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https://www.readbyqxmd.com/read/29761914/molecular-features-in-young-vs-elderly-breast-cancer-patients-and-the-impacts-on-survival-disparities-by-age-at-diagnosis
#1
Mei-Xia Wang, Jun-Ting Ren, Lu-Ying Tang, Ze-Fang Ren
Young and elderly breast cancer patients are more likely to have a poorer outcome than middle-aged patients. The intrinsic molecular features for this disparity are unclear. We obtained data from the Cancer Genome Atlas (TCGA) on May 15, 2017 to test the potential mediation effects of the molecular features on the association between age and prognosis with a four-step approach. The relative contributions of the molecular features (PAM50 subtype, risk stratification, DNAm age, and mutations in TP53, PIK3CA, MLL3, CDH1, GATA3, and MAP3K1) to age disparities in survival were estimated by Cox proportional hazard models with or without the features...
May 15, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29675884/specific-breast-cancer-prognosis-subtype-distinctions-based-on-dna-methylation-patterns
#2
Shumei Zhang, Yihan Wang, Yue Gu, Jiang Zhu, Ce Ci, Zhongfu Guo, Chuangeng Chen, Yanjun Wei, Wenhua Lv, Hongbo Liu, Dongwei Zhang, Yan Zhang
Tumor heterogeneity is an obstacle to effective breast cancer diagnosis and therapy. DNA methylation is an important regulator of gene expression, thus characterizing tumor heterogeneity by epigenetic features can be clinically informative. In this study, we explored specific prognosis-subtypes based on DNA methylation status using 669 breast cancers from TCGA database. Nine subgroups were distinguished by consensus clustering using 3869 CpGs that significantly influenced survival. The specific DNA methylation patterns were reflected by different races, ages, tumor stages, receptor status, histological types, metastasis status and prognosis...
April 19, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29650789/reparameterization-of-pam50-expression-identifies-novel-breast-tumor-dimensions-and-leads-to-discovery-of-a-genomewide-significant-breast-cancer-locus-at-12q15
#3
Michael J Madsen, Stacey Knight, Carol Sweeney, Rachel E Factor, Mohamed E Salama, Inge J Stijleman, Venkatesh Rajamanickam, Bryan E Welm, Sasi Arunachalam, Brandt Jones, Rakesh Rachamadugu, Kerry Rowe, Melissa Cessna, Alun Thomas, Lawrence H Kushi, Bette Caan, Philip S Bernard, Nicola J Camp
BACKGROUND: Breast tumor subtyping has failed to provide impact in susceptibility genetics. The PAM50 assay categorizes breast tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like. However, tumors are often more complex than simple categorization can describe. The identification of heritable tumor characteristics has potential to decrease heterogeneity and increase power for gene-finding. METHODS: We used 911 sporadic breast tumors with PAM50 expression data to derive tumor dimensions using principal components (PC)...
April 12, 2018: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29622545/pam50-and-risk-of-recurrence-scores-for-interval-breast-cancers
#4
Samantha Puvanesarajah, Sarah J Nyante, Cherie M Kuzmiak, Mengjie Chen, Chiu-Kit Tse, Xuezheng Sun, Emma H Allott, Erin L Kirk, Lisa A Carey, Charles M Perou, Andrew F Olshan, Louise M Henderson, Melissa A Troester
Breast cancers detected after a negative breast screening examination and prior to the next screening are referred to as interval cancers. These cancers generally have poor clinical characteristics compared to screen-detected cancers, but associations between interval cancer and genomic cancer characteristics are not well understood. Mammographically-screened women diagnosed with primary invasive breast cancer from 1993-2013 (n=370) were identified by linking the Carolina Breast Cancer Study and the Carolina Mammography Registry...
April 5, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29596496/radiogenomics-analysis-identifies-correlations-of-digital-mammography-with-clinical-molecular-signatures-in-breast-cancer
#5
Jose-Gerardo Tamez-Peña, Juan-Andrés Rodriguez-Rojas, Hugo Gomez-Rueda, Jose-Maria Celaya-Padilla, Roxana-Alicia Rivera-Prieto, Rebeca Palacios-Corona, Margarita Garza-Montemayor, Servando Cardona-Huerta, Victor Treviño
In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control...
