keyword
MENU ▼
Read by QxMD icon Read
search

Breast cancer genomic testing

keyword
https://www.readbyqxmd.com/read/29769129/a-powerful-nonparametric-method-for-detecting-differentially-co-expressed-genes-distance-correlation-screening-and-edge-count-test
#1
Qingyang Zhang
BACKGROUND: Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks...
May 16, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29768301/germline-genome-wide-association-studies-in-women-receiving-neoadjuvant-chemotherapy-with-or-without-bevacizumab
#2
James N Ingle, Krishna R Kalari, Donald Lawrence Wickerham, Gunter von Minckwitz, Peter A Fasching, Yoichi Furukawa, Taisei Mushiroda, Matthew P Goetz, Poulami Barman, Erin E Carlson, Priya Rastogi, Joseph P Costantino, Junmei Cairns, Soonmyung Paik, Harry D Bear, Michiaki Kubo, Liewei Wang, Norman Wolmark, Richard M Weinshilboum
Neoadjuvant chemotherapy (NAC) for breast cancer is widely utilized, and we performed genome-wide association studies (GWAS) to determine whether germ-line genetic variability was associated with benefit in terms of pathological complete response (pCR), disease-free survival, and overall survival in patients entered on the NSABP B-40 NAC trial, wherein patients were randomized to receive, or not, bevacizumab in addition to chemotherapy. Patient DNA samples were genotyped with the Illumina OmniExpress BeadChip...
June 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29768063/overexpression-of-hoxc10-promotes-glioblastoma-cell-progression-to-a-poor-prognosis-via-the-pi3k-akt-signaling-pathway
#3
Yong Guan, Yajie He, Shaoping Lv, Xiaoqun Hou, Luo Li, Jianjun Song
OBJECTIVE: The HOX gene is expressed in neoplasias occurred in multiple tissues, such as the colon, lung, and breast. However, the effects of the HOX gene on glioblastoma (GBM) remain poorly understood. We examined HOXC10 expression in GBM tissues and cells, analyzed its effect on GBM prognosis, and finally assessed its possible underlying mechanisms in this study. METHODS: HOXC10 expression levels and its prognostic effects on GBM tissues were analyzed based on The Cancer Genome Atlas (TCGA) and ONCOMINE database...
May 16, 2018: Journal of Drug Targeting
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
#4
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/29757984/integrative-bioinformatics-and-functional-analyses-of-geo-encode-and-tcga-reveal-fadd-as-a-direct-target-of-the-tumor-suppressor-brca1
#5
Dinh-Duc Nguyen, Dong Gyu Lee, Sinae Kim, Keunsoo Kang, Je-Keun Rhee, Suhwan Chang
BRCA1 is a multifunctional tumor suppressor involved in several essential cellular processes. Although many of these functions are driven by or related to its transcriptional/epigenetic regulator activity, there has been no genome-wide study to reveal the transcriptional/epigenetic targets of BRCA1. Therefore, we conducted a comprehensive analysis of genomics/transcriptomics data to identify novel BRCA1 target genes. We first analyzed ENCODE data with BRCA1 chromatin immunoprecipitation (ChIP)-sequencing results and identified a set of genes with a promoter occupied by BRCA1...
May 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29750305/alterations-in-mrna-profiles-of-trastuzumab%C3%A2-resistant-her%C3%A2-2%C3%A2-positive-breast-cancer
#6
Bin Zhao, Yang Zhao, Yan Sun, Haitao Niu, Long Sheng, Dongfang Huang, Li Li
Breast cancer is one of the most common malignancies in women. Neoadjuvant trastuzumab therapy improves the prognosis of certain Her‑2‑positive breast cancer patients, however around two‑thirds of patients with Her‑2‑positive breast cancer do not benefit from Her‑2‑targeted therapy. To investigate the key mechanisms in trastuzumab resistance, potential biomarkers for neoadjuvant trastuzumab sensitivity were investigated using the gene expression omnibus (GEO) database for mRNA microarray data of Her‑2‑positive breast cancer patients who received neoadjuvant trastuzumab therapy...
May 7, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29737473/uptake-of-brca-1-2-and-oncotype-dx-testing-by-medical-and-surgical-oncologists
#7
Yonina R Murciano-Goroff, Anne Marie McCarthy, Mirar N Bristol, Peter Groeneveld, Susan M Domchek, U Nkiru Motanya, Katrina Armstrong
PURPOSE: The diffusion of genomic testing is critical to the success of precision medicine, but there is limited information on oncologists' uptake of genetic technology. We aimed to assess the frequency with which medical oncologists and surgeons order BRCA 1/2 and Oncotype DX testing for breast cancer patients. METHODS: We surveyed 732 oncologists and surgeons treating breast cancer patients. Physicians were from Florida, New York, New Jersey, and Pennsylvania, and were listed in the 2010 AMA Masterfile or identified by patients...
