Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non-Hispanic and Hispanic women
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ determined by the Linear Array HPV Genotyping Tests
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: increased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens | ||
| Prevotella |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: decreased abundance in HPV+
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low grade dysplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade dysplasia confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: increased abundance in low grade dysplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens | ||
| Parvimonas | ||
| Gemella asaccharolytica | ||
| Mobiluncus mulieris | ||
| Fannyhessea vaginae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: decreased abundance in low grade dysplasia
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high grade dysplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high grade dysplasia confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: increased abundance in high grade dysplasia
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: decreased abundance in high grade dysplasia
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,cervical cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- invasive cervical carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: increased abundance in invasive cervical carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia sanguinegens |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: decreased abundance in invasive cervical carcinoma
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ determined by the Linear Array HPV Genotyping Tests
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, ethnic group
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control prior to adjusting
Abundance in Group 1: increased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Olsenella | ||
| Shuttleworthia | ||
| Lactobacillus | ||
| Prevotella | ||
| Peptostreptococcus anaerobius | ||
| Megasphaera |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: decreased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Hoylesella timonensis | ||
| Prevotella bivia | ||
| Peptoniphilus grossensis | ||
| Anaerococcus obesiensis | ||
| Anaerococcus | ||
| Gardnerella | ||
| Bifidobacterium |
Revision editor(s): WikiWorks
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical glandular intraepithelial neoplasia cervical glandular intraepithelial neoplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low grade dysplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low grade dysplasia confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: increased abundance in low grade dysplasia
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: decreased abundance in low grade dysplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Peptoniphilus coxii | ||
| Lactobacillus crispatus |
Revision editor(s): WikiWorks
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high grade dysplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high grade dysplasia confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: increased abundance in high grade dysplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella amnii | ||
| Lactobacillus iners | ||
| Clostridium | ||
| Gardnerella | ||
| Megasphaera | ||
| Sneathia sanguinegens | ||
| Parvimonas | ||
| Sneathia | ||
| Shuttleworthia |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: decreased abundance in high grade dysplasia
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,cervical cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- invasive cervical carcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Curated date: 2021/01/10
Curator: Cynthia Anderson
Revision editor(s): Lwaldron, Cynthia Anderson, WikiWorks
Source: Figure 4
Description: Enrichment in bacterial taxa among the groups when compared to HPV-negative control after adjusting for age, BMI, and ethnicity
Abundance in Group 1: decreased abundance in invasive cervical carcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus | ||
| Bifidobacterium | ||
| Gardnerella | ||
| Lactobacillus | ||
| Lactobacillus crispatus | ||
| Moryella | ||
| Peptoniphilus grossensis | ||
| Prevotella bivia |
Revision editor(s): Lwaldron, Cynthia Anderson, WikiWorks
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- human papilloma virus infection , cervical cancer HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,cervical cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- abnormal pH
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- normal pH
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ determined by the Linear Array HPV Genotyping Tests, low grade dysplasia,high grade dysplasia, invasive cervical carcinoma confirmed by histology of colonoscopy-directed biopsy,
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic
Abundance in Group 1: increased abundance in normal pH
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic
Abundance in Group 1: decreased abundance in normal pH
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Escherichia | ||
| Brenneria | ||
| Shigella | ||
| Clostridium | ||
| Lactobacillus gasseri |
Revision editor(s): WikiWorks
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-Hispanic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hispanic
- Group 0 sample size Number of subjects in the control (unexposed) group
- 53
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4
Description: Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic
Abundance in Group 1: increased abundance in Hispanic
Revision editor(s): WikiWorks
Signature 2
Source: Figure 4
Description: Enrichment in bacterial taxa in patients with abnormal pH vs. normal pH and Hispanic vs. non-Hispanic
Abundance in Group 1: decreased abundance in Hispanic
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Hoylesella buccalis | ||
| Anaerococcus vaginalis | ||
| Lactobacillus gasseri |
Revision editor(s): WikiWorks
