# Molecular Phenotyping of ARDS, Pneumonia, and Sepsis using Latent Class Analysis and Metagenomic Sequencing

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $171,888

## Abstract

ABSTRACT
 This application to RFA HL-23-001 proposes a California Clinical Center for participation in the Acute
Respiratory Distress Syndrome (ARDS), Pneumonia, and Sepsis (APS) Consortium study. Our Clinical Center
consists of 4 sites: University of California, San Francisco (UCSF; lead site); UCSF Fresno; Zuckerberg San
Francisco General Hospital; and Stanford University. Our Clinical Center will contribute to the design and
conduct of the APS Consortium’s prospective, longitudinal observational cohort study which will enroll 5000
adults with ARDS, pneumonia, and/or sepsis overall, with follow up of approximately half of survivors at 3, 6 and
12 months. We will enroll 1000 participants in this Consortium during the project period and work with our
colleagues on the APS Consortium Steering Committee to design and implement the project. Our 4 sites have
a strong track record of working well together to enroll a diverse population of critically ill patients with ARDS,
pneumonia, and sepsis in interventional trials and observational studies, including collection of extensive clinical
data and biospecimens and successful outpatient follow-up. Moreover, our group pioneered the identification of
molecular phenotypes in ARDS and the use of metagenomic sequencing in pneumonia and sepsis, as evidence
of our relevant content expertise. Thus, we are well-prepared to contribute to the APS Consortium as a Clinical
Center.
 This application proposes a Consortium-wide study (Aim 1) that seeks to determine whether previously
observed latent molecular phenotypes of ARDS are present in critically ill patients across syndromic diagnostic
criteria for ARDS, pneumonia and sepsis, and whether these molecular phenotypes have consistent prognostic
value across syndromic diagnostic criteria. This application also proposes a Clinical Center-specific study (Aim
2) that seeks to determine whether integration of metagenomic data capturing both host and microbe enhances
mechanistic understanding and prognostic utility of ARDS, pneumonia, and sepsis molecular phenotypes.
Completion of these aims will lay the groundwork for a new taxonomy of critical illness, moving critical care
towards a precision medicine paradigm in which we can better match novel therapies with distinct clinical and
biological phenotypes, with the ultimate goal of improving outcomes for our patients.

## Key facts

- **NIH application ID:** 10649372
- **Project number:** 1U01HL168415-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Carolyn Calfee
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $171,888
- **Award type:** 1
- **Project period:** 2023-05-01 → 2029-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10649372

## Citation

> US National Institutes of Health, RePORTER application 10649372, Molecular Phenotyping of ARDS, Pneumonia, and Sepsis using Latent Class Analysis and Metagenomic Sequencing (1U01HL168415-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10649372. Licensed CC0.

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