Abstract P3-16-01: Using the new pan-cancer clinical data resource (TCGA-CDR) to identify breast cancer genomic correlates associating with different survival outcome endpoints

2018 ◽  
Author(s):  
J Liu ◽  
T Lichtenberg ◽  
KA Hoadley ◽  
A Cherniack ◽  
L Poisson ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Clinical Data ◽  
Survival Outcome ◽  
Data Resource ◽  
Pan Cancer

Abstract 3287: An integrated TCGA pan-cancer clinical data resource to drive high quality survival outcome analytics

2018 ◽  
Author(s):  
Jianfang Liu ◽  
Tara Lichtenberg ◽  
Katherine A. Hoadley ◽  
Laila M. Poisson ◽  
Alexander J. Lazar ◽  
...  
Keyword(s):  
Clinical Data ◽  
Survival Outcome ◽  
High Quality ◽  
Data Resource ◽  
Pan Cancer

scholarly journals An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

Cell ◽  
2018 ◽  
Vol 173 (2) ◽  
pp. 400-416.e11 ◽  
Author(s):  
Jianfang Liu ◽  
Tara Lichtenberg ◽  
Katherine A. Hoadley ◽  
Laila M. Poisson ◽  
Alexander J. Lazar ◽  
...  
Keyword(s):  
Clinical Data ◽  
Survival Outcome ◽  
High Quality ◽  
Data Resource ◽  
Pan Cancer

scholarly journals Observed Survival Interval: A Supplement to TCGA Pan-Cancer Clinical Data Resource

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 280 ◽  
Author(s):  
Jie Xiong ◽  
Zhitong Bing ◽  
Shengyu Guo
Keyword(s):  
Clinical Data ◽  
The Cancer Genome Atlas ◽  
Time Interval ◽  
Omics Data ◽  
Pathological Stage ◽  
Sequencing Data ◽  
Patient Death ◽  
Data Resource ◽  
Pan Cancer ◽  
Survival Interval

To drive high-quality omics translational research using The Cancer Genome Atlas (TCGA) data, a TCGA Pan-Cancer Clinical Data Resource was proposed. However, there is an out-of-step issue between clinical outcomes and the omics data of TCGA for skin cutaneous melanoma (SKCM), due to the majority of metastatic samples. In clinical cases, the survival time started from the initial SKCM diagnosis, while the omics data were characterized at TCGA sampling. This study aimed to address this issue by proposing an observed survival interval (OBS), which was defined as the time interval from TCGA sampling to patient death or last follow-up. We compared the OBS with the usual recommended overall survival (OS) by associating them with both clinical data and microRNA sequencing data of TCGA-SKCM. We found that the OS of primary SKCM was significantly shorter than that of metastatic SKCM, while the opposite happened if OBS was compared. OS was associated with the pathological stage of both primary and metastatic SKCM, while OBS was associated with the pathological stage of primary SKCM but not that of metastatic SKCM. Five previously cross-validated survival-associated microRNAs were found to be associated with the OBS rather than OS in metastatic SKCM. Thus, the OBS was more appropriate for associating microRNA-omics data of TCGA-SKCM than OS, and it is a timely supplement to TCGA Pan-Cancer Clinical Data Resource.

scholarly journals The BIRC Family Genes Expression in Patients with Triple Negative Breast Cancer

2021 ◽  
Vol 22 (4) ◽  
pp. 1820
Author(s):  
Anna Makuch-Kocka ◽  
Janusz Kocki ◽  
Anna Brzozowska ◽  
Jacek Bogucki ◽  
Przemysław Kołodziej ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Clinical Data ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Lymphatic Vessels ◽  
The Cancer Genome Atlas ◽  
Expression Level ◽  
Cancer Tissue ◽  
Expression Levels