May 8, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29736694/pre-surgical-trial-of-the-akt-inhibitor-mk-2206-in-patients-with-operable-invasive-breast-cancer-a-new-york-cancer-consortium-trial
#8
K Kalinsky, J A Sparano, X Zhong, E Andreopoulou, B Taback, L Wiechmann, S M Feldman, P Ananthakrishnan, A Ahmad, S Cremers, A N Sireci, J R Cross, D K Marks, P Mundi, E Connolly, K D Crew, M A Maurer, H Hibshoosh, S Lee, D L Hershman
INTRODUCTION: The PI3K/AKT/mTOR pathway is an oncogenic driver in breast cancer (BC). In this multi-center, pre-surgical study, we evaluated the tissue effects of the AKT inhibitor MK-2206 in women with stage I-III BC. MATERIALS AND METHODS: Two doses of weekly oral MK2206 were administered at days - 9 and - 2 before surgery. The primary endpoint was reduction of pAktSer473 in breast tumor tissue from diagnostic biopsy to surgery. Secondary endpoints included changes in PI3K/AKT pathway tumor markers, tumor proliferation (ki-67), insulin growth factor pathway blood markers, pharmacokinetics (PK), genomics, and MK-2206 tolerability...
May 7, 2018: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/29728051/ensemble-outlier-detection-and-gene-selection-in-triple-negative-breast-cancer-data
#9
Marta B Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel, Susana Vinga
BACKGROUND: Learning accurate models from 'omics data is bringing many challenges due to their inherent high-dimensionality, e.g. the number of gene expression variables, and comparatively lower sample sizes, which leads to ill-posed inverse problems. Furthermore, the presence of outliers, either experimental errors or interesting abnormal clinical cases, may severely hamper a correct classification of patients and the identification of reliable biomarkers for a particular disease. We propose to address this problem through an ensemble classification setting based on distinct feature selection and modeling strategies, including logistic regression with elastic net regularization, Sparse Partial Least Squares - Discriminant Analysis (SPLS-DA) and Sparse Generalized PLS (SGPLS), coupled with an evaluation of the individuals' outlierness based on the Cook's distance...
May 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29721472/practical-consensus-recommendations-on-management-of-hr-ve-early-breast-cancer-with-specific-reference-to-genomic-profiling
#10
S Aggarwal, A Vaid, A Ramesh, Purvish M Parikh, S Purohit, B Avasthi, S Gupta, S Ranjan, V Kaushal, S Salim, R Singh, S Minhas, D Doval
Breast cancer is a heterogeneous disease and patients are managed clinically based on ER, PR, HER2 expression, and key risk factors. The use of gene expression assays for early stage disease is already common practice. These tests have found a place in risk stratifying the heterogeneous group of stage I-II breast cancers for recurrence, for predicting chemotherapy response, and for predicting breast cancer-related mortality. Most guidelines for hormone receptor (HR)-positive early breast cancer recommend addition of adjuvant chemotherapy for most women, leading to overtreatment, which causes considerable morbidity and cost...
April 2018: South Asian Journal of Cancer
https://www.readbyqxmd.com/read/29721079/dna-methylation-signatures-predicting-bevacizumab-efficacy-in-metastatic-breast-cancer
#11
Simon Peter Gampenrieder, Gabriel Rinnerthaler, Hubert Hackl, Walter Pulverer, Andreas Weinhaeusel, Suzana Ilic, Clemens Hufnagl, Cornelia Hauser-Kronberger, Alexander Egle, Angela Risch, Richard Greil
Background: Biomarkers predicting response to bevacizumab in breast cancer are still missing. Since epigenetic modifications can contribute to an aberrant regulation of angiogenesis and treatment resistance, we investigated the influence of DNA methylation patterns on bevacizumab efficacy. Methods: Genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in archival FFPE specimens of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy ( learning set )...
2018: Theranostics
https://www.readbyqxmd.com/read/29720474/functional-and-genomic-characterization-of-a-xenograft-model-system-for-the-study-of-metastasis-in-triple-negative-breast-cancer
#12
Cameron N Johnstone, Andrew D Pattison, Kylie L Gorringe, Paul F Harrison, David R Powell, Peter Lock, David Baloyan, M Ernst, Alastair G Stewart, Traude H Beilharz, Robin L Anderson
Triple-negative breast cancer represents 10-20% of all human ductal adenocarcinomas and has a poor prognosis relative to other subtypes. Hence, new molecular targets for therapeutic intervention are necessary. Analyses of panels of human or mouse cancer lines derived from the same individual that differ in their cellular phenotypes but not in genetic background have been instrumental in defining the molecular players that drive the various hallmarks of cancer.To determine the molecular regulators of metastasis in triple-negative breast cancer, we completed a rigorous in vitro and in vivo characterization of four populations of the MDA-MB-231 human breast cancer line ranging in aggressiveness from non-metastatic to spontaneously metastatic to lung, liver, spleen and lymph node...
