for people ages up to 21 years (full criteria)
at San Francisco, California
study started
Principal Investigator
Matthew Zinter, MD
Photo of Matthew Zinter
Matthew Zinter



This is a multicenter prospective collection of leftover respiratory tract secretions, paired blood and NP swabs, and clinical circumstances from pediatric HCT patients, followed by next generation genomic sequencing, transcriptome analysis, protein biomarker measurement, and statistical modeling.


This study is a multicenter cross-sectional observational analysis of unused lower respiratory tract secretions collected from children with a history of HCT who are undergoing evaluation for pulmonary complications. Patients will be screened and enrolled by study coordinators at each site, who will collect and submit biospecimens as well as patient characteristics and clinical outcomes. Metagenomic NGS will be performed on these biospecimens in an attempt to identify microbial pathogens and markers of host response to infection, including immune activation, inflammation, and cell damage. This study will then correlate these results with patient characteristics, clinical microbiology test results, and clinical outcomes in order to evaluate the utility of metagenomics NGS in improving the diagnosis of LRTI in our pediatric HCT population.


Lower Respiratory Tract Infections Infection Communicable Diseases Respiratory Tract Infections Next Generation Genomic Sequencing HCT recipients ages ≤21 years


You can join if…

Open to people ages up to 21 years

  • Patients will be ≤21 years of age with a history of HCT of any type at any point in the past, and are planned to undergo clinically-indicated collection of any lower respiratory specimen, including but not limited to bronchoalveolar lavage (either via a plugged telescoping catheter such as a CombiCath, or with fiberoptic bronchoscopy) and tracheal aspirate.
  • For the purposes of this study, induced or spontaneous sputum is not considered a lower respiratory tract specimen.
  • Patients may have any underlying indication for clinical testing of lower respiratory secretions, including but not limited to suspected infection, non-infectious inflammation, obstructive or restrictive lung disease, pulmonary edema, pleural effusions, alveolar hemorrhage, aspiration, or pulmonary vascular disease.
  • Patients who have not undergone HCT but plan to undergo HCT in the future, hereafter referred to as pre-HCT patients, may also be enrolled.
  • Pre-HCT patients must have intention to undergo stem cell transplantation in the future and include but are not limited to patients with primary immunodeficiency, patients with malignancy undergoing induction or consolidation chemotherapy, and HCT patients with selected cell sources who are undergoing pre-transplant conditioning but have not yet received their cellular infusion.

You CAN'T join if...

  • Patients will not be >21 years of age.
  • Patients who do not have a clinical indication for obtaining lower respiratory secretions for testing as part of their direct patient care will be excluded.
  • Patients who do not have sufficient respiratory secretions remaining after collection and aliquoting for indicated clinical tests ordered by the treating clinician will also be excluded.
  • Patients who undergo lower respiratory testing solely to evaluate for relapsed malignancy will be excluded.


  • University of California, San Francisco accepting new patients
    San Francisco California 94143 United States

Lead Scientist at UCSF

  • Matthew Zinter, MD
    I study the pathobiology of critical illness, including organ dysfunction and infection, in children with cancer, immunodeficiencies, and those who have undergone hematopoietic stem cell transplantation.


accepting new patients
Start Date
Pediatric Blood and Marrow Transplant Foundation, Inc.
Study Type
Last Updated