Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition
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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
Quality issues
Experiment 1
Curated date: 2021/03/18
Curator: Cynthia Anderson
Revision editor(s): Fatima, Cynthia Anderson, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- ANOVA
- 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 3A
Description: Differential florae types in the comparison of the microbiota between high-risk human papillomavirus (HPV) persistent infection higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
Revision editor(s): Fatima, Cynthia Anderson
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection (HPV has regressed within 1 year) with high grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Figure 3B
Description: comparison of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: decreased abundance in transient HPV+ with HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Xanthomonadaceae | ||
| [Clostridium] innocuum |
Revision editor(s): Cynthia Anderson
Experiment 3
Subjects
- 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
- transient HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection (HPV has regressed within 1 year) with low grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3C
Description: Comparison of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group
Abundance in Group 1: decreased abundance in transient HPV+ with LSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia | ||
| Shuttleworthella | ||
| Veillonella | ||
| [Clostridium] innocuum | ||
| Megasphaera | ||
| Devosia | ||
| Xanthomonadaceae | ||
| Gardnerella |
Revision editor(s): Cynthia Anderson
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with high grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3D
Description: Comparison of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera | ||
| Peptostreptococcus | ||
| Shuttleworthella | ||
| Sneathia |
Revision editor(s): Fatima, Cynthia Anderson
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- persistent HPV+ infection ( same HPV subtype has infected for >12 months) with high grade squamus intraepithelial lesion
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Signature 1
Source: Figure 4A
Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: increased abundance in persistent HPV+ with HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus agalactiae |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4A
Description: Abundance analysis of the microbiota between high-risk human papillomavirus (HPV) persistent infection with higher-grade squamous intraepithelial lesion (HSIL) and the high-risk HPV persistent infection with lower-grade squamous intraepithelial lesion (LSIL) group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
Revision editor(s): Cynthia Anderson
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with low grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4B
Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: increased abundance in persistent HPV+ with LSIL
| NCBI | Quality Control | Links |
|---|---|---|
| [Ruminococcus] torques |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4B
Description: Abundance analysis of the microbiota between the high-risk HPV persistent infection with LSIL group and high-risk HPV transient infection with HSIL group
Abundance in Group 1: decreased abundance in persistent HPV+ with LSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Trichinella pseudospiralis | ||
| Quinella | ||
| Tyzzerella | ||
| Flavobacterium gelidilacus | ||
| Parabacteroides faecis | ||
| Dechloromonas |
Revision editor(s): Cynthia Anderson
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- transient HPV+ with LSIL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- transient HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection with high grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4C
Description: Abundance analysis of the microbiota between high-risk HPV transient infection with HSIL group and high-risk HPV transient infection with LSIL group
Abundance in Group 1: increased abundance in transient HPV+ with HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Flavobacteriia | ||
| Flavobacteriales | ||
| Cloacibacterium | ||
| Lactobacillus | ||
| Dyella koreensis | ||
| Flavobacterium gelidilacus | ||
| Dyella | ||
| Parabacteroides faecis |
Revision editor(s): Cynthia Anderson
Experiment 8
Subjects
- 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
- transient HPV+ with LSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV transient infection with low grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4D
Description: Abundance analysis of the microbiota between high-risk HPV transient infection with LSIL group and the non-infected HPV group
Abundance in Group 1: decreased abundance in transient HPV+ with LSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Devosia riboflavina | ||
| Candidatus Saccharibacteria | ||
| Sneathia | ||
| Lactobacillus | ||
| Pseudomonas | ||
| Shuttleworthella | ||
| Leptotrichiaceae | ||
| Oscillospiraceae | ||
| Pseudomonadaceae |
Revision editor(s): Cynthia Anderson
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- persistent HPV+ with HSIL
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high-risk HPV persistent infection with low grade squamus intraepithelial lesion
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: increased abundance in persistent HPV+ with HSIL
| NCBI | Quality Control | Links |
|---|---|---|
| Solirubrobacterales | ||
| Morganella |
Revision editor(s): Cynthia Anderson
Signature 2
Source: Figure 4E
Description: Abundance analysis of the microbiota between high-risk HPV persistent infection with HSIL and the non-infected HPV group
Abundance in Group 1: decreased abundance in persistent HPV+ with HSIL
Revision editor(s): Cynthia Anderson
