The Oral Microbiome and Upper Aerodigestive Squamous Cell Cancer

Study Overview
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Brief Summary
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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
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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.

Official Title
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The Oral Microbiome and Upper Aerodigestive Squamous Cell Cancer

Conditions
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Oral Cancer

Intervention / Treatment
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* Other: Classification of Oral Microbiome Using 16S rRNA gene sequence-based approach
* Other: Classification of Oral Microbiome Using taxonomic approach


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Diagnosis of Upper Aerodigestive Squamous Cell Cancer and registered in: The American Cancer Society Cancer Prevention Study II (CPS-II) The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial.

Ages Eligible for Study
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Minimum Age: 40 Years
Maximum Age: 92 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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Accepts Healthy Volunteers

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Upper aerodigestive squamous cell cancers (UADSCC) cases<br>From PLCO and ACS CPS II, identified 140 UADSCC cases. These cases are frequency matched 3:1 (420 controls) by incidence density sampling for study (ACS. PLCO), | Other: Classification of Oral Microbiome Using 16S rRNA gene sequence-based approach<br>* 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.<br>Other: Classification of Oral Microbiome Using taxonomic approach<br>* 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.<br>|
| Controls<br>From PLCO and ACS CPS II, we have identified 140 UADSCC cases. These cases are frequency matched 3:1 (420 controls) by incidence density sampling for study (ACS. PLCO), | Other: Classification of Oral Microbiome Using 16S rRNA gene sequence-based approach<br>* 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.<br>Other: Classification of Oral Microbiome Using taxonomic approach<br>* 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.<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| 16S rRNA gene survey approach for microbiome characterization | Data alignment and clustering to determine microbiome species diversity | 4 Years | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Oral Microbiome, reflux disorders, esophageal microbiome, Alcohol Use, Tobacco Use