2018: PloS One
https://www.readbyqxmd.com/read/29588372/prognostic-value-of-ki67-analysed-by-cytology-or-histology-in-primary-breast-cancer
#6
Stephanie Robertson, Gustav Stålhammar, Eva Darai-Ramqvist, Mattias Rantalainen, Nicholas P Tobin, Jonas Bergh, Johan Hartman
AIMS: The accuracy of biomarker assessment in breast pathology is vital for therapy decisions. The therapy predictive and prognostic biomarkers oestrogen receptor (ER), progesterone receptor, HER2 and Ki67 may act as surrogates to gene expression profiling of breast cancer. The aims of this study were to investigate the concordance of consecutive biomarker assessment by immunocytochemistry on preoperative fine-needle aspiration cytology versus immunohistochemistry (IHC) on the corresponding resected breast tumours...
March 27, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29573665/outcomes-of-single-versus-double-hormone-receptor-positive-breast-cancer-a-geicam-9906-sub-study
#7
J L Ethier, A Ocaña, A Rodríguez Lescure, A Ruíz, E Alba, L Calvo, M Ruíz-Borrego, A Santaballa, C A Rodríguez, C Crespo, M Ramos, J Gracia Marco, A Lluch, I Álvarez, M Casas, M Sánchez-Aragó, E Carrasco, R Caballero, E Amir, M Martin
BACKGROUND: Retrospective data suggest better outcomes for patients with double hormonal receptor (oestrogen [ER] and progesterone receptor [PgR])-positive (dHR+) early breast cancer, compared with single hormonal receptor-positive, sHR+, (ER+/PgR- or ER-/PgR+) disease. Here, we evaluate the classification according to intrinsic subtypes and clinical outcomes of sHR+ versus dHR+ in HER2-negative breast cancer patients enrolled in GEICAM/9906 study (NCT00129922). METHODS: Archival tumours were retrieved retrospectively for the analysis of ER, PgR and HER2 status and classified into intrinsic subtypes using the PAM50 gene expression assay...
May 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29507663/a-comprehensive-function-analysis-of-lmo2-in-different-breast-cancer-subtypes
#8
Ye Liu, Mei Yuan, Chao Wu, Tianhui Zhu, Wei Sun
Breast cancer is the most common invasive cancer in women worldwide, and can be subdivided into Luminal A, Luminal B, Her2, and Basal subtype (the PAM50 subtyping system). The lmo2 gene was traditionally recognized as a proto-oncogene in hematopoietic system but its functions in breast cancers remained largely unclear. Based on the Cancer Genome Atlas (TCGA) breast cancer dataset, herein we found that the significantly LMO2-correlated genes in normal or malignant samples were enriched in rather divergent cellular pathways, suggesting the function complexity of LMO2 in breast tissues...
February 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29504910/brca-pathway-a-structural-integration-and-visualization-system-of-tcga-breast-cancer-data-on-kegg-pathways
#9
Inyoung Kim, Saemi Choi, Sun Kim
BACKGROUND: Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become huge, e.g., TCGA, and the data types to be analyzed have come in many varieties, including mutations, copy number variations, and transcriptome. We also need to consider a complex relationship with regulators of genes, particularly Transcription Factors(TF)...
February 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29467948/challenges-in-using-liquid-biopsies-for-gene-expression-profiling
#10
Tania B Porras, Pushpinder Kaur, Alexander Ring, Naomi Schechter, Julie E Lang
Circulating tumor cells (CTCs) have potential utility as a surrogate biomarker of tumor biology via a liquid biopsy. The aim of this study was to evaluate if the nCounter NanoString assay could be used for accurate gene expression profiling of CTCs using the PAM50 research-use-only CodeSet. Analysis was performed on CTCs isolated by the ANGLE Parsortix system from healthy blood spiked with the breast cancer cell lines Hs578T, SkBr3, MDA-MB-231 or MCF7. Using cell lines as gold standard positive controls and Parsortix processed blood without spiking (unspiked) as negative controls, we found an average of 12 significantly differentially expressed genes among spiked samples versus unspiked controls...
