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Njunge JM, Tickell K, Diallo AH, Sayeem Bin Shahid ASM, Gazi MA, Saleem A, Kazi Z, Ali S, Tigoi C, Mupere E, Lancioni CL, Yoshioka E, Chisti MJ, Mburu M, Ngari M, Ngao N, Gichuki B, Omer E, Gumbi W, Singa B, Bandsma R, Ahmed T, Voskuijl W, Williams TN, Macharia A, Makale J, Mitchel A, Williams J, Gogain J, Janjic N, Mandal R, Wishart DS, Wu H, Xia L, Routledge M, Gong YY, Espinosa C, Aghaeepour N, Liu J, Houpt E, Lawley TD, Browne H, Shao Y, Rwigi D, Kariuki K, Kaburu T, Uhlig HH, Gartner L, Jones K, Koulman A, Walson J, Berkley J. The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia. Gates Open Res 2022; 6:77. [PMID: 36415883 PMCID: PMC9646488 DOI: 10.12688/gatesopenres.13635.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2022] [Indexed: 08/10/2023] Open
Abstract
Introduction: Many acutely ill children in low- and middle-income settings have a high risk of mortality both during and after hospitalisation despite guideline-based care. Understanding the biological mechanisms underpinning mortality may suggest optimal pathways to target for interventions to further reduce mortality. The Childhood Acute Illness and Nutrition (CHAIN) Network ( www.chainnnetwork.org) Nested Case-Cohort Study (CNCC) aims to investigate biological mechanisms leading to inpatient and post-discharge mortality through an integrated multi-omic approach. Methods and analysis; The CNCC comprises a subset of participants from the CHAIN cohort (1278/3101 hospitalised participants, including 350 children who died and 658 survivors, and 270/1140 well community children of similar age and household location) from nine sites in six countries across sub-Saharan Africa and South Asia. Systemic proteome, metabolome, lipidome, lipopolysaccharides, haemoglobin variants, toxins, pathogens, intestinal microbiome and biomarkers of enteropathy will be determined. Computational systems biology analysis will include machine learning and multivariate predictive modelling with stacked generalization approaches accounting for the different characteristics of each biological modality. This systems approach is anticipated to yield mechanistic insights, show interactions and behaviours of the components of biological entities, and help develop interventions to reduce mortality among acutely ill children. Ethics and dissemination. The CHAIN Network cohort and CNCC was approved by institutional review boards of all partner sites. Results will be published in open access, peer reviewed scientific journals and presented to academic and policy stakeholders. Data will be made publicly available, including uploading to recognised omics databases. Trial registration NCT03208725.
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Affiliation(s)
- James M. Njunge
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kirkby Tickell
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - Abdoulaye Hama Diallo
- Department of Public Health, Faculty of Health Sciences, University of Ouagadougou, Ouagadougou, Burkina Faso
| | | | - Md. Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ali Saleem
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Zaubina Kazi
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Syed Ali
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Caroline Tigoi
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ezekiel Mupere
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Emily Yoshioka
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Moses Mburu
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Moses Ngari
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Narshion Ngao
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Bonface Gichuki
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Elisha Omer
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Wilson Gumbi
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benson Singa
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Bandsma
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Wieger Voskuijl
- Amsterdam UMC location, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Centre for Global Child Health & Emma Children’s Hospital, Amsterdam, The Netherlands
| | - Thomas N. Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Institute of Global Health Innovation, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Alex Macharia
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Hang Wu
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Lei Xia
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Michael Routledge
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yun Yun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Camilo Espinosa
- Departments of Anesthesiology, Pain, and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nima Aghaeepour
- Departments of Anesthesiology, Pain, and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | | | - Yan Shao
- Wellcome Sanger Institute, Hinxton, UK
| | - Doreen Rwigi
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kevin Kariuki
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Timothy Kaburu
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lisa Gartner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kelsey Jones
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Gastroenterology Department, Great Ormond Street Hospital for Children, London, UK
| | - Albert Koulman
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- NIHR BRC Nutritional Biomarker Laboratory, University of Cambridge, Cambridge, UK
| | - Judd Walson
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - James Berkley
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Center for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
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3
