Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Example Utah high-risk breast cancer pedigree 1817. a. Confirmed and sampled breast cancer cases are indicated in black (55 sampled out of 138 total confirmed UCR cases). Star, triangle and hexagon symbols indicate pedigree branches. b. shows only those cases from (a) with tumor expression data available and indicates PAM50 intrinsic subtype by color. Cases whose tumors are extreme for PC3 are indicated by ‘3’; extreme for PC5 are indicated by ‘5’. c. shows only the PC3-extreme cases from (b). A ‘+’ indicates those cases that share the genomewide significant region at 12q15.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques: Expressing

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: Summary of the 11 high-risk Utah pedigrees Tumor count by intrinsic subtype per pedigree.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques:

Journal: Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Article Title: Reparameterization of PAM50 expression identifies novel breast tumor dimensions and leads to discovery of a genomewide significant breast cancer locus at 12q15

doi: 10.1158/1055-9965.EPI-17-0887

Figure Lengend Snippet: A slice from a three-dimensional scatterplot of PC1, PC2, and PC4 shows that they recapitulate the PAM50 intrinsic subtypes. Reinforcing the constrasts illustrated in Figure 2, PC1 here clearly distinguishes Basal-like from Luminal A tumors. PC2 and PC4 aid in distinguishing HER2-enriched from Luminal B tumors. Combined, these three components define clusters corresponding to the intrinsic subtypes.

Article Snippet: Gene expression data was generated using the PAM50 RT-qPCR research assay( 12 ) in the Bernard Lab at the Huntsman Cancer Institute( 15 ).

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: A novel exosome-derived prognostic signature and risk stratification for breast cancer based on multi-omics and systematic biological heterogeneity

doi: 10.1016/j.csbj.2023.05.013

Figure Lengend Snippet: Association of exoSIG risk score with characteristics of breast cancer patients. (A & B) Univariate and multivariate cox hazard ratio (HR) distributions of exoSIG risk scores versus seven clinical characteristics. (C) Risk grouping based on exoSIG risk scores. Up-panel: correlation between risk grouping and risk score; Middle-panel: correlation between survival status and survival time; Low-panel: Heatmap of expression patterns of 10 exoMols in risk patients. (D) Distribution of different clinical characteristics in the low-risk and high-risk patients. (E) Correlation of clinical characteristics of breast cancer patients with exoSIG risk scores. Breast cancer patients with ER-, PR-, high stage, high age, PAM50-LumB, and PAM50-Basal subtype had higher exoSIG risk scores.

Article Snippet: Clinical survival features of high-risk patients were worse than those of low-risk patients, such as estrogen-receptor (ER) status (Chi-square test, P < 0.001), progesterone-receptor (PR) status (Chi-square test, P < 0.001), node coded (Chi-square test, P < 0.05), AJCC stage (Chi-square test, P < 0.001), 50-gene signature (PAM50) (Chi-square test, P < 0.001) and age (Student T test, P < 0.01) ( C).

Techniques: Expressing