Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.

Journal

medRxiv : the preprint server for health sciences
Titre abrégé: medRxiv
Pays: United States
ID NLM: 101767986

Informations de publication

Date de publication:
11 Apr 2023
Historique:
pubmed: 23 3 2023
medline: 23 3 2023
entrez: 22 3 2023
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1101/2023.03.07.23286920 PMID: 36945505 PMC: PMC10029035
pubmed: 36945505
doi: 10.1101/2023.03.07.23286920
pmc: PMC10029035
pii:
doi:

Types de publication

Preprint

Langues

eng

Déclaration de conflit d'intérêts

Competing Interests Antonio Parraga-Leo and Patricia Diaz-Gimeno are receiving hononaria from the IVI Foundation. The remaining authors declare no Competing Financial or Non-Financial Interests.

Auteurs

Jonathan L Golob (JL)

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 (TT)

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 (AS)

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 (A)

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.

Verena Chung (V)

Sage Bionetworks, Seattle, WA. USA.

Connie W Y Ha (CWY)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.

Ronald J Wong (RJ)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.
March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA.

Kaitlin J Flynn (KJ)

Sage Bionetworks, Seattle, WA. USA.

Antonio Parraga-Leo (A)

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 (C)

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 (SS)

Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA.

Gaia Andreoletti (G)

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 (I)

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.

Julie Bletz (J)

Sage Bionetworks, Seattle, WA. USA.

Amber Nelson (A)

Sage Bionetworks, Seattle, WA. USA.

Jifan Gao (J)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA.

Zhoujingpeng Wei (Z)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA.

Guanhua Chen (G)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA.

Zheng-Zheng Tang (ZZ)

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA.

Pierfrancesco Novielli (P)

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 (D)

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 (E)

Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA.

Nicola Amoroso (N)

March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA.

Alfonso Monaco (A)

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 (M)

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 (M)

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 (R)

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 (S)

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 (A)

Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA.

Isaac Bigcraft (I)

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 (S)

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 (D)

Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA.

Eunyoung Kim (E)

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.

Jongbum Jeon (J)

Sage Bionetworks, Seattle, WA. USA.

Soobok Joe (S)

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 (KR)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.

Sherrianne Ng (S)

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 (YS)

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 (P)

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 (PR)

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 (DA)

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 (G)

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 (SV)

Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA.

Jake Albrecht (J)

Sage Bionetworks, Seattle, WA. USA.

Nardhy Gomez-Lopez (N)

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 (R)

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 (DK)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.

Nima Aghaeepour (N)

Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA.

Adi L Tarca (AL)

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 (JC)

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 (M)

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.

Classifications MeSH