gignoux, Christopher R., additional, Almand, Austin T., additional, Steel, J. Jordan, additional, Sitko, John C., additional, Rohrer, Joseph W., additional, Wickert, Douglas P., additional, Almand, Erin A., additional, Pollock, David D., additional, and Rissland, Olivia S., additional

Published
2022
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47. Building a Vertically-Integrated Genomic Learning Health System: The Colorado Center for Personalized Medicine Biobank

Author

Wiley, Laura K, primary, Shortt, Jonathan A, additional, Roberts, Emily R, additional, Lowery, Jan, additional, Kudron, Elizabeth, additional, Lin, Meng, additional, Mayer, David A, additional, Wilson, Melissa P, additional, Brunetti, Tonya M, additional, Chavan, Sameer, additional, Phang, Tzu L, additional, Pozdeyev, Nikita, additional, Lesny, Joseph, additional, Wicks, Stephen J, additional, Moore, Ethan, additional, Morgenstern, Joshua L, additional, Roff, Alanna N, additional, Shalowitz, Elise L, additional, Stewart, Adrian, additional, Williams, Cole, additional, Edelmann, Michelle N, additional, Hull, Madelyne, additional, Patton, J. Tacker, additional, Axell, Lisen, additional, Ku, Lisa, additional, Lee, Yee Ming, additional, Jirikowic, Jean, additional, Tanaka, Anna, additional, Todd, Emily, additional, White, Sarah, additional, Peterson, Brett, additional, Hearst, Emily, additional, Zane, Richard, additional, Greene, Casey S, additional, Mathias, Rasika, additional, Coors, Marilyn, additional, Taylor, Matthew RG, additional, Ghosh, Debashis, additional, Kahn, Michael G, additional, Brooks, Ian M, additional, Aquilante, Christina L, additional, Kao, David, additional, Rafaels, Nicholas, additional, Crooks, Kristy, additional, Hess, Steve, additional, Barnes, Kathleen C, additional, and Gignoux, Christopher R, additional

Published
2022
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48. List of Contributors

Author

Allison, Kimberly H., primary, Allyse, Megan A., additional, Arcenas, Rodney C., additional, Bartel, Michael J., additional, Behdad, Amir, additional, Bennett, Katie M., additional, Berg, Jonathan S., additional, Best, D. Hunter, additional, Betz, Bryan L., additional, Booker, Jessica K., additional, Borowski, Kristi S., additional, Bourlet, Thomas, additional, Brissot, Pierre, additional, Brown, Noah A., additional, Bula, Marcin, additional, Caprioli, Richard M., additional, Chakraborty, Subhankar, additional, Coleman, William B., additional, Crooks, Kristy R., additional, Dong, Jianli, additional, Drabkin, Harry A., additional, Duncan, Daniel L., additional, Fareed, Jawed, additional, Ferreira-Gonzalez, Andrea, additional, Funke, Birgit H., additional, Furtado, Larissa V., additional, Gallinella, Giorgio, additional, Gonzalo, Sonzalo, additional, Grattard, Florence, additional, Gutierrez, Danielle B., additional, Haskell, Gloria T., additional, Hedayat, Amin A., additional, Highsmith, W. Edward, additional, Hsiao, Susan J., additional, Iqbal, Omer, additional, Ismail, Nahed, additional, Jouanolle, Anne-Marie, additional, Kerr, Sarah E., additional, Loréal, Olivier, additional, McLaughlin, Heather M., additional, Memmi, Meriam, additional, Michalak, Tomasz I., additional, Miller, Melissa B., additional, Mulrooney-Cousins, Patricia M., additional, Nikiforov, Yuri E., additional, Norris, Jeremy L., additional, Patel, Nirali M., additional, Perrotta, Peter L., additional, Pinsky, Benjamin A., additional, Pirmohamed, Munir, additional, Plongla, Rongpong, additional, Pozzetto, Bruno, additional, Pratt, Victoria M., additional, Procop, Gary W., additional, Raimondo, Massimo, additional, Rao, ✠Kathleen W., additional, Scott, Stuart A., additional, Shi, Chanjuan, additional, Shiau, Carolyn J., additional, Si, Yue, additional, Smith, Steven C., additional, Smolkin, Matthew B., additional, Stellrecht, Kathleen A., additional, Tan, Susanna K., additional, Thomas, Jessica S., additional, Tomlins, Scott A., additional, Trembath, Dimitri G., additional, Tsao, Ming-Sound, additional, Tsongalis, Gregory J., additional, Turner, Richard M., additional, Turner, Scott A., additional, Udager, Aaron M., additional, Verhoeven, Paul, additional, Walker, David H., additional, Wick, Myra J., additional, Willoughby, Kathryn, additional, Yan, Shaofeng, additional, and Yen-Lieberman, Belinda, additional

Published
2017
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49. A practice change intervention to improve antenatal care addressing alcohol consumption by women during pregnancy: research protocol for a randomised stepped-wedge cluster trial

Author

Kingsland, Melanie, Doherty, Emma, Anderson, Amy E., Crooks, Kristy, Tully, Belinda, Tremain, Danika, Tsang, Tracey W., Attia, John, Wolfenden, Luke, Dunlop, Adrian J., Bennett, Nicole, Hunter, Mandy, Ward, Sarah, Reeves, Penny, Symonds, Ian, Rissel, Chris, Azzopardi, Carol, Searles, Andrew, Gillham, Karen, Elliott, Elizabeth J., and Wiggers, John

Published
2018
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