Functional Dyspepsia Microbiome Study
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|ClinicalTrials.gov Identifier: NCT02340312|
Recruitment Status : Recruiting
First Posted : January 16, 2015
Last Update Posted : January 16, 2015
|Condition or disease||Intervention/treatment|
|Functional Dyspepsia||Procedure: EGD Other: Collection of Stool Specimens|
Show Detailed Description
|Study Type :||Observational|
|Estimated Enrollment :||200 participants|
|Official Title:||Evaluation of the Duodenal Microbiome in Pediatric Functional Dyspepsia|
|Study Start Date :||January 2015|
|Estimated Primary Completion Date :||January 2020|
- Procedure: EGD
In this study patients are being scoped(EGD) as standard of care and being asked to allow .5 aggregate of tissue biopsy to be taken for research purposes.
- Other: Collection of Stool Specimens
We will be collecting stool samples from each participant for research purposes. Within two weeks after EGD tissue collection.
- Microbiome Analysis [ Time Frame: within 12 months from collection ]Fecal samples and 8 mucosal biopsies (descending duodenum) will be obtained from each subject. Samples will be processed and DNA isolated per standard lab techniques.16S rDNA sequence analysis of microbial communities within patient samples will be analyzed utilizing our HiSeq 1500 rapid run technologies. We will perform 2 X 150 bp paired end sequencing which will give exceptional coverage (reads > 30,000). We will sequence the V4 region of 16s RNA (E. coli 515-806), which is the method optimized for Illumina HiSeq 1500 currently. We will also sequence simultaneously the V3 region of 16s RNA to provide a dual-control analysis of samples. Confirmatory PCR will be employed when appropriate. Data will be reported as total counts for each identified bacterial species.
- Inflammatory Cell Density [ Time Frame: within 12 months from collection ]
Routine histology slides previously stained with hematoxylin and eosin will be utilized for determination of eosinophil density.
IHC techniques will be utilized for determination of mast cell density. Serial 3-μm paraffin sections will be air dried and heat fixed on slides. The sections will be deparaffinized with xylene and iodine and rehydrated in a graded series of alcohol. Utilizing tryptase monoclonal mouse antihuman mast cell tryptase antibody (clone AA1, Dako, Carpinteria, CA), sections will be stained on an automated Dako Autostainer 3400 using Dako's LSAB+ kit with streptoavidin conjugated to horseradish peroxidase.
To determine density for each cell type, the entire specimen will be scanned to determine the subjective area of greatest involvement. Density will be determined by counting cells within 5 consecutive high-power fields (400X magnification). Peak and mean cell densities expressed as cells/hpf will be determined. This will be completed before study end.
- Immunohistochemistry (IHC) [ Time Frame: within 12 months from collection ]IHC staining will be performed and may include DCLK1, BDNF, TRPV1, and/or CRH-R1, respectively, depending on the results of an on-going pilot study. Staining intensity will be evaluated in a blinded fashion by a pathologist to assign scores for average IHC signal intensity (i.e. 0= none, 1= mild, 2= moderate, and 3= strong) as well as the percentage of tissue cells or fibers showing positive immunoreactivity. A sem-quantitative scoring system will be applied in which the final immunoreactive score will equal the product of the percentage of positive cells times the average staining intensity. Percentage of positive cells or fibers will be graded as follows: 0= negative-10%, 1= 11-33%, 2= 33-66%, and 3= > 67%. Immunoreactivity will be considered positive when the combined score ranges between 2-6 and negative with a score of 0-1. Other IHC stains may be performed should they become relevant as indicated by the literature. This will be performed before study end.
- T-scores for the BASC will be collected as part of this study on the Data Collection Form. [ Time Frame: within 6 months from completion ]This information is used to assess psychosocial information from the patient.This will be collected and recorded before study end.
Biospecimen Retention: Samples With DNA
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): NCT02340312
|Contact: Craig A Friesen, M.D.||email@example.com|
|Contact: Trevor J Cole, B.S.||firstname.lastname@example.org|
|United States, Missouri|
|The Children's Mercy Hospital||Recruiting|
|Kansas City, Missouri, United States, 64108|
|Contact: Trevor J Cole, B.S. 816-983-6025 email@example.com|