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Stevenson DK, Gotlib IH, Buthmann JL, Marié I, Aghaeepour N, Gaudilliere B, Angst MS, Darmstadt GL, Druzin ML, Wong RJ, Shaw GM, Katz M. Stress and Its Consequences-Biological Strain. Am J Perinatol 2024; 41:1282-1284. [PMID: 35292943 DOI: 10.1055/a-1798-1602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Understanding the role of stress in pregnancy and its consequences is important, particularly given documented associations between maternal stress and preterm birth and other pathological outcomes. Physical and psychological stressors can elicit the same biological responses, known as biological strain. Chronic stressors, like poverty and racism (race-based discriminatory treatment), may create a legacy or trajectory of biological strain that no amount of coping can relieve in the absence of larger-scale socio-behavioral or societal changes. An integrative approach that takes into consideration simultaneously social and biological determinants of stress may provide the best insights into the risk of preterm birth. The most successful computational approaches and the most predictive machine-learning models are likely to be those that combine information about the stressors and the biological strain (for example, as measured by different omics) experienced during pregnancy.
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Affiliation(s)
- David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Ian H Gotlib
- Department of Psychology, Stanford University School of Humanities and Science, Stanford, California
| | - Jessica L Buthmann
- Department of Psychology, Stanford University School of Humanities and Science, Stanford, California
| | - Ivana Marié
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California
| | - Gary L Darmstadt
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Maurice L Druzin
- Department of Obstetrics and Gynecology-Maternal-Fetal Medicine, Stanford University School of Medicine, Stanford, California
| | - Ronald J Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Gary M Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Michael Katz
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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2
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Stevenson DK, Winn VD, Shaw GM, England SK, Wong RJ. Solving the Puzzle of Preterm Birth. Clin Perinatol 2024; 51:291-300. [PMID: 38705641 DOI: 10.1016/j.clp.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Solving the puzzle of preterm birth has been challenging and will require novel integrative solutions as preterm birth likely arises from many etiologies. It has been demonstrated that many sociodemographic and psychological determinants of preterm birth relate to its complex biology. It is this understanding that has enabled the development of a novel preventative strategy, which integrates the omics profile (genome, epigenome, transcriptome, proteome, metabolome, microbiome) with sociodemographic, environmental, and psychological determinants of individual pregnant people to solve the puzzle of preterm birth.
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Affiliation(s)
- David K Stevenson
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Biomedical Innovations Building (BMI), 240 Pasteur Drive, Room 2652, Stanford, CA 94305, USA.
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Division of Reproductive, Stem Cell and Perinatal Biology, Stanford University of School of Medicine, Biomedical Innovations Building (BMI), 240 Pasteur Drive, Module 2700, Stanford, CA 94305, USA
| | - Gary M Shaw
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Biomedical Innovations Building (BMI), 240 Pasteur Drive, Room 2652, Stanford, CA 94305, USA
| | - Sarah K England
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, 425 S. Euclid Avenue, CB 8064, St. Louis, MO 63110, USA
| | - Ronald J Wong
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Biomedical Innovations Building (BMI), 240 Pasteur Drive, Room 2652, Stanford, CA 94305, USA
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3
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Feyaerts D, Marić I, Arck PC, Prins JR, Gomez-Lopez N, Gaudillière B, Stelzer IA. Predicting Spontaneous Preterm Birth Using the Immunome. Clin Perinatol 2024; 51:441-459. [PMID: 38705651 DOI: 10.1016/j.clp.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Throughout pregnancy, the maternal peripheral circulation contains valuable information reflecting pregnancy progression, detectable as tightly regulated immune dynamics. Local immune processes at the maternal-fetal interface and other reproductive and non-reproductive tissues are likely to be the pacemakers for this peripheral immune "clock." This cellular immune status of pregnancy can be leveraged for the early risk assessment and prediction of spontaneous preterm birth (sPTB). Systems immunology approaches to sPTB subtypes and cross-tissue (local and peripheral) interactions, as well as integration of multiple biological data modalities promise to improve our understanding of preterm birth pathobiology and identify potential clinically actionable biomarkers.
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Affiliation(s)
- Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ivana Marić
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA 94304, USA
| | - Petra C Arck
- Department of Obstetrics and Fetal Medicine and Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20251 Hamburg, Germany
| | - Jelmer R Prins
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Postbus 30.001, 9700RB, Groningen, The Netherlands
| | - Nardhy Gomez-Lopez
- Department of Obstetrics and Gynecology, Washington University School of Medicine, 425 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, 425 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA 94305, USA; Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ina A Stelzer
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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4
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Mirzaei A, Hiller BC, Stelzer IA, Thiele K, Tan Y, Becker M. Computational Approaches for Connecting Maternal Stress to Preterm Birth. Clin Perinatol 2024; 51:345-360. [PMID: 38705645 DOI: 10.1016/j.clp.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Multiple studies have hinted at a complex connection between maternal stress and preterm birth (PTB). This article describes the potential of computational methods to provide new insights into this relationship. For this, we outline existing approaches for stress assessments and various data modalities available for profiling stress responses, and review studies that sought either to establish a connection between stress and PTB or to predict PTB based on stress-related factors. Finally, we summarize the challenges of computational methods, highlighting potential future research directions within this field.