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Njunge JM, Tickell K, Diallo AH, Sayeem Bin Shahid ASM, Gazi MA, Saleem A, Kazi Z, Ali S, Tigoi C, Mupere E, Lancioni CL, Yoshioka E, Chisti MJ, Mburu M, Ngari M, Ngao N, Gichuki B, Omer E, Gumbi W, Singa B, Bandsma R, Ahmed T, Voskuijl W, Williams TN, Macharia A, Makale J, Mitchel A, Williams J, Gogain J, Janjic N, Mandal R, Wishart DS, Wu H, Xia L, Routledge M, Gong YY, Espinosa C, Aghaeepour N, Liu J, Houpt E, Lawley TD, Browne H, Shao Y, Rwigi D, Kariuki K, Kaburu T, Uhlig HH, Gartner L, Jones K, Koulman A, Walson J, Berkley J. The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia. Gates Open Res 2022; 6:77. [PMID: 36415883 PMCID: PMC9646488 DOI: 10.12688/gatesopenres.13635.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2022] [Indexed: 02/15/2024] Open
Abstract
Introduction: Many acutely ill children in low- and middle-income settings have a high risk of mortality both during and after hospitalisation despite guideline-based care. Understanding the biological mechanisms underpinning mortality may suggest optimal pathways to target for interventions to further reduce mortality. The Childhood Acute Illness and Nutrition (CHAIN) Network ( www.chainnnetwork.org) Nested Case-Cohort Study (CNCC) aims to investigate biological mechanisms leading to inpatient and post-discharge mortality through an integrated multi-omic approach. Methods and analysis; The CNCC comprises a subset of participants from the CHAIN cohort (1278/3101 hospitalised participants, including 350 children who died and 658 survivors, and 270/1140 well community children of similar age and household location) from nine sites in six countries across sub-Saharan Africa and South Asia. Systemic proteome, metabolome, lipidome, lipopolysaccharides, haemoglobin variants, toxins, pathogens, intestinal microbiome and biomarkers of enteropathy will be determined. Computational systems biology analysis will include machine learning and multivariate predictive modelling with stacked generalization approaches accounting for the different characteristics of each biological modality. This systems approach is anticipated to yield mechanistic insights, show interactions and behaviours of the components of biological entities, and help develop interventions to reduce mortality among acutely ill children. Ethics and dissemination. The CHAIN Network cohort and CNCC was approved by institutional review boards of all partner sites. Results will be published in open access, peer reviewed scientific journals and presented to academic and policy stakeholders. Data will be made publicly available, including uploading to recognised omics databases. Trial registration NCT03208725.
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Affiliation(s)
- James M. Njunge
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kirkby Tickell
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - Abdoulaye Hama Diallo
- Department of Public Health, Faculty of Health Sciences, University of Ouagadougou, Ouagadougou, Burkina Faso
| | | | - Md. Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ali Saleem
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Zaubina Kazi
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Syed Ali
- Department of Pediatrics and Child Health, Aga Khan University Hospital, Karachi, Karachi, Pakistan
| | - Caroline Tigoi
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ezekiel Mupere
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Emily Yoshioka
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Moses Mburu
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Moses Ngari
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Narshion Ngao
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Bonface Gichuki
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Elisha Omer
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Wilson Gumbi
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Benson Singa
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Bandsma
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biomedical Sciences, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Wieger Voskuijl
- Amsterdam UMC location, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Centre for Global Child Health & Emma Children’s Hospital, Amsterdam, The Netherlands
| | - Thomas N. Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Institute of Global Health Innovation, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Alex Macharia
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | | | | | | | | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Hang Wu
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Lei Xia
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Michael Routledge
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yun Yun Gong
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Camilo Espinosa
- Departments of Anesthesiology, Pain, and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nima Aghaeepour
- Departments of Anesthesiology, Pain, and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | | | - Yan Shao
- Wellcome Sanger Institute, Hinxton, UK
| | - Doreen Rwigi
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kevin Kariuki
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Timothy Kaburu
- The Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics and Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Lisa Gartner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kelsey Jones
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Gastroenterology Department, Great Ormond Street Hospital for Children, London, UK
| | - Albert Koulman
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- NIHR BRC Nutritional Biomarker Laboratory, University of Cambridge, Cambridge, UK
| | - Judd Walson
- Global Health and Epidemiology, University of Washington, Seattle, Seattle, USA
| | - James Berkley
- The Childhood Acute Illness and Nutrition Network, Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Center for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| |
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