<clinical_study>
  <!-- This xml conforms to an XML Schema at:
    https://clinicaltrials.gov/ct2/html/images/info/public.xsd -->
  <required_header>
    <download_date>ClinicalTrials.gov processed this data on September 20, 2023</download_date>
    <link_text>Link to the current ClinicalTrials.gov record.</link_text>
    <url>https://clinicaltrials.gov/ct2/show/NCT04425343</url>
  </required_header>
  <id_info>
    <org_study_id>F-H-17-11-03</org_study_id>
    <nct_id>NCT04425343</nct_id>
  </id_info>
  <brief_title>Microbial Profiling in Pockets Related to Chronic Periodontitis Patients Using 16s RNA Metagenomics Sequencing</brief_title>
  <official_title>Microbial Profiling in Pockets Related to Chronic Periodontitis Patients in UAE Population Using 16s RNA Metagenomics Sequencing</official_title>
  <sponsors>
    <lead_sponsor>
      <agency>Ajman University</agency>
      <agency_class>Other</agency_class>
    </lead_sponsor>
  </sponsors>
  <source>Ajman University</source>
  <oversight_info>
    <has_dmc>Yes</has_dmc>
    <is_fda_regulated_drug>No</is_fda_regulated_drug>
    <is_fda_regulated_device>No</is_fda_regulated_device>
  </oversight_info>
  <brief_summary>
    <textblock>
      The study was developed in compliance with the Helsinki Declaration on medical research&#xD;
      involving the Ethics Committee at Ajman University (2017-A-DN-04). Informed consent from all&#xD;
      the participants was obtained before participation in the study. The participants were&#xD;
      systemically healthy with no history of antibiotics for the past three months. Patients&#xD;
      recruited for the study were diagnosed as Stage II Generalized periodontitis according to the&#xD;
      classification from the 2017 world workshop on the &quot;classification of periodontal and&#xD;
      peri-implant disease and conditions&quot;. Periodontal status indicating the severity of&#xD;
      interdental clinical attachment loss of 3-4mm, radiographic bone loss between 15%-33% and&#xD;
      with no tooth loss were included. The complexity of periodontitis with a maximum probing&#xD;
      depth of ≤ 5mm with horizontal bone loss and having an extent and distribution with &gt;30%&#xD;
      teeth involved were included in the study. A total of 80 plaque samples were collected with&#xD;
      the clinical characteristics of the patient comprising of age between 25-39 years, 36 females&#xD;
      and 44 males. The subgingival plaque was collected using a sterile curette from the buccal&#xD;
      aspect of maxillary molars and lingual aspect of mandibular incisors, in a vial containing&#xD;
      200µl of Buffer CL.&#xD;
    </textblock>
  </brief_summary>
  <detailed_description>
    <textblock>
      The collected plaque samples were then freshly prepared for the DNA isolation using ABIOpure&#xD;
      TM Total DNA (version 2.0) (Cat No: M501DP100) according to the manufacturer's instruction.&#xD;
      All the samples were assessed for DNA quantification using spectrophotometry and further&#xD;
      quantified using the fluorometric method. This was performed using DeNovix DS-11 FX&#xD;
      (DeNovix). Further to the DNA quantification, assessment of DNA integrity was resolved on a&#xD;
      0.8% agarose gel with ethidium bromide. For NGS library preparation, all the samples&#xD;
      underwent PCR amplification of the 16S rRNA gene in the isolated bacterial DNA. The primers&#xD;
      used had targeted in the V3-V4 region of the 16S rRNA gene. The full length primer sequences,&#xD;
      using standard IUPAC nucleotide nomenclature, to follow the protocol targeting this region&#xD;
      are:&#xD;
&#xD;
      16SAmpliconPCRForwardPrimer=5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG&#xD;
      16SAmpliconPCRReversePrimer=5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC Gel&#xD;
      electrophoresis method was used for the size selection and the bioinformatics pipeline used&#xD;
      for processing microbiome 16S sequence data was QIIME&#xD;
    </textblock>
  </detailed_description>
  <overall_status>Completed</overall_status>
  <start_date type="Actual">November 10, 2017</start_date>
  <completion_date type="Actual">October 7, 2019</completion_date>
  <primary_completion_date type="Actual">September 15, 2018</primary_completion_date>
  <phase>N/A</phase>
  <study_type>Interventional</study_type>
  <has_expanded_access>No</has_expanded_access>
  <study_design_info>
    <allocation>Randomized</allocation>
    <intervention_model>Single Group Assignment</intervention_model>
