Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid
Condition: Pulmonary Infection
Study type: Observational

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.
    

Intervention name(s): massively paralleled sequencing
Intervention type(s): Diagnostic Test
Intervention description(s): 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.
Observational model: Other
Time perspective: Prospective
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.
      
Biospecimen 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.