The Oral Microbiome and Upper Aerodigestive Squamous Cell Cancer
Condition: Oral Cancer
MeSH terms: Mouth Neoplasms; Neoplasms, Squamous Cell; Carcinoma, Squamous Cell
Study type: Observational

Summary: 
      The human oral cavity is a diverse habitat that contains approximately 700 prokaryotic
      species. The oral microbiome is comprised of 44% named species, 12% isolates representing
      unnamed species, and 44% phylotypes known only from 16S rRNA based cloning studies
      (http://www.homd.org/). Species from 11 phyla have been identified: Firmicutes,
      Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, Fusobacteria, TM7,
      Synergistetes, Chlamydiae, Chloroflexi and SR1 (http://www.homd.org/). Because these
      observations have been mainly based on data generated from traditional Sanger sequencing, the
      diversity of oral microbiome is highly likely underestimated. Application of high throughput
      sequencing to the oral microbiome similar to the scale of the microbiome studies of other
      body sites (GI tract, skin, and vagina) under the Human Microbiome Project is necessary to
      obtain data essential for understanding the diversity and community structure of the oral
      microbiome in health and disease.
    

Detailed description: 
      The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and The American
      Cancer Society Cancer Prevention Study II (CPS-II) investigators have identified 140 UADSCC
      cases that have been frequency matched 3:1 (420 controls) by incidence density sampling for
      study (ACS. PLCO), gender, ethnic background, and age, within 10 years.
    

Intervention name(s): Classification of Oral Microbiome Using 16S rRNA gene sequence-based approach; Classification of Oral Microbiome Using taxonomic approach
Intervention type(s): Other; Other
Intervention description(s): The sequence-based approach is selected because it classifies samples by considering the entire difference (genetic distance) in 16S rRNA gene sequences among samples analyzed, unbiased by artificial details such as taxonomies, sequence length, or even quality scores.; The taxonomic approach is a complement to the sequence-based approach in that it will further identify specific taxonomic groups or species that can explain the difference found by overall analyses.
Observational model: Case-Control
Time perspective: Prospective
Sampling method: Non-Probability Sample
Study population: 
        The American Cancer Society Cancer (ACS) Prevention Study II Nutrition Cohort (CPS-II) was
        established in 1992; the cohort includes over 86,000 men and 97,000 women from 21 U.S.
        states who completed a mailed questionnaire in 1992. In total, 72 UADSCC were eligible for
        study, with completed informed consent and prediagnostic oral wash collection.

        The Prostate, Lung, Colon and Ovarian (PLCO) Cancer Screening Trial is a randomized
        controlled trial of approximately 155,000 men and women. Participants are randomized to
        either a screening or control arm. n total, 68 UADSCC were eligible for study, including
        completed informed consent and prediagnostic oral wash collection.
      
Biospecimen description: 
      140 UADSCC cases and 420 controls using Roche 454 16S rRNA gene sequencing.
    
Keywords: Oral Microbiome; reflux disorders; esophageal microbiome; Alcohol Use; Tobacco Use