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Affiliation(s)
- Amin Mirzaei
- Department of Computer Science and Electrical Engineering, Institute for Visual and Analytic Computing, Universität Rostock, Albert-Einstein-Straße 22, 18059 Rostock, Germany
| | - Bjarne C Hiller
- Department of Computer Science and Electrical Engineering, Institute for Visual and Analytic Computing, Universität Rostock, Albert-Einstein-Straße 22, 18059 Rostock, Germany
| | - Ina A Stelzer
- Department of Pathology, University of California San Diego, GPL/CMM-West, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kristin Thiele
- Division for Experimental Feto-Maternal Medicine, Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Center for Obstetrics and Pediatrics, Martinistrasse 52, 20246 Hamburg, Germany
| | - Yuqi Tan
- Department of Microbiology and Immunology, Stanford University School of Medicine, CSSR3220, 269 Campus Drive, Stanford, CA 94305, USA
| | - Martin Becker
- Department of Computer Science and Electrical Engineering, Institute for Visual and Analytic Computing, Universität Rostock, Albert-Einstein-Straße 22, 18059 Rostock, Germany.
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5
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Seong D, Espinosa C, Aghaeepour N. Computational Approaches for Predicting Preterm Birth and Newborn Outcomes. Clin Perinatol 2024; 51:461-473. [PMID: 38705652 PMCID: PMC11070639 DOI: 10.1016/j.clp.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Preterm birth (PTB) and its associated morbidities are a leading cause of infant mortality and morbidity. Accurate predictive models and a better biological understanding of PTB-associated morbidities are critical in reducing their adverse effects. Increasing availability of multimodal high-dimensional data sets with concurrent advances in artificial intelligence (AI) have created a rich opportunity to gain novel insights into PTB, a clinically complex and multifactorial disease. Here, the authors review the use of AI to analyze 3 modes of data: electronic health records, biological omics, and social determinants of health metrics.
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Affiliation(s)
- David Seong
- Immunology Program, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Medical Scientist Training Program, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA
| | - Camilo Espinosa
- Immunology Program, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Biomedical Data Science, Stanford University, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA; Department of Biomedical Data Science, Stanford University, 300 Pasteur Drive, Grant S280, Stanford, CA 94305-5117, USA.
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6
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med 2024; 5:101350. [PMID: 38134931 PMCID: PMC10829755 DOI: 10.1016/j.xcrm.2023.101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/15/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA.
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; March of Dimes Prematurity Research Center at Stanford University, Stanford, CA, USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain; IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Boris Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Pierfrancesco Novielli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Donato Romano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Ester Pantaleo
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Mirco Vacca
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sabina Tangaro
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Abigail Kuntzleman
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Isaac Bigcraft
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Stephen Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Daehun Bae
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Eunyoung Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA
| | - Sherrianne Ng
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Patricia Diaz-Gimeno
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Gustavo Stolovitzky
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA; Thomas J. Watson Research Center, IBM, Yorktown Heights, NY, USA; Sema4, Stamford, CT, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Detroit Medical Center, Detroit, MI, USA; Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
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7
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Ravindra NG, Espinosa C, Berson E, Phongpreecha T, Zhao P, Becker M, Chang AL, Shome S, Marić I, De Francesco D, Mataraso S, Saarunya G, Thuraiappah M, Xue L, Gaudillière B, Angst MS, Shaw GM, Herzog ED, Stevenson DK, England SK, Aghaeepour N. Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity. NPJ Digit Med 2023; 6:171. [PMID: 37770643 PMCID: PMC10539360 DOI: 10.1038/s41746-023-00911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
Preterm birth (PTB) is the leading cause of infant mortality globally. Research has focused on developing predictive models for PTB without prioritizing cost-effective interventions. Physical activity and sleep present unique opportunities for interventions in low- and middle-income populations (LMICs). However, objective measurement of physical activity and sleep remains challenging and self-reported metrics suffer from low-resolution and accuracy. In this study, we use physical activity data collected using a wearable device comprising over 181,944 h of data across N = 1083 patients. Using a new state-of-the art deep learning time-series classification architecture, we develop a 'clock' of healthy dynamics during pregnancy by using gestational age (GA) as a surrogate for progression of pregnancy. We also develop novel interpretability algorithms that integrate unsupervised clustering, model error analysis, feature attribution, and automated actigraphy analysis, allowing for model interpretation with respect to sleep, activity, and clinical variables. Our model performs significantly better than 7 other machine learning and AI methods for modeling the progression of pregnancy. We found that deviations from a normal 'clock' of physical activity and sleep changes during pregnancy are strongly associated with pregnancy outcomes. When our model underestimates GA, there are 0.52 fewer preterm births than expected (P = 1.01e - 67, permutation test) and when our model overestimates GA, there are 1.44 times (P = 2.82e - 39, permutation test) more preterm births than expected. Model error is negatively correlated with interdaily stability (P = 0.043, Spearman's), indicating that our model assigns a more advanced GA when an individual's daily rhythms are less precise. Supporting this, our model attributes higher importance to sleep periods in predicting higher-than-actual GA, relative to lower-than-actual GA (P = 1.01e - 21, Mann-Whitney U). Combining prediction and interpretability allows us to signal when activity behaviors alter the likelihood of preterm birth and advocates for the development of clinical decision support through passive monitoring and exercise habit and sleep recommendations, which can be easily implemented in LMICs.
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Affiliation(s)
- Neal G Ravindra
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Eloïse Berson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - Peinan Zhao
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Sayane Shome
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Ivana Marić
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Davide De Francesco
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Geetha Saarunya
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Melan Thuraiappah
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Lei Xue
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Erik D Herzog
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Sarah K England
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford School of Medicine, Stanford, CA, USA.
