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Mortality prediction in sepsis via gene expression analysis: a community approach

View ORCID ProfileTimothy E Sweeney, Thanneer M Perumal, Ricardo Henao, Marshall Nichols, Judith A Howrylak, Augustine M Choi, Jesús F Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E Davenport, Katie L Burnham, Charles J Hinds, Julian C Knight, Christopher W Woods, Stephen F Kingsmore, Geoffrey S Ginsburg, Hector R Wong, Grant P Parnell, Benjamin Tang, Lyle L Moldawer, Frederick E Moore, Larsson Omberg, Purvesh Khatri, Ephraim L Tsalik, Lara M Mangravite, Raymond J Langley
doi: https://doi.org/10.1101/095489
Timothy E Sweeney
1Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
2Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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  • ORCID record for Timothy E Sweeney
Thanneer M Perumal
3Sage Bionetworks, Seattle, WA 98109, USA.
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Ricardo Henao
4Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
5Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.
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Marshall Nichols
4Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
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Judith A Howrylak
6Division of Pulmonary and Critical Care Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, USA.
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Augustine M Choi
7Department of Medicine, Cornell Medical Center, New York, NY 10065, USA.
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Jesús F Bermejo-Martin
8Hospital Clínico Universitario de Valladolid/IECSCYL, Avda Ramón y Cajal 3, 47005 Valladolid, Spain.
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Raquel Almansa
8Hospital Clínico Universitario de Valladolid/IECSCYL, Avda Ramón y Cajal 3, 47005 Valladolid, Spain.
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Eduardo Tamayo
8Hospital Clínico Universitario de Valladolid/IECSCYL, Avda Ramón y Cajal 3, 47005 Valladolid, Spain.
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Emma E Davenport
9Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA.
10Partners Center for Personalized Genetic Medicine, Boston, USA.
11Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA.
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Katie L Burnham
12Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Charles J Hinds
13William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University, London, UK.
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Julian C Knight
12Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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Christopher W Woods
4Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
14Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.
15Durham Veteran’s Affairs Health Care System, Durham, NC 27705, USA.
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Stephen F Kingsmore
16Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA.
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Geoffrey S Ginsburg
4Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
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Hector R Wong
17Division of Critical Care Medicine, Cincinnati Children’s Hospital Medical Center and Cincinnati Children’s Research Foundation, Cincinnati, OH, 45223, USA.
18Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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Grant P Parnell
19Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, Australia.
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Benjamin Tang
19Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Sydney, Australia.
20Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia.
21Nepean Genomic Research Group, Nepean Clinical School, University of Sydney, Sydney, Australia.
22Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia.
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Lyle L Moldawer
23Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA.
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Frederick E Moore
23Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610, USA.
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Larsson Omberg
3Sage Bionetworks, Seattle, WA 98109, USA.
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Purvesh Khatri
1Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
2Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Ephraim L Tsalik
4Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
14Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA.
15Durham Veteran’s Affairs Health Care System, Durham, NC 27705, USA.
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Lara M Mangravite
3Sage Bionetworks, Seattle, WA 98109, USA.
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Raymond J Langley
24Department of Pharmacology, University of South Alabama. Mobile, Alabama, USA.
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Abstract

Improved risk stratification and prognosis in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal performance, and do not specifically reveal the underlying dysregulation of sepsis. Here three scientific groups were invited to independently generate prognostic models for 30-day mortality using 12 discovery cohorts (N=650) containing transcriptomic data collected from primarily community-onset sepsis patients. Predictive performance was validated in 5 cohorts of community-onset sepsis patients (N=189) in which the models showed summary AUROCs ranging from 0.765-0.89. Similar performance was observed in 4 cohorts of hospital-acquired sepsis (N=282). Combining the new gene-expression-based prognostic models with prior clinical severity scores led to significant improvement in prediction of 30-day mortality (p<0.01). These models provide an opportunity to develop molecular bedside tests that may improve risk stratification and mortality prediction in patients with sepsis, improving both resource allocation and prognostic enrichment in clinical trials.

Footnotes

  • ↵** These authors jointly directed this work

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Posted December 19, 2016.
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Mortality prediction in sepsis via gene expression analysis: a community approach
Timothy E Sweeney, Thanneer M Perumal, Ricardo Henao, Marshall Nichols, Judith A Howrylak, Augustine M Choi, Jesús F Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E Davenport, Katie L Burnham, Charles J Hinds, Julian C Knight, Christopher W Woods, Stephen F Kingsmore, Geoffrey S Ginsburg, Hector R Wong, Grant P Parnell, Benjamin Tang, Lyle L Moldawer, Frederick E Moore, Larsson Omberg, Purvesh Khatri, Ephraim L Tsalik, Lara M Mangravite, Raymond J Langley
bioRxiv 095489; doi: https://doi.org/10.1101/095489
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Mortality prediction in sepsis via gene expression analysis: a community approach
Timothy E Sweeney, Thanneer M Perumal, Ricardo Henao, Marshall Nichols, Judith A Howrylak, Augustine M Choi, Jesús F Bermejo-Martin, Raquel Almansa, Eduardo Tamayo, Emma E Davenport, Katie L Burnham, Charles J Hinds, Julian C Knight, Christopher W Woods, Stephen F Kingsmore, Geoffrey S Ginsburg, Hector R Wong, Grant P Parnell, Benjamin Tang, Lyle L Moldawer, Frederick E Moore, Larsson Omberg, Purvesh Khatri, Ephraim L Tsalik, Lara M Mangravite, Raymond J Langley
bioRxiv 095489; doi: https://doi.org/10.1101/095489

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