The BIRC (baculoviral IAP repeat-containing; BIRC) family genes encode for Inhibitor of Apoptosis (IAP) proteins. The dysregulation of the expression levels of the genes in question in cancer tissue as compared to normal tissue suggests that the apoptosis process in cancer cells was disturbed, which may be associated with the development and chemoresistance of triple negative breast cancer (TNBC). In our study, we determined the expression level of eight genes from the BIRC family using the Real-Time PCR method in patients with TNBC and compared the obtained results with clinical data. Additionally, using bioinformatics tools (Ualcan and The Breast Cancer Gene-Expression Miner v4.5 (bc-GenExMiner v4.5)), we compared our data with the data in the Cancer Genome Atlas (TCGA) database. We observed diverse expression pattern among the studied genes in breast cancer tissue. Comparing the expression level of the studied genes with the clinical data, we found that in patients diagnosed with breast cancer under the age of 50, the expression levels of all studied genes were higher compared to patients diagnosed after the age of 50. We observed that in patients with invasion of neoplastic cells into lymphatic vessels and fat tissue, the expression levels of BIRC family genes were lower compared to patients in whom these features were not noted. Statistically significant differences in gene expression were also noted in patients classified into three groups depending on the basis of the Scarff-Bloom and Richardson (SBR) Grading System.

scholarly journals Breast cancer demographics, screening and survival outcome at a regional Australian cancer centre: a retrospective study

2016 ◽  
Vol 27 ◽  
pp. vi479
Author(s):  
H.A. Mandaliya ◽  
C. Oldmeadow ◽  
T. Evans ◽  
P. Troke ◽  
M. George
Keyword(s):  
Breast Cancer ◽  
Retrospective Study ◽  
Survival Outcome ◽  
Cancer Centre

scholarly journals Variation in the use of radiotherapy fractionation for breast cancer: Survival outcome and cost implications

2020 ◽  
Vol 152 ◽  
pp. 70-77
Author(s):  
Vikneswary Batumalai ◽  
Geoff P Delaney ◽  
Joseph Descallar ◽  
Gabriel Gabriel ◽  
Karen Wong ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Survival ◽  
Survival Outcome ◽  
Breast Cancer Survival ◽  
Cost Implications

scholarly journals Epidemiology and survival outcome of breast cancer in a nationwide study

Oncotarget ◽  
2017 ◽  
Vol 8 (10) ◽  
pp. 16939-16950 ◽  
Author(s):  
Fu-Chao Liu ◽  
Huan-Tang Lin ◽  
Chang-Fu Kuo ◽  
Lai-Chu See ◽  
Meng-Jiun Chiou ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Outcome ◽  
Nationwide Study

scholarly journals Quantitative hormone receptor (HR) expression and gene expression analysis in HR+ inflammatory breast cancer (IBC) vs non-IBC

2020 ◽  
Author(s):  
Toshiaki Iwase ◽  
Kenichi Harano ◽  
Hiroko Masuda ◽  
Kumiko Kida ◽  
Kenneth R. Hess ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Inflammatory Breast Cancer ◽  
Hormone Receptor ◽  
Survival Outcome ◽  
Stage Iii ◽  
Prognostic Role ◽  
Poor Survival ◽  
Poor Survival Outcome

Abstract Purpose: The purpose of this study was to determine the prognostic role of hormone receptor (HR) on inflammatory breast cancer (IBC) to elucidate its aggressive biological behavior.Methods: We evaluated the expression of estrogen receptor (ER) and progesterone receptor (PR) by immunohistochemical staining and determined the predictive and prognostic role of HR expression on 189 patients with HR+/HER2– IBC and 677 patients with HR+/HER2– stage III non-IBC. Furthermore, we performed gene expression (GE) analyses for 137 patients with HR+/HER2– IBC and 252 patients with corresponding non-IBC to detect genes that are specifically overexpressed in IBC.Results: The expression of ER% was significantly associated with longer distant disease-free survival and overall survival. However, there was no significant relationship between ER% and NAC outcome. In the GE study, 84 genes were identified as significantly distinguishing HR+ IBC from non-IBC. Among the top 15 canonical pathways expressed in IBC, the ERK/MAPK, PDGF, insulin receptor, and IL-7 signaling pathways were associated with the ER signaling pathway. Upregulation of the MYC gene was observed in three of these four pathways. Furthermore, HR+/HER2– IBC had significantly higher MYC amplification, and the genetic alteration was associated with poor survival outcome.Conclusions: Increased HR positivity was significantly associated with improved survival in both HR+/HER2– IBC and HR+/HER2– stage III non-IBC patients. HR+/HER2– IBC had several activated pathways with MYC upregulation, and the genetic alteration was associated with poor survival outcome. The results indicate that MYC may be a key gene for understanding the biology of HR+/HER2– IBC.

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