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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8
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Barak O, Lovelace T, Piekos S, Chu T, Cao Z, Sadovsky E, Mouillet JF, Ouyang Y, Parks WT, Hood L, Price ND, Benos PV, Sadovsky Y. Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes. BMC Med 2023; 21:349. [PMID: 37679695 PMCID: PMC10485945 DOI: 10.1186/s12916-023-03054-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Placental dysfunction, a root cause of common syndromes affecting human pregnancy, such as preeclampsia (PE), fetal growth restriction (FGR), and spontaneous preterm delivery (sPTD), remains poorly defined. These common, yet clinically disparate obstetrical syndromes share similar placental histopathologic patterns, while individuals within each syndrome present distinct molecular changes, challenging our understanding and hindering our ability to prevent and treat these syndromes. METHODS Using our extensive biobank, we identified women with severe PE (n = 75), FGR (n = 40), FGR with a hypertensive disorder (FGR + HDP; n = 33), sPTD (n = 72), and two uncomplicated control groups, term (n = 113), and preterm without PE, FGR, or sPTD (n = 16). We used placental biopsies for transcriptomics, proteomics, metabolomics data, and histological evaluation. After conventional pairwise comparison, we deployed an unbiased, AI-based similarity network fusion (SNF) to integrate the datatypes and identify omics-defined placental clusters. We used Bayesian model selection to compare the association between the histopathological features and disease conditions vs SNF clusters. RESULTS Pairwise, disease-based comparisons exhibited relatively few differences, likely reflecting the heterogeneity of the clinical syndromes. Therefore, we deployed the unbiased, omics-based SNF method. Our analysis resulted in four distinct clusters, which were mostly dominated by a specific syndrome. Notably, the cluster dominated by early-onset PE exhibited strong placental dysfunction patterns, with weaker injury patterns in the cluster dominated by sPTD. The SNF-defined clusters exhibited better correlation with the histopathology than the predefined disease groups. CONCLUSIONS Our results demonstrate that integrated omics-based SNF distinctively reclassifies placental dysfunction patterns underlying the common obstetrical syndromes, improves our understanding of the pathological processes, and could promote a search for more personalized interventions.
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Affiliation(s)
- Oren Barak
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Tyler Lovelace
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Joint CMU-Pitt PhD Program in Computational Biology, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
| | - Samantha Piekos
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Zhishen Cao
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Elena Sadovsky
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - W Tony Parks
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Simcoe Hall, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Leroy Hood
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
| | - Nathan D Price
- Institute for Systems Biology, 401 Terri Avenue North, Seattle, WA, 98109, USA
- Thorne HealthTech, 152 West 57th Street, New York, NY, 10019, USA
| | - Panayiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Joint CMU-Pitt PhD Program in Computational Biology, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15260, USA
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, FL, 32610, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 300 Halket Street, Pittsburgh, PA, 15213, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA, 15219, USA.
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9
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Shamshuzzoha M, Islam MM. Early Prediction Model of Macrosomia Using Machine Learning for Clinical Decision Support. Diagnostics (Basel) 2023; 13:2754. [PMID: 37685292 PMCID: PMC10487237 DOI: 10.3390/diagnostics13172754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 09/10/2023] Open
Abstract
The condition of fetal overgrowth, also known as macrosomia, can cause serious health complications for both the mother and the infant. It is crucial to identify high-risk macrosomia-relevant pregnancies and intervene appropriately. Despite this need, there are several gaps in research related to macrosomia, including limited predictive models, insufficient machine learning applications, ineffective interventions, and inadequate understanding of how to integrate machine learning models into clinical decision-making. To address these gaps, we developed a machine learning-based model that uses maternal characteristics and medical history to predict macrosomia. Three different algorithms, namely logistic regression, support vector machine, and random forest, were used to develop the model. Based on the evaluation metrics, the logistic regression algorithm provided the best results among the three. The logistic regression algorithm was chosen as the final algorithm to predict macrosomia. The hyper parameters of the logistic regression model were tuned using cross-validation to achieve the best possible performance. Our results indicate that machine learning-based models have the potential to improve macrosomia prediction and enable appropriate interventions for high-risk pregnancies, leading to better health outcomes for both mother and fetus. By leveraging machine learning algorithms and addressing research gaps related to macrosomia, we can potentially reduce the health risks associated with this condition and make informed decisions about high-risk pregnancies.
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Affiliation(s)
| | - Md. Motaharul Islam
- Department of CSE, United International University, Madani Avenue, Dhaka 1212, Bangladesh;
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10
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Edwards TL, Greene CA, Piekos JA, Hellwege JN, Hampton G, Jasper EA, Velez Edwards DR. Challenges and Opportunities for Data Science in Women's Health. Annu Rev Biomed Data Sci 2023; 6:23-45. [PMID: 37040736 PMCID: PMC10877578 DOI: 10.1146/annurev-biodatasci-020722-105958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The intersection of women's health and data science is a field of research that has historically trailed other fields, but more recently it has gained momentum. This growth is being driven not only by new investigators who are moving into this area but also by the significant opportunities that have emerged in new methodologies, resources, and technologies in data science. Here, we describe some of the resources and methods being used by women's health researchers today to meet challenges in biomedical data science. We also describe the opportunities and limitations of applying these approaches to advance women's health outcomes and the future of the field, with emphasis on repurposing existing methodologies for women's health.