January 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29450494/comparison-of-the-performance-of-6-prognostic-signatures-for-estrogen-receptor-positive-breast-cancer-a-secondary-analysis-of-a-randomized-clinical-trial
#11
Ivana Sestak, Richard Buus, Jack Cuzick, Peter Dubsky, Ralf Kronenwett, Carsten Denkert, Sean Ferree, Dennis Sgroi, Catherine Schnabel, Frederick L Baehner, Elizabeth Mallon, Mitch Dowsett
Importance: Multiple molecular signatures are available for managing estrogen receptor (ER)-positive breast cancer but with little direct comparative information to guide the patient's choice. Objective: To conduct a within-patient comparison of the prognostic value of 6 multigene signatures in women with early ER-positive breast cancer who received endocrine therapy for 5 years. Design, Setting, and Participants: This retrospective biomarker analysis included 774 postmenopausal women with ER-positive ERBB2 (formerly HER2)-negative breast cancer...
April 1, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/29433456/exome-sequencing-of-primary-breast-cancers-with-paired-metastatic-lesions-reveals-metastasis-enriched-mutations-in-the-a-kinase-anchoring-protein-family-akaps
#12
Una Kjällquist, Rikard Erlandsson, Nicholas P Tobin, Amjad Alkodsi, Ikram Ullah, Gustav Stålhammar, Eva Karlsson, Thomas Hatschek, Johan Hartman, Sten Linnarsson, Jonas Bergh
BACKGROUND: Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease...
February 12, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29409530/frequency-of-breast-cancer-subtypes-among-african-american-women-in-the-amber-consortium
#13
Emma H Allott, Joseph Geradts, Stephanie M Cohen, Thaer Khoury, Gary R Zirpoli, Wiam Bshara, Warren Davis, Angela Omilian, Priya Nair, Rochelle P Ondracek, Ting-Yuan David Cheng, C Ryan Miller, Helena Hwang, Leigh B Thorne, Siobhan O'Connor, Traci N Bethea, Mary E Bell, Zhiyuan Hu, Yan Li, Erin L Kirk, Xuezheng Sun, Edward A Ruiz-Narvaez, Charles M Perou, Julie R Palmer, Andrew F Olshan, Christine B Ambrosone, Melissa A Troester
BACKGROUND: Breast cancer subtype can be classified using standard clinical markers (estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)), supplemented with additional markers. However, automated biomarker scoring and classification schemes have not been standardized. The aim of this study was to optimize tumor classification using automated methods in order to describe subtype frequency in the African American Breast Cancer Epidemiology and Risk (AMBER) consortium...
February 6, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29386247/the-role-of-the-ar-er-ratio-in-er-positive-breast-cancer-patients
#14
Nelson Rangel, Milena Rondon-Lagos, Laura Annaratone, Simona Osella-Abate, Jasna Metovic, Maria Piera Mano, Luca Bertero, Paola Cassoni, Anna Sapino, Isabella Castellano
The significance of androgen receptor (AR) in breast cancer (BC) management is not fully defined, and it is still ambiguous how the level of AR expression influences oestrogen receptor-positive (ER+) tumours. The aim of the present study was to analyse the prognostic impact of AR/ER ratio, evaluated by immunohistochemistry (IHC), correlating this value with clinical, pathological and molecular characteristics. We retrospectively selected a cohort of 402 ER+BC patients. On each tumour, IHC analyses for AR, ER, PgR, HER2 and Ki67 were performed and AR+ cases were used to calculate the AR/ER value...
March 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29369732/pam50-risk-of-recurrence-score-predicts-10-year-distant-recurrence-in-a-comprehensive-danish-cohort-of-postmenopausal-women-allocated-to-5-years-of-endocrine-therapy-for-hormone-receptor-positive-early-breast-cancer
#15
Anne-Vibeke Lænkholm, Maj-Britt Jensen, Jens Ole Eriksen, Birgitte Bruun Rasmussen, Ann S Knoop, Wesley Buckingham, Sean Ferree, Carl Schaper, Torsten O Nielsen, Taryn Haffner, Torben Kibøl, Maj-Lis Møller Talman, Anne Marie Bak Jylling, Tomasz Piotr Tabor, Bent Ejlertsen
Purpose The PAM50-based Prosigna risk of recurrence (ROR) score has been validated in randomized clinical trials to predict 10-year distant recurrence (DR). The value of Prosigna for predicting DR was examined in a comprehensive nationwide Danish cohort consisting of postmenopausal women with hormone receptor-positive early breast cancer treated with 5 years of endocrine therapy alone. Patients and Methods Using the population-based Danish Breast Cancer Cooperative Group database, follow-up data were collected on all patients diagnosed from 2000 through 2003 who, by nationwide guidelines, were treated with endocrine therapy for 5 years...