    <intervention_model_description>. Patients recruited for the study were diagnosed as Stage II Generalized periodontitis according to the classification from the 2017 world workshop on the &quot;classification of periodontal and peri-implant disease and conditions&quot;. Periodontal status indicating the severity of interdental clinical attachment loss of 3-4mm, radiographic bone loss between 15%-33% and with no tooth loss were included. The complexity of periodontitis with a maximum probing depth of ≤ 5mm with horizontal bone loss and having an extent and distribution with &gt;30% teeth involved were included in the study.</intervention_model_description>
    <primary_purpose>Health Services Research</primary_purpose>
    <masking>Single (Investigator)</masking>
    <masking_description>. A total of 80 plaque samples were collected with the clinical characteristics of the patient comprising of age between 25-39 years, 36 females and 44 males</masking_description>
  </study_design_info>
  <primary_outcome>
    <measure>Microbial Taxonomical Composition</measure>
    <time_frame>From Baseline to 3 months</time_frame>
    <description>The composition was determined using subgingival plaque samples and performing 16s metagenomic sequencing</description>
  </primary_outcome>
  <number_of_arms>2</number_of_arms>
  <enrollment type="Actual">80</enrollment>
  <condition>Periodontal Diseases</condition>
  <arm_group>
    <arm_group_label>Periodontitis, Adult</arm_group_label>
    <arm_group_type>Experimental</arm_group_type>
    <description>Plaque samples were taken from subgingival pocket and send to the lab for metagenomic analysis</description>
  </arm_group>
  <arm_group>
    <arm_group_label>Metgenomic analysis</arm_group_label>
    <arm_group_type>Experimental</arm_group_type>
    <description>Analysis for whole bacterial count</description>
  </arm_group>
  <intervention>
    <intervention_type>Genetic</intervention_type>
    <intervention_name>16s RNA Metagenomics sequencing</intervention_name>
    <description>The subgingival plaque was collected using a sterile curette from the buccal aspect of maxillary molars and lingual aspect of mandibular incisors, in a vial containing 200µl of Buffer CL.</description>
    <arm_group_label>Metgenomic analysis</arm_group_label>
    <arm_group_label>Periodontitis, Adult</arm_group_label>
    <other_name>DNA isolation</other_name>
  </intervention>
  <eligibility>
    <criteria>
      <textblock>
        Inclusion Criteria:&#xD;
&#xD;
          -  Patients recruited for the study were diagnosed as Stage II Generalized periodontitis&#xD;
&#xD;
          -  Medically fit&#xD;
&#xD;
        Exclusion Criteria:&#xD;
&#xD;
          -  Patients having gingivitis or stage III periodontitis&#xD;
&#xD;
          -  Medically unfit&#xD;
      </textblock>
    </criteria>
    <gender>All</gender>
    <minimum_age>18 Years</minimum_age>
    <maximum_age>60 Years</maximum_age>
    <healthy_volunteers>Accepts Healthy Volunteers</healthy_volunteers>
  </eligibility>
  <overall_official>
    <last_name>Sudhir Varma, MDS</last_name>
    <role>Principal Investigator</role>
    <affiliation>Assistant Professor</affiliation>
  </overall_official>
  <location>
    <facility>
      <name>Ajman University of Science and Technology</name>
      <address>
        <city>Ajman</city>
        <zip>009716</zip>
        <country>United Arab Emirates</country>
      </address>
    </facility>
  </location>
  <location_countries>
    <country>United Arab Emirates</country>
  </location_countries>
  <verification_date>June 2020</verification_date>
  <study_first_submitted>June 7, 2020</study_first_submitted>
  <study_first_submitted_qc>June 9, 2020</study_first_submitted_qc>
  <study_first_posted type="Actual">June 11, 2020</study_first_posted>
  <last_update_submitted>June 9, 2020</last_update_submitted>
  <last_update_submitted_qc>June 9, 2020</last_update_submitted_qc>
  <last_update_posted type="Actual">June 11, 2020</last_update_posted>
  <responsible_party>
    <responsible_party_type>Principal Investigator</responsible_party_type>
    <investigator_affiliation>Ajman University</investigator_affiliation>
    <investigator_full_name>sudhir rama varma</investigator_full_name>
    <investigator_title>Assistant Professor</investigator_title>
  </responsible_party>
  <keyword>metagenomics</keyword>
  <keyword>16S</keyword>
  <keyword>Periodontitis, Adult</keyword>
  <condition_browse>
    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm            -->
    <mesh_term>Periodontitis</mesh_term>
    <mesh_term>Periodontal Diseases</mesh_term>
    <mesh_term>Chronic Periodontitis</mesh_term>
  </condition_browse>
  <patient_data>
    <sharing_ipd>No</sharing_ipd>
    <ipd_description>Microbial Taxonomical Composition</ipd_description>
  </patient_data>
  <!-- Results have not yet been posted for this study                                          -->
</clinical_study>


download date: ClinicalTrials.gov processed this data on September 20, 2023
link text: Link to the current ClinicalTrials.gov record.
url: https://clinicaltrials.gov/ct2/show/NCT04425343
org study id: F-H-17-11-03
nct id: NCT04425343
lead sponsor: 
has dmc: Yes
is fda regulated drug: No
is fda regulated device: No
The study was developed in compliance with the Helsinki Declaration on medical research
      involving the Ethics Committee at Ajman University (2017-A-DN-04). Informed consent from all
      the participants was obtained before participation in the study. The participants were
      systemically healthy with no history of antibiotics for the past three months. Patients
      recruited for the study were diagnosed as Stage II Generalized periodontitis according to the
      classification from the 2017 world workshop on the "classification of periodontal and
      peri-implant disease and conditions". Periodontal status indicating the severity of
      interdental clinical attachment loss of 3-4mm, radiographic bone loss between 15%-33% and
      with no tooth loss were included. The complexity of periodontitis with a maximum probing
      depth of ≤ 5mm with horizontal bone loss and having an extent and distribution with >30%
      teeth involved were included in the study. A total of 80 plaque samples were collected with
      the clinical characteristics of the patient comprising of age between 25-39 years, 36 females
      and 44 males. The subgingival plaque was collected using a sterile curette from the buccal
      aspect of maxillary molars and lingual aspect of mandibular incisors, in a vial containing
      200µl of Buffer CL.
The collected plaque samples were then freshly prepared for the DNA isolation using ABIOpure
      TM Total DNA (version 2.0) (Cat No: M501DP100) according to the manufacturer's instruction.
      All the samples were assessed for DNA quantification using spectrophotometry and further
      quantified using the fluorometric method. This was performed using DeNovix DS-11 FX
      (DeNovix). Further to the DNA quantification, assessment of DNA integrity was resolved on a
      0.8% agarose gel with ethidium bromide. For NGS library preparation, all the samples
      underwent PCR amplification of the 16S rRNA gene in the isolated bacterial DNA. The primers
      used had targeted in the V3-V4 region of the 16S rRNA gene. The full length primer sequences,
      using standard IUPAC nucleotide nomenclature, to follow the protocol targeting this region
      are:

      16SAmpliconPCRForwardPrimer=5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG
      16SAmpliconPCRReversePrimer=5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC Gel
      electrophoresis method was used for the size selection and the bioinformatics pipeline used
      for processing microbiome 16S sequence data was QIIME
allocation: Randomized
intervention model: Single Group Assignment
intervention model description: . Patients recruited for the study were diagnosed as Stage II Generalized periodontitis according to the classification from the 2017 world workshop on the "classification of periodontal and peri-implant disease and conditions". Periodontal status indicating the severity of interdental clinical attachment loss of 3-4mm, radiographic bone loss between 15%-33% and with no tooth loss were included. The complexity of periodontitis with a maximum probing depth of ≤ 5mm with horizontal bone loss and having an extent and distribution with >30% teeth involved were included in the study.
primary purpose: Health Services Research
masking: Single (Investigator)
masking description: . A total of 80 plaque samples were collected with the clinical characteristics of the patient comprising of age between 25-39 years, 36 females and 44 males
measure: Microbial Taxonomical Composition
time frame: From Baseline to 3 months
description: The composition was determined using subgingival plaque samples and performing 16s metagenomic sequencing
arm group label: Periodontitis, Adult
arm group type: Experimental
description: Plaque samples were taken from subgingival pocket and send to the lab for metagenomic analysis
arm group label: Metgenomic analysis
arm group type: Experimental
description: Analysis for whole bacterial count
intervention type: Genetic
intervention name: 16s RNA Metagenomics sequencing
description: The subgingival plaque was collected using a sterile curette from the buccal aspect of maxillary molars and lingual aspect of mandibular incisors, in a vial containing 200µl of Buffer CL.
arm group label: Metgenomic analysis
arm group label: Periodontitis, Adult
other name: DNA isolation
criteria: 
gender: All
minimum age: 18 Years
maximum age: 60 Years
healthy volunteers: Accepts Healthy Volunteers
last name: Sudhir Varma, MDS
role: Principal Investigator
affiliation: Assistant Professor
facility: 
country: United Arab Emirates
responsible party type: Principal Investigator
investigator affiliation: Ajman University
investigator full name: sudhir rama varma
investigator title: Assistant Professor
mesh term: Periodontitis
mesh term: Periodontal Diseases
mesh term: Chronic Periodontitis
sharing ipd: No
ipd description: Microbial Taxonomical Composition