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Affiliation(s)
- Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Catherine A Greene
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacqueline A Piekos
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gabrielle Hampton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
| | - Elizabeth A Jasper
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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11
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Mishra A, Hirani S, Hirani S, Shaikh MYD, Khanholkar S, Prasad R, Wanjari M. Arnold-Chiari Malformations in Pregnancy and Labor: Challenges and Management Strategies. Cureus 2023; 15:e43688. [PMID: 37724202 PMCID: PMC10505272 DOI: 10.7759/cureus.43688] [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] [Received: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
Arnold-Chiari malformations (ACMs) present unique challenges in pregnancy and labor, requiring a comprehensive understanding and multidisciplinary approach to care. This review article provides an overview of ACMs, including their definition, classification, and prevalence. The challenges in diagnosing ACMs during pregnancy, the available imaging modalities, and screening recommendations are discussed. The impact of ACMs on maternal health, fetal development, and the management strategies employed during pregnancy and labor are explored. Emphasis is placed on the importance of a multidisciplinary approach involving neurologists, obstetricians, and other specialists. Medical management options for symptom relief, surgical interventions, and anesthetic considerations during labor and delivery are also addressed. The importance of postpartum care, breastfeeding considerations, and long-term follow-up for women with ACMs who desire future pregnancies are highlighted. Finally, areas for further research and advancements in ACM management are identified. By improving our understanding and management of ACMs in pregnancy and labor, healthcare professionals can optimize care and improve outcomes for mothers and babies affected by this condition.
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Affiliation(s)
- Aditi Mishra
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Shoyeb Hirani
- Medicine, Mahatma Gandhi Medical College and Hospital, Aurangabad, IND
| | - Sajid Hirani
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Mohammed Yusuf D Shaikh
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Shubham Khanholkar
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Roshan Prasad
- Internal Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Mayur Wanjari
- Research and Development, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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12
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Espinosa CA, Khan W, Khanam R, Das S, Khalid J, Pervin J, Kasaro MP, Contrepois K, Chang AL, Phongpreecha T, Michael B, Ellenberger M, Mehmood U, Hotwani A, Nizar A, Kabir F, Wong RJ, Becker M, Berson E, Culos A, De Francesco D, Mataraso S, Ravindra N, Thuraiappah M, Xenochristou M, Stelzer IA, Marić I, Dutta A, Raqib R, Ahmed S, Rahman S, Hasan ASMT, Ali SM, Juma MH, Rahman M, Aktar S, Deb S, Price JT, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Stringer JSA, Gaudilliere B, Snyder MP, Angst MS, Rahman A, Baqui AH, Jehan F, Nisar MI, Vwalika B, Sazawal S, Shaw GM, Stevenson DK, Aghaeepour N. Multiomic signals associated with maternal epidemiological factors contributing to preterm birth in low- and middle-income countries. SCIENCE ADVANCES 2023; 9:eade7692. [PMID: 37224249 PMCID: PMC10208584 DOI: 10.1126/sciadv.ade7692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
Preterm birth (PTB) is the leading cause of death in children under five, yet comprehensive studies are hindered by its multiple complex etiologies. Epidemiological associations between PTB and maternal characteristics have been previously described. This work used multiomic profiling and multivariate modeling to investigate the biological signatures of these characteristics. Maternal covariates were collected during pregnancy from 13,841 pregnant women across five sites. Plasma samples from 231 participants were analyzed to generate proteomic, metabolomic, and lipidomic datasets. Machine learning models showed robust performance for the prediction of PTB (AUROC = 0.70), time-to-delivery (r = 0.65), maternal age (r = 0.59), gravidity (r = 0.56), and BMI (r = 0.81). Time-to-delivery biological correlates included fetal-associated proteins (e.g., ALPP, AFP, and PGF) and immune proteins (e.g., PD-L1, CCL28, and LIFR). Maternal age negatively correlated with collagen COL9A1, gravidity with endothelial NOS and inflammatory chemokine CXCL13, and BMI with leptin and structural protein FABP4. These results provide an integrated view of epidemiological factors associated with PTB and identify biological signatures of clinical covariates affecting this disease.
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Affiliation(s)
- Camilo A. Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sayan Das
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Javairia Khalid
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Margaret P. Kasaro
- University of North Carolina Global Projects Zambia, Lusaka, Zambia
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alan L. Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Basil Michael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mathew Ellenberger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Ambreen Nizar
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Eloise Berson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Davide De Francesco
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Neal Ravindra
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Melan Thuraiappah
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ina A. Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivana Marić
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Arup Dutta
- Centre for Public Health Kinetics, New Delhi, Delhi, India
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Said M. Ali
- Public Health Laboratory—Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Mohamed H. Juma
- Public Health Laboratory—Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Monjur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shaki Aktar
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Saikat Deb
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Public Health Laboratory—Ivo de Carneri, Pemba, Zanzibar, Tanzania
| | - Joan T. Price
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Obstetrics and Gynaecology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Paul H. Wise
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginia D. Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maurice L. Druzin
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald S. Gibbs
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary L. Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jeffrey S. A. Stringer
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Abdullah H. Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan
| | - Bellington Vwalika
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Obstetrics and Gynaecology, University of Zambia School of Medicine, Lusaka, Zambia
| | - Sunil Sazawal
- Centre for Public Health Kinetics, New Delhi, Delhi, India
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
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13
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Giles ML, Sing Way S, Marchant A, Aghaepour N, James T, Schaltz-Buchholzer F, Zazara D, Arck P, Kollmann TR. Maternal vaccination to prevent adverse pregnancy outcomes: An underutilized molecular immunological intervention? J Mol Biol 2023; 435:168097. [PMID: 37080422 DOI: 10.1016/j.jmb.2023.168097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
Adverse pregnancy outcomes including maternal mortality, stillbirth, preterm birth, intrauterine growth restriction cause millions of deaths each year. More effective interventions are urgently needed. Maternal immunization could be one such intervention protecting the mother and newborn from infection through its pathogen-specific effects. However, many adverse pregnancy outcomes are not directly linked to the infectious pathogens targeted by existing maternal vaccines but rather are linked to pathological inflammation unfolding during pregnancy. The underlying pathogenesis driving such unfavourable outcomes have only partially been elucidated but appear to relate to altered immune regulation by innate as well as adaptive immune responses, ultimately leading to aberrant maternal immune activation. Maternal immunization, like all immunization, impacts the immune system beyond pathogen-specific immunity. This raises the possibility that maternal vaccination could potentially be utilised as a pathogen-agnostic immune modulatory intervention to redirect abnormal immune trajectories towards a more favourable phenotype providing pregnancy protection. In this review we describe the epidemiological evidence surrounding this hypothesis, along with the mechanistic plausibility and present a possible path forward to accelerate addressing the urgent need of adverse pregnancy outcomes.
