The Microbiota of Breast Tissue and Its Association with Breast Cancer/Experiment 2
Subjects
- Location of subjects
- Canada
- 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
- Breast Mamma,Mammary part of chest,Mammary region,Breast,breast
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breast cancer breast cancer,breast tumor,cancer of breast,malignant breast neoplasm,malignant breast tumor,malignant neoplasm of breast,malignant neoplasm of the breast,malignant tumor of breast,malignant tumor of the breast,mammary cancer,mammary neoplasm,mammary tumor,primary breast cancer,Breast cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with benign tumors
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Normal adjacent tissue, collected outside the marginal zone (approximately 5 cm away from the tumor), from patients with benign tumors.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- 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
- V6
- 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).
- centered log-ratio
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Supplementary Table S4
Description: ALDEx2 summary comparing relative abundances in breast tissue from healthy women, those with benign tumours and those with cancerous tumours. Bacterial profiles in normal adjacent breast tissue from women with benign tumours are more similar to normal adjacent tissue from women with cancerous tumours rather than healthy controls.
Abundance in Group 1: increased abundance in patients with benign tumors
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillus | ||
| Staphylococcus |
Revision editor(s): Ecsharp
Signature 2
Source: Supplementary Table S4
Description: ALDEx2 summary comparing relative abundances in breast tissue from healthy women, those with benign tumours and those with cancerous tumours. Bacterial profiles in normal adjacent breast tissue from women with benign tumours are more similar to normal adjacent tissue from women with cancerous tumours rather than healthy controls.
Abundance in Group 1: decreased abundance in patients with benign tumors
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Lactococcus |
Revision editor(s): Ecsharp