March 10, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29228969/race-associated-biological-differences-among-luminal-a-and-basal-like-breast-cancers-in-the-carolina-breast-cancer-study
#16
Humberto Parada, Xuezheng Sun, Jodie M Fleming, ClarLynda R Williams-DeVane, Erin L Kirk, Linnea T Olsson, Charles M Perou, Andrew F Olshan, Melissa A Troester
BACKGROUND: We examined racial differences in the expression of eight genes and their associations with risk of recurrence among 478 white and 495 black women who participated in the Carolina Breast Cancer Study Phase 3. METHODS: Breast tumor samples were analyzed for PAM50 subtype and for eight genes previously found to be differentially expressed by race and associated with breast cancer survival: ACOX2, MUC1, FAM177A1, GSTT2, PSPH, PSPHL, SQLE, and TYMS. The expression of these genes according to race was assessed using linear regression and each gene was evaluated in association with recurrence using Cox regression...
December 11, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29220095/digital-image-analysis-of-ki67-in-hot-spots-is-superior-to-both-manual-ki67-and-mitotic-counts-in-breast-cancer
#17
Gustav Stålhammar, Stephanie Robertson, Lena Wedlund, Michael Lippert, Mattias Rantalainen, Jonas Bergh, Johan Hartman
AIMS: During pathological examination of breast tumours, proliferative activity is routinely evaluated by a count of mitoses. Adding immunohistochemical stains of Ki67 provides extra prognostic and predictive information. However, the currently used methods for these evaluations suffer from imperfect reproducibility. It is still unclear whether analysis of Ki67 should be performed in hot spots, in the tumour periphery, or as an average of the whole tumour section. The aim of this study was to compare the clinical relevance of mitoses, Ki67 and phosphohistone H3 in two cohorts of primary breast cancer specimens (total n = 294)...
December 8, 2017: Histopathology
https://www.readbyqxmd.com/read/29218898/building-trans-omics-evidence-using-imaging-and-omics-to-characterize-cancer-profiles
#18
Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju
Utilization of single modality data to build predictive models in cancer results in a rather narrow view of most patient profiles. Some clinical facet s relate strongly to histology image features, e.g. tumor stages, whereas others are associated with genomic and proteomic variations (e.g. cancer subtypes and disease aggression biomarkers). We hypothesize that there are coherent "trans-omics" features that characterize varied clinical cohorts across multiple sources of data leading to more descriptive and robust disease characterization...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29202609/the-ability-of-pam50-risk-of-recurrence-score-to-predict-10-year-distant-recurrence-in-hormone-receptor-positive-postmenopausal-women-with-special-histological-subtypes
#19
Anne-Vibeke Laenkholm, Maj-Britt Jensen, Jens Ole Eriksen, Wesley Buckingham, Sean Ferree, Torsten O Nielsen, Bent Ejlertsen
INTRODUCTION: The Prosigna-PAM50 risk of recurrence (ROR) score has been validated in randomized clinical trials to predict 10-year distant recurrence (DR) in hormone receptor-positive breast cancer. Here, we examine the ability of Prosigna for predicting DR at 10 years in a subgroup of postmenopausal breast cancer patients with special histological subtypes. METHODS: Using the population based Danish Breast Cancer Group database, follow-up data were collected on all patients diagnosed from 2000 to 2003 with estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2) normal breast cancer who by nationwide guidelines were treated with 5 year of endocrine therapy (N = 2558)...
January 2018: Acta Oncologica
https://www.readbyqxmd.com/read/29175678/systematic-review-of-the-clinical-and-economic-value-of-gene-expression-profiles-for-invasive-early-breast-cancer-available-in-europe
#20
REVIEW
E J Blok, E Bastiaannet, W B van den Hout, G J Liefers, V T H B M Smit, J R Kroep, C J H van de Velde
Gene expression profiles with prognostic capacities have shown good performance in multiple clinical trials. However, with multiple assays available and numerous types of validation studies performed, the added value for daily clinical practice is still unclear. In Europe, the MammaPrint, OncotypeDX, PAM50/Prosigna and Endopredict assays are commercially available. In this systematic review, we aim to assess these assays on four important criteria: Assay development and methodology, clinical validation, clinical utility and economic value...
January 2018: Cancer Treatment Reviews
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