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Affiliation(s)
| | - Sing Sing Way
- Center for Inflammation and Tolerance; Cincinnati Children's Hospital, Cincinnati USA
| | | | - Nima Aghaepour
- Stanford University School of Medicine, Stanford, CA, USA
| | - Tomin James
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Dimitra Zazara
- Division of Experimental Feto-Maternal Medicine, Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg, Hamburg, Germany
| | - Petra Arck
- Division of Experimental Feto-Maternal Medicine, Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg, Hamburg, Germany
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14
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.07.23286920. [PMID: 36945505 PMCID: PMC10029035 DOI: 10.1101/2023.03.07.23286920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We present a crowdsourcing approach to predict: (a) preterm or (b) early preterm birth from 9 publicly available vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from raw sequences via an open-source tool, MaLiAmPi. We validated the crowdsourced models on novel datasets representing 331 samples from 148 pregnant individuals. From 318 DREAM challenge participants we received 148 and 121 submissions for our two separate prediction sub-challenges with top-ranking submissions achieving bootstrapped AUROC scores of 0.69 and 0.87, respectively. Alpha diversity, VALENCIA community state types, and composition (via phylotype relative abundance) were important features in the top performing models, most of which were tree based methods. This work serves as the foundation for subsequent efforts to translate predictive tests into clinical practice, and to better understand and prevent preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Pierfrancesco Novielli
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Donato Romano
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Ester Pantaleo
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
| | - Nicola Amoroso
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Alfonso Monaco
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Mirco Vacca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Maria De Angelis
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Bellotti
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Sabina Tangaro
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Abigail Kuntzleman
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
| | - Isaac Bigcraft
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Stephen Techtmann
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Daehun Bae
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Eunyoung Kim
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | | | - Soobok Joe
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Kevin R Theis
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Sherrianne Ng
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | - Yun S Lee Li
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Patricia Diaz-Gimeno
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Phillip R Bennett
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David A MacIntyre
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Gustavo Stolovitzky
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | | | - Nardhy Gomez-Lopez
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Romero
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Adi L Tarca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - James C Costello
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
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15
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Becker M, Nassar H, Espinosa C, Stelzer IA, Feyaerts D, Berson E, Bidoki NH, Chang AL, Saarunya G, Culos A, De Francesco D, Fallahzadeh R, Liu Q, Kim Y, Marić I, Mataraso SJ, Payrovnaziri SN, Phongpreecha T, Ravindra NG, Stanley N, Shome S, Tan Y, Thuraiappah M, Xenochristou M, Xue L, Shaw G, Stevenson D, Angst MS, Gaudilliere B, Aghaeepour N. Large-scale correlation network construction for unraveling the coordination of complex biological systems. NATURE COMPUTATIONAL SCIENCE 2023; 3:346-359. [PMID: 38116462 PMCID: PMC10727505 DOI: 10.1038/s43588-023-00429-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 03/10/2023] [Indexed: 12/21/2023]
Abstract
Advanced measurement and data storage technologies have enabled high-dimensional profiling of complex biological systems. For this, modern multiomics studies regularly produce datasets with hundreds of thousands of measurements per sample, enabling a new era of precision medicine. Correlation analysis is an important first step to gain deeper insights into the coordination and underlying processes of such complex systems. However, the construction of large correlation networks in modern high-dimensional datasets remains a major computational challenge owing to rapidly growing runtime and memory requirements. Here we address this challenge by introducing CorALS (Correlation Analysis of Large-scale (biological) Systems), an open-source framework for the construction and analysis of large-scale parametric as well as non-parametric correlation networks for high-dimensional biological data. It features off-the-shelf algorithms suitable for both personal and high-performance computers, enabling workflows and downstream analysis approaches. We illustrate the broad scope and potential of CorALS by exploring perspectives on complex biological processes in large-scale multiomics and single-cell studies.
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Affiliation(s)
- Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Computer Science and Electrical Engineering, University of Rostock, Rostock, Germany
- These authors contributed equally: Martin Becker, Huda Nassar, Camilo Espinosa
| | - Huda Nassar
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
- These authors contributed equally: Martin Becker, Huda Nassar, Camilo Espinosa
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
- These authors contributed equally: Martin Becker, Huda Nassar, Camilo Espinosa
| | - Ina A. Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Eloise Berson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Neda H. Bidoki
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Alan L. Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Geetha Saarunya
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Davide De Francesco
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Qun Liu
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Yeasul Kim
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Ivana Marić
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Samson J. Mataraso
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Seyedeh Neelufar Payrovnaziri
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Neal G. Ravindra
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Natalie Stanley
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sayane Shome
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Yuqi Tan
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Melan Thuraiappah
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lei Xue
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Gary Shaw
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - David Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, USA
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16
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De Francesco D, Reiss JD, Roger J, Tang AS, Chang AL, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le BL, Ravindra NG, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein MG, Oskotsky T, Marić I, Gaudilliere B, Carvalho B, Bateman BT, Angst MS, Prince LS, Blumenfeld YJ, Benitz WE, Fuerch JH, Shaw GM, Sylvester KG, Stevenson DK, Sirota M, Aghaeepour N. Data-driven longitudinal characterization of neonatal health and morbidity. Sci Transl Med 2023; 15:eadc9854. [PMID: 36791208 PMCID: PMC10197092 DOI: 10.1126/scitranslmed.adc9854] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 01/11/2023] [Indexed: 02/17/2023]
Abstract
Although prematurity is the single largest cause of death in children under 5 years of age, the current definition of prematurity, based on gestational age, lacks the precision needed for guiding care decisions. Here, we propose a longitudinal risk assessment for adverse neonatal outcomes in newborns based on a deep learning model that uses electronic health records (EHRs) to predict a wide range of outcomes over a period starting shortly before conception and ending months after birth. By linking the EHRs of the Lucile Packard Children's Hospital and the Stanford Healthcare Adult Hospital, we developed a cohort of 22,104 mother-newborn dyads delivered between 2014 and 2018. Maternal and newborn EHRs were extracted and used to train a multi-input multitask deep learning model, featuring a long short-term memory neural network, to predict 24 different neonatal outcomes. An additional cohort of 10,250 mother-newborn dyads delivered at the same Stanford Hospitals from 2019 to September 2020 was used to validate the model. Areas under the receiver operating characteristic curve at delivery exceeded 0.9 for 10 of the 24 neonatal outcomes considered and were between 0.8 and 0.9 for 7 additional outcomes. Moreover, comprehensive association analysis identified multiple known associations between various maternal and neonatal features and specific neonatal outcomes. This study used linked EHRs from more than 30,000 mother-newborn dyads and would serve as a resource for the investigation and prediction of neonatal outcomes. An interactive website is available for independent investigators to leverage this unique dataset: https://maternal-child-health-associations.shinyapps.io/shiny_app/.
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Affiliation(s)
- Davide De Francesco
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Jonathan D. Reiss
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacquelyn Roger
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143, USA
| | - Alice S. Tang
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143, USA
- Graduate Program in Bioengineering, University of California, San Francisco, CA 94158, USA
| | - Alan L. Chang
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Susanna Morin
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143, USA
| | - Eloïse Berson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melan Thuraiappah
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Brian L. Le
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Neal G. Ravindra
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Seyedeh Neelufar Payrovnaziri
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Samson Mataraso
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Yeasul Kim
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Lei Xue
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Melissa G. Rosenstein
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94158, USA
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Ivana Marić
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brendan Carvalho
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T. Bateman
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lawrence S. Prince
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yair J. Blumenfeld
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William E. Benitz
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janene H. Fuerch
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karl G. Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA
- Department of Pediatrics, University of California, San Francisco, CA 94143, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain 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, Stanford, CA 94305, USA
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17
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Pammi M, Aghaeepour N, Neu J. Multiomics, artificial intelligence, and precision medicine in perinatology. Pediatr Res 2023; 93:308-315. [PMID: 35804156 PMCID: PMC9825681 DOI: 10.1038/s41390-022-02181-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/12/2022] [Accepted: 05/30/2022] [Indexed: 01/11/2023]
Abstract
Technological advances in omics evaluation, bioinformatics, and artificial intelligence have made us rethink ways to improve patient outcomes. Collective quantification and characterization of biological data including genomics, epigenomics, metabolomics, and proteomics is now feasible at low cost with rapid turnover. Significant advances in the integration methods of these multiomics data sets by machine learning promise us a holistic view of disease pathogenesis and yield biomarkers for disease diagnosis and prognosis. Using machine learning tools and algorithms, it is possible to integrate multiomics data with clinical information to develop predictive models that identify risk before the condition is clinically apparent, thus facilitating early interventions to improve the health trajectories of the patients. In this review, we intend to update the readers on the recent developments related to the use of artificial intelligence in integrating multiomic and clinical data sets in the field of perinatology, focusing on neonatal intensive care and the opportunities for precision medicine. We intend to briefly discuss the potential negative societal and ethical consequences of using artificial intelligence in healthcare. We are poised for a new era in medicine where computational analysis of biological and clinical data sets will make precision medicine a reality. IMPACT: Biotechnological advances have made multiomic evaluations feasible and integration of multiomics data may provide a holistic view of disease pathophysiology. Artificial Intelligence and machine learning tools are being increasingly used in healthcare for diagnosis, prognostication, and outcome predictions. Leveraging artificial intelligence and machine learning tools for integration of multiomics and clinical data will pave the way for precision medicine in perinatology.
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Affiliation(s)
- Mohan Pammi
- Section of Neonatology, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.
| | - Nima Aghaeepour
- Departments of Anesthesiology, Pediatrics, and Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Josef Neu
- Section of Neonatology, Department of Pediatrics, University of Florida, Gainesville, FL, USA
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18
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Ozen M, Aghaeepour N, Marić I, Wong RJ, Stevenson DK, Jantzie LL. Omics approaches: interactions at the maternal-fetal interface and origins of child health and disease. Pediatr Res 2023; 93:366-375. [PMID: 36216868 PMCID: PMC9549444 DOI: 10.1038/s41390-022-02335-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/08/2022] [Accepted: 09/18/2022] [Indexed: 11/09/2022]
Abstract
Immunoperinatology is an emerging field. Transdisciplinary efforts by physicians, physician-scientists, basic science researchers, and computational biologists have made substantial advancements by identifying unique immunologic signatures of specific diseases, discovering innovative preventative or treatment strategies, and establishing foundations for individualized neonatal intensive care of the most vulnerable neonates. In this review, we summarize the immunobiology and immunopathology of pregnancy, highlight omics approaches to study the maternal-fetal interface, and their contributions to pregnancy health. We examined the importance of transdisciplinary, multiomic (such as genomics, transcriptomics, proteomics, metabolomics, and immunomics) and machine-learning strategies in unraveling the mechanisms of adverse pregnancy, neonatal, and childhood outcomes and how they can guide the development of novel therapies to improve maternal and neonatal health. IMPACT: Discuss immunoperinatology research from the lens of omics and machine-learning approaches. Identify opportunities for omics-based approaches to delineate infection/inflammation-associated maternal, neonatal, and later life adverse outcomes (e.g., histologic chorioamnionitis [HCA]).
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Affiliation(s)
- Maide Ozen
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Nima Aghaeepour
- Department of Anesthesiology, Pain, and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Ivana Marić
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald J Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren L Jantzie
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kennedy Krieger Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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19
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Muglia LJ, Benhalima K, Tong S, Ozanne S. Maternal factors during pregnancy influencing maternal, fetal, and childhood outcomes. BMC Med 2022; 20:418. [PMID: 36320027 PMCID: PMC9623926 DOI: 10.1186/s12916-022-02632-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Enhancing pregnancy health is known to improve the mother's and offspring's life-long well-being. The maternal environment, encompassing genetic factors, impacts of social determinants, the nutritional/metabolic milieu, and infections and inflammation, have immediate consequences for the in utero development of the fetus and long-term programming into childhood and adulthood. Moreover, adverse pregnancy outcomes such as preterm birth or preeclampsia, often attributed to the maternal environmental factors listed above, have been associated with poor maternal cardiometabolic health after pregnancy. In this BMC Medicine article collection, we explore a broad spectrum of maternal characteristics across pregnancy and postnatal phenotypes, anticipating substantial cross-fertilization of new understanding and shared mechanisms around diverse outcomes. Advances in the ability to leverage 'omics across different platforms (genome, transcriptome, proteome, metabolome, microbiome, lipidome), large high-dimensional population databases, and unique cohorts are generating exciting new insights: The first articles in this collection highlight the role of placental biomarkers of preterm birth, metabolic influences on fetal and childhood growth, and the impact of common pre-existing maternal disorders, obesity and smoking on pregnancy outcomes, and the child's health. As the collection grows, we look forward to seeing the connections emerge across maternal, fetal, and childhood outcomes that will foster new insights and preventative strategies for women.
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Affiliation(s)
- Louis J Muglia
- Burroughs Wellcome Fund, Research Triangle Park, Durham, NC, USA.
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | | | - Stephen Tong
- University of Melbourne, Melbourne, Australia
- Mercy Perinatal, Heidelberg, Australia
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20
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Fredriksson A, Fulcher IR, Russell AL, Li T, Tsai YT, Seif SS, Mpembeni RN, Hedt-Gauthier B. Machine learning for maternal health: Predicting delivery location in a community health worker program in Zanzibar. Front Digit Health 2022; 4:855236. [PMID: 36060544 PMCID: PMC9428344 DOI: 10.3389/fdgth.2022.855236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Background Maternal and neonatal health outcomes in low- and middle-income countries (LMICs) have improved over the last two decades. However, many pregnant women still deliver at home, which increases the health risks for both the mother and the child. Community health worker programs have been broadly employed in LMICs to connect women to antenatal care and delivery locations. More recently, employment of digital tools in maternal health programs have resulted in better care delivery and served as a routine mode of data collection. Despite the availability of rich, patient-level data within these digital tools, there has been limited utilization of this type of data to inform program delivery in LMICs. Methods We use program data from 38,787 women enrolled in Safer Deliveries, a community health worker program in Zanzibar, to build a generalizable prediction model that accurately predicts whether a newly enrolled pregnant woman will deliver in a health facility. We use information collected during the enrollment visit, including demographic data, health characteristics and current pregnancy information. We apply four machine learning methods: logistic regression, LASSO regularized logistic regression, random forest and an artificial neural network; and three sampling techniques to address the imbalanced data: undersampling of facility deliveries, oversampling of home deliveries and addition of synthetic home deliveries using SMOTE. Results Our models correctly predicted the delivery location for 68%–77% of the women in the test set, with slightly higher accuracy when predicting facility delivery versus home delivery. A random forest model with a balanced training set created using undersampling of existing facility deliveries accurately identified 74.4% of women delivering at home. Conclusions This model can provide a “real-time” prediction of the delivery location for new maternal health program enrollees and may enable early provision of extra support for individuals at risk of not delivering in a health facility, which has potential to improve health outcomes for both mothers and their newborns. The framework presented here is applicable in other contexts and the selection of input features can easily be adapted to match data availability and other outcomes, both within and beyond maternal health.
