Working…
COVID-19 is an emerging, rapidly evolving situation.
Get the latest public health information from CDC: https://www.coronavirus.gov.

Get the latest research information from NIH: https://www.nih.gov/coronavirus.
ClinicalTrials.gov
ClinicalTrials.gov Menu

Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Read our disclaimer for details.
 
ClinicalTrials.gov Identifier: NCT03995030
Recruitment Status : Active, not recruiting
First Posted : June 21, 2019
Last Update Posted : February 27, 2020
Sponsor:
Information provided by (Responsible Party):
New York Medical College

Brief Summary:
Patients who are post hematopoietic stem cell transplantation who require a bronchoalveolar lavage (BAL) for standard clinical car will have extra fluid collected and sent for massively parallel sequencing to see if it is as sensitive for detecting a microbial pulmonary infection compared to standard cultures.

Condition or disease Intervention/treatment
Pulmonary Infection Diagnostic Test: massively paralleled sequencing

Detailed Description:

5.1 Subjects will undergo bronchoscopy and BAL based on clinical indications. Techniques and equipment will be per current clinical practice at Westchester Medical Center (WMC). The bronchoscope is usually introduced either via an artificial airway (endotracheal tube or laryngeal mask airway). The lavage is performed with sterile normal saline. The site of performing the lavage is selected based on radiologic or clinical data and on the appearance of the airways during the bronchoscopy. The typical volume of the lavage is 3 aliquots of 1 ml/kg each, with a max of 20 ml per aliquot.

5.2 When 10 ml or more of BAL fluid is received by the WMC laboratory, the BAL fluid will be divided by the WMC laboratory for all physician ordered clinical laboratory tests and for massively parallel sequencing research tests. This will ensure that sufficient BAL material is available for all clinical tests.

5.3 The BAL fluid for research will be held by the WMC laboratory and picked up by research personnel for processing at New York Medical College Genomics Core Facility.

5.4 The research portion will be further divided for isolation of viral, bacterial, and fungal nucleic acid isolation. A control sample of fluid used for the BAL will be prepared in parallel. Bacterial/fungal DNA and viral DNA and RNA will be isolated. Whole genome sequencing libraries will be generated and sequenced in batches on the Illumina MiSeq.

FASTQ files will be demultiplexed and then aligned to microbial genomes using Phylosift.11 DNA sequences present in both the patient and control samples will be discarded as contaminant. The preponderant organism(s) identified will be matched to the results of the culture based techniques used to verify the culture independent results.

Layout table for study information
Study Type : Observational
Estimated Enrollment : 10 participants
Observational Model: Other
Time Perspective: Prospective
Official Title: Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid in Children, Adolescents and Young Adults Post Hematopoietic Stem Cell Transplant
Actual Study Start Date : September 15, 2016
Actual Primary Completion Date : January 31, 2019
Estimated Study Completion Date : December 31, 2020

Intervention Details:
  • Diagnostic Test: massively paralleled sequencing
    Whole genome sequencing libraries will be generated and sequenced in batches on the Illumina MiSeq. FASTQ files will be demultiplexed and then aligned to microbial genomes using Phylosift.


Primary Outcome Measures :
  1. Percentage concordance between massively paralleled sequencing (MPS) and standard microbiological technique results. [ Time Frame: 10 days ]
    Children, adolescents and young adult (CAYA) hematopoietic stem cell transplantation (HSCT) subjects with clinical symptoms/indications will undergo bronchoalveolar lavage (BAL), with samples from those with sufficient BAL fluid yield (>10ml) undergoing both massively paralleled sequencing and standard microbiological technique comparison.


Biospecimen Retention:   Samples With DNA

Extra BAL fluids will be sent to for massively parallel sequencing research tests at New York Medical College Genomics Core Facility.

The research portion will be further divided for isolation of viral, bacterial, and fungal nucleic acid isolation. A control sample of fluid used for the BAL will be prepared in parallel. Bacterial/fungal DNA and viral DNA and RNA will be isolated. Whole genome sequencing libraries will be generated and sequenced in batches on the Illumina MiSeq.



Information from the National Library of Medicine

Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the contacts provided below. For general information, Learn About Clinical Studies.


Layout table for eligibility information
Ages Eligible for Study:   up to 29 Years   (Child, Adult)
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Non-Probability Sample
Study Population
Patients less than 30 years old who have had a hematopoietic stem cell transplantation and require a BAL for clinical diagnosis.
Criteria

Inclusion criteria

  • Patient age < 30 years
  • Recipient of an autologous or allogeneic stem cell transplant in the previous 365 days
  • Requires a bronchoalveolar lavage for clinical indications
  • Signed consent Exclusion criteria
  • Lack of signed informed consent

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its ClinicalTrials.gov identifier (NCT number): NCT03995030


Sponsors and Collaborators
New York Medical College
Investigators
Layout table for investigator information
Principal Investigator: Jeremy Rosenblum, MD New York Medical College
Layout table for additonal information
Responsible Party: New York Medical College
ClinicalTrials.gov Identifier: NCT03995030    
Other Study ID Numbers: NYMC 181
First Posted: June 21, 2019    Key Record Dates
Last Update Posted: February 27, 2020
Last Verified: February 2020
Individual Participant Data (IPD) Sharing Statement:
Plan to Share IPD: Yes
Plan Description: Will submit manuscript for peer-reviewed publication.
Supporting Materials: Clinical Study Report (CSR)
Time Frame: submit for publication Q4 2019

Layout table for additional information
Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No