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Start Over Author "Chris Hughes" Journal nature communications
3 results on '"Chris Hughes"'

1. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Author

Victoria N. Parikh, Alexander G. Ioannidis, David Jimenez-Morales, John E. Gorzynski, Hannah N. De Jong, Xiran Liu, Jonasel Roque, Victoria P. Cepeda-Espinoza, Kazutoyo Osoegawa, Chris Hughes, Shirley C. Sutton, Nathan Youlton, Ruchi Joshi, David Amar, Yosuke Tanigawa, Douglas Russo, Justin Wong, Jessie T. Lauzon, Jacob Edelson, Daniel Mas Montserrat, Yongchan Kwon, Simone Rubinacci, Olivier Delaneau, Lorenzo Cappello, Jaehee Kim, Massa J. Shoura, Archana N. Raja, Nathaniel Watson, Nathan Hammond, Elizabeth Spiteri, Kalyan C. Mallempati, Gonzalo Montero-Martín, Jeffrey Christle, Jennifer Kim, Anna Kirillova, Kinya Seo, Yong Huang, Chunli Zhao, Sonia Moreno-Grau, Steven G. Hershman, Karen P. Dalton, Jimmy Zhen, Jack Kamm, Karan D. Bhatt, Alina Isakova, Maurizio Morri, Thanmayi Ranganath, Catherine A. Blish, Angela J. Rogers, Kari Nadeau, Samuel Yang, Andra Blomkalns, Ruth O’Hara, Norma F. Neff, Christopher DeBoever, Sándor Szalma, Matthew T. Wheeler, Christian M. Gates, Kyle Farh, Gary P. Schroth, Phil Febbo, Francis deSouza, Omar E. Cornejo, Marcelo Fernandez-Vina, Amy Kistler, Julia A. Palacios, Benjamin A. Pinsky, Carlos D. Bustamante, Manuel A. Rivas, and Euan A. Ashley

Subjects
Science
Abstract

There is a genetic component to the risk of severe COVID-19, but the genetic effects are difficult to separate from social constructs that covary with genetic ancestry. To address this, the authors identify determinants of COVID-19 severity using admixture mapping, viral phylodynamics, and host immune and metagenomic sequencing.

Published
2022
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2. Modeling biological and genetic diversity in upper tract urothelial carcinoma with patient derived xenografts

Author

Kwanghee Kim, Wenhuo Hu, François Audenet, Nima Almassi, Aphrothiti J. Hanrahan, Katie Murray, Aditya Bagrodia, Nathan Wong, Timothy N. Clinton, Shawn Dason, Vishnu Mohan, Sylvia Jebiwott, Karan Nagar, Jianjiong Gao, Alex Penson, Chris Hughes, Benjamin Gordon, Ziyu Chen, Yiyu Dong, Philip A. Watson, Ricardo Alvim, Arijh Elzein, Sizhi P. Gao, Emiliano Cocco, Alessandro D. Santin, Irina Ostrovnaya, James J. Hsieh, Irit Sagi, Eugene J. Pietzak, A. Ari Hakimi, Jonathan E. Rosenberg, Gopa Iyer, Herbert A. Vargas, Maurizio Scaltriti, Hikmat Al-Ahmadie, David B. Solit, and Jonathan A. Coleman

Subjects
Science
Abstract

The advancement of upper tract urothelial carcinoma (UTUC) research is hampered by the lack of disease-specific models. Here, the authors report patient derived xenograft and cell line models of UTUC, and show that these models retain the genomic and biological heterogeneity of human disease.

Published
2020
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3. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy

Author

Victoria N. Parikh, Alexander G. Ioannidis, David Jimenez-Morales, John E. Gorzynski, Hannah N. De Jong, Xiran Liu, Jonasel Roque, Victoria P. Cepeda-Espinoza, Kazutoyo Osoegawa, Chris Hughes, Shirley C. Sutton, Nathan Youlton, Ruchi Joshi, David Amar, Yosuke Tanigawa, Douglas Russo, Justin Wong, Jessie T. Lauzon, Jacob Edelson, Daniel Mas Montserrat, Yongchan Kwon, Simone Rubinacci, Olivier Delaneau, Lorenzo Cappello, Jaehee Kim, Massa J. Shoura, Archana N. Raja, Nathaniel Watson, Nathan Hammond, Elizabeth Spiteri, Kalyan C. Mallempati, Gonzalo Montero-Martín, Jeffrey Christle, Jennifer Kim, Anna Kirillova, Kinya Seo, Yong Huang, Chunli Zhao, Sonia Moreno-Grau, Steven G. Hershman, Karen P. Dalton, Jimmy Zhen, Jack Kamm, Karan D. Bhatt, Alina Isakova, Maurizio Morri, Thanmayi Ranganath, Catherine A. Blish, Angela J. Rogers, Kari Nadeau, Samuel Yang, Andra Blomkalns, Ruth O’Hara, Norma F. Neff, Christopher DeBoever, Sándor Szalma, Matthew T. Wheeler, Christian M. Gates, Kyle Farh, Gary P. Schroth, Phil Febbo, Francis deSouza, Omar E. Cornejo, Marcelo Fernandez-Vina, Amy Kistler, Julia A. Palacios, Benjamin A. Pinsky, Carlos D. Bustamante, Manuel A. Rivas, and Euan A. Ashley

Subjects
Genome, Multidisciplinary, SARS-CoV-2, Prevention, Human Genome, General Physics and Astronomy, COVID-19, General Chemistry, Genome, Viral, General Biochemistry, Genetics and Molecular Biology, Infectious Diseases, Good Health and Well Being, Clinical Research, Pneumonia & Influenza, Genetics, Humans, Viral, Infection, Lung, Pandemics, Genome-Wide Association Study
Abstract

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Published
2021

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