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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

Tracking Information
First Submitted Date June 6, 2019
First Posted Date June 21, 2019
Last Update Posted Date February 27, 2020
Actual Study Start Date September 15, 2016
Actual Primary Completion Date January 31, 2019   (Final data collection date for primary outcome measure)
Current Primary Outcome Measures
 (submitted: June 19, 2019)
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.
Original Primary Outcome Measures Same as current
Change History
Current Secondary Outcome Measures Not Provided
Original Secondary Outcome Measures Not Provided
Current Other Pre-specified Outcome Measures Not Provided
Original Other Pre-specified Outcome Measures Not Provided
 
Descriptive Information
Brief Title Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid
Official Title Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid in Children, Adolescents and Young Adults Post Hematopoietic Stem Cell Transplant
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.
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.

Study Type Observational
Study Design Observational Model: Other
Time Perspective: Prospective
Target Follow-Up Duration Not Provided
Biospecimen Retention:   Samples With DNA
Description:

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.

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.
Condition Pulmonary Infection
Intervention 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.
Study Groups/Cohorts Not Provided
Publications * Not Provided

*   Includes publications given by the data provider as well as publications identified by ClinicalTrials.gov Identifier (NCT Number) in Medline.
 
Recruitment Information
Recruitment Status Active, not recruiting
Estimated Enrollment
 (submitted: June 19, 2019)
10
Original Estimated Enrollment Same as current
Estimated Study Completion Date December 31, 2020
Actual Primary Completion Date January 31, 2019   (Final data collection date for primary outcome measure)
Eligibility 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
Sex/Gender
Sexes Eligible for Study: All
Ages up to 29 Years   (Child, Adult)
Accepts Healthy Volunteers No
Contacts Contact information is only displayed when the study is recruiting subjects
Listed Location Countries Not Provided
Removed Location Countries  
 
Administrative Information
NCT Number NCT03995030
Other Study ID Numbers NYMC 181
Has Data Monitoring Committee No
U.S. FDA-regulated Product
Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
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
Responsible Party New York Medical College
Study Sponsor New York Medical College
Collaborators Not Provided
Investigators
Principal Investigator: Jeremy Rosenblum, MD New York Medical College
PRS Account New York Medical College
Verification Date February 2020