April 30, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29715116/first-french-pilot-quality-assessment-of-the-endopredict-test-for-early-luminal-breast-carcinoma
#13
Jacqueline Lehmann-Che, Catherine Miquel, Jennifer Wong, Celine Callens, Etienne Rouleau, Veronique Quillien, Nicolas Lozano, Anne Cayre, Ludovic Lacroix, Ivan Bieche, Philippe Bertheau, Luis Teixeira, Frederique Penault Llorca, Pierre Jean Lamy, Patricia DE Cremoux
BACKGROUND/AIM: Genomic signatures are needed for the determination of prognosis in patients with early stage, estrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancers. EndoPredict test is a RNA-based multigene assay that assesses the risk of 10-year relapse in this context. Quality assessment is a mandatory requirement for a laboratory to address the analytical quality of these molecular analyses. The aim of the study was to demonstrate the robustness of this prognostic test, its usefulness for the patient's treatment strategy, at the national level...
May 2018: Anticancer Research
https://www.readbyqxmd.com/read/29700634/frequency-of-pathogenic-germline-mutations-in-cancer-susceptibility-genes-in-breast-cancer-patients
#14
Raman Preet Kaur, Gowhar Shafi, Raja Paramjeet Singh Benipal, Anjana Munshi
In this study, we evaluated the incidence of pathogenic germline mutations in 30 breast cancer susceptibility genes in breast cancer patients. Our aim was to understand the involvement of the inherited mutations in these genes in a breast cancer cohort. Two hundred ninety-six female breast cancer patients including 4.5% of familial breast cancer cases were included in the study. 200 ng of genomic DNA was used to evaluate the pathogenic mutations, detected using Global Screening Array (GSA) microchip (Illumina Inc...
April 26, 2018: Medical Oncology
https://www.readbyqxmd.com/read/29665859/morphology-and-genomic-hallmarks-of-breast-tumours-developed-by-atm-deleterious-variant-carriers
#15
Anne-Laure Renault, Noura Mebirouk, Laetitia Fuhrmann, Guillaume Bataillon, Eve Cavaciuti, Dorothée Le Gal, Elodie Girard, Tatiana Popova, Philippe La Rosa, Juana Beauvallet, Séverine Eon-Marchais, Marie-Gabrielle Dondon, Catherine Dubois d'Enghien, Anthony Laugé, Walid Chemlali, Virginie Raynal, Martine Labbé, Ivan Bièche, Sylvain Baulande, Jacques-Olivier Bay, Pascaline Berthet, Olivier Caron, Bruno Buecher, Laurence Faivre, Marc Fresnay, Marion Gauthier-Villars, Paul Gesta, Nicolas Janin, Sophie Lejeune, Christine Maugard, Sébastien Moutton, Laurence Venat-Bouvet, Hélène Zattara, Jean-Pierre Fricker, Laurence Gladieff, Isabelle Coupier, Georgia Chenevix-Trench, Janet Hall, Anne Vincent-Salomon, Dominique Stoppa-Lyonnet, Nadine Andrieu, Fabienne Lesueur
BACKGROUND: The ataxia telangiectasia mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear histopathological and molecular features of breast tumours occurring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumour signature may help in patient management. METHODS: To characterise hallmarks of ATM-associated tumours, we performed systematic pathology review of tumours from 21 participants from ataxia-telangiectasia families and 18 participants from HBOC families, as well as copy number profiling on a subset of 23 tumours...
April 17, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29659677/targeting-the-human-epidermal-growth-factor-receptor-2-her2-oncogene-in-colorectal-cancer
#16
S Siena, A Sartore-Bianchi, S Marsoni, H I Hurwitz, S J McCall, F Penault-Llorca, S Srock, A Bardelli, L Trusolino
BACKGROUND: Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver, and a well-established therapeutic target in breast and gastric cancers. Using functional and genomic analyses of patient-derived xenografts, we previously showed that a subset (approximately 5%) of metastatic colorectal cancer (CRC) tumors are driven by amplification or mutation of HER2. MATERIALS AND METHODS: This paper reviews the role of HER2 as an oncogenic driver, a prognostic and predictive biomarker, and a clinically actionable target in CRC, considering the specifics of HER2 testing in this tumor type...
April 6, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29618289/testing-equality-of-means-in-partially-paired-data-with-incompleteness-in-single-response
#17
Qianya Qi, Li Yan, Lili Tian
In testing differentially expressed genes between tumor and healthy tissues, data are usually collected in paired form. However, incomplete paired data often occur. While extensive statistical researches exist for paired data with incompleteness in both arms, hