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Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid
| Condition or disease | Intervention/treatment |
|---|---|
| Pulmonary Infection | Diagnostic Test: massively paralleled sequencing |
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 |
| 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 |
- 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.
| Tracking Information | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| First Submitted Date | June 6, 2019 | ||||||||
| First Posted Date | June 21, 2019 | ||||||||
| Last Update Posted Date | September 9, 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 |
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.
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| 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. |
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| Study Type | Observational | ||||||||
| Study Design | Observational Model: Other Time Perspective: Prospective |
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| 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. |
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| 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.
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| Study Groups/Cohorts | Not Provided | ||||||||
| Publications * | Not Provided | ||||||||
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* Includes publications given by the data provider as well as publications identified by ClinicalTrials.gov Identifier (NCT Number) in Medline. |
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| Recruitment Information | |||||||||
| Recruitment Status | Active, not recruiting | ||||||||
| Estimated Enrollment |
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
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| Sex/Gender |
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| 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 |
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| IPD Sharing Statement |
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| Responsible Party | New York Medical College | ||||||||
| Study Sponsor | New York Medical College | ||||||||
| Collaborators | Not Provided | ||||||||
| Investigators |
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| PRS Account | New York Medical College | ||||||||
| Verification Date | September 2020 | ||||||||