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Affiliation(s)
- Alma Fredriksson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Correspondence: Alma Fredriksson
| | - Isabel R. Fulcher
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
- Harvard Data Science Initiative, Cambridge, MA, United States
| | | | - Tracey Li
- D-tree International, Dar es Salaam, Tanzania
| | - Yi-Ting Tsai
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | | | - Rose N. Mpembeni
- Department of Epidemiology and Biostatistics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bethany Hedt-Gauthier
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, United States
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21
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Black swans and ambitious overgeneralization in newborn intensive care. Pediatr Res 2022; 92:357-359. [PMID: 34601493 DOI: 10.1038/s41390-021-01771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 11/09/2022]
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22
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Vicoveanu P, Vasilache IA, Scripcariu IS, Nemescu D, Carauleanu A, Vicoveanu D, Covali AR, Filip C, Socolov D. Use of a Feed-Forward Back Propagation Network for the Prediction of Small for Gestational Age Newborns in a Cohort of Pregnant Patients with Thrombophilia. Diagnostics (Basel) 2022; 12:diagnostics12041009. [PMID: 35454057 PMCID: PMC9025417 DOI: 10.3390/diagnostics12041009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/25/2023] Open
Abstract
(1) Background: Fetal growth restriction is a relatively common disorder in pregnant patients with thrombophilia. New artificial intelligence algorithms are a promising option for the prediction of adverse obstetrical outcomes. The aim of this study was to evaluate the predictive performance of a Feed-Forward Back Propagation Network (FFBPN) for the prediction of small for gestational age (SGA) newborns in a cohort of pregnant patients with thrombophilia. (2) Methods: This observational retrospective study included all pregnancies in women with thrombophilia who attended two tertiary maternity hospitals in Romania between January 2013 and December 2020. Bivariate associations of SGA and each predictor variable were evaluated. Clinical and paraclinical predictors were further included in a FFBPN, and its predictive performance was assessed. (3) Results: The model had an area under the curve (AUC) of 0.95, with a true positive rate of 86.7%, and a false discovery rate of 10.5%. The overall accuracy of our model was 90%. (4) Conclusion: This is the first study in the literature that evaluated the performance of a FFBPN for the prediction of pregnant patients with thrombophilia at a high risk of giving birth to SGA newborns, and its promising results could lead to a tailored prenatal management.
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Affiliation(s)
- Petronela Vicoveanu
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
| | - Ingrid Andrada Vasilache
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
- Correspondence:
| | - Ioana Sadiye Scripcariu
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
| | - Dragos Nemescu
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
| | - Alexandru Carauleanu
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
| | - Dragos Vicoveanu
- Faculty of Electrical Engineering and Computer Science, Stefan cel Mare University of Suceava, 720229 Suceava, Romania;
| | - Ana Roxana Covali
- Department of Radiology, Elena Doamna Obsterics and Gynecology University Hospital, 700398 Iasi, Romania;
| | - Catalina Filip
- Department of Vascular Surgery, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Demetra Socolov
- Department of Obstetrics and Gynecology, ‘Grigore T. Popa’ University of Medicine and Pharmacy, 700115 Iasi, Romania; (P.V.); (I.S.S.); (D.N.); (A.C.); (D.S.)
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23
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AlSaad R, Malluhi Q, Boughorbel S. PredictPTB: an interpretable preterm birth prediction model using attention-based recurrent neural networks. BioData Min 2022; 15:6. [PMID: 35164820 PMCID: PMC8842907 DOI: 10.1186/s13040-022-00289-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/23/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Early identification of pregnant women at risk for preterm birth (PTB), a major cause of infant mortality and morbidity, has a significant potential to improve prenatal care. However, we lack effective predictive models which can accurately forecast PTB and complement these predictions with appropriate interpretations for clinicians. In this work, we introduce a clinical prediction model (PredictPTB) which combines variables (medical codes) readily accessible through electronic health record (EHR) to accurately predict the risk of preterm birth at 1, 3, 6, and 9 months prior to delivery. METHODS The architecture of PredictPTB employs recurrent neural networks (RNNs) to model the longitudinal patient's EHR visits and exploits a single code-level attention mechanism to improve the predictive performance, while providing temporal code-level and visit-level explanations for the prediction results. We compare the performance of different combinations of prediction time-points, data modalities, and data windows. We also present a case-study of our model's interpretability illustrating how clinicians can gain some transparency into the predictions. RESULTS Leveraging a large cohort of 222,436 deliveries, comprising a total of 27,100 unique clinical concepts, our model was able to predict preterm birth with an ROC-AUC of 0.82, 0.79, 0.78, and PR-AUC of 0.40, 0.31, 0.24, at 1, 3, and 6 months prior to delivery, respectively. Results also confirm that observational data modalities (such as diagnoses) are more predictive for preterm birth than interventional data modalities (e.g., medications and procedures). CONCLUSIONS Our results demonstrate that PredictPTB can be utilized to achieve accurate and scalable predictions for preterm birth, complemented by explanations that directly highlight evidence in the patient's EHR timeline.
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Affiliation(s)
- Rawan AlSaad
- College of Engineering, Qatar University, Doha, Qatar
| | | | - Sabri Boughorbel
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
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Next generation strategies for preventing preterm birth. Adv Drug Deliv Rev 2021; 174:190-209. [PMID: 33895215 DOI: 10.1016/j.addr.2021.04.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/22/2022]
Abstract
Preterm birth (PTB) is defined as delivery before 37 weeks of gestation. Globally, 15 million infants are born prematurely, putting these children at an increased risk of mortality and lifelong health challenges. Currently in the U.S., there is only one FDA approved therapy for the prevention of preterm birth. Makena is an intramuscular progestin injection given to women who have experienced a premature delivery in the past. Recently, however, Makena failed a confirmatory trial, resulting the Center for Drug Evaluation and Research's (CDER) recommendation for the FDA to withdrawal Makena's approval. This recommendation would leave clinicians with no therapeutic options for preventing PTB. Here, we outline recent interdisciplinary efforts involving physicians, pharmacologists, biologists, chemists, and engineers to understand risk factors associated with PTB, to define mechanisms that contribute to PTB, and to develop next generation therapies for preventing PTB. These advances have the potential to better identify women at risk for PTB, prevent the onset of premature labor, and, ultimately, save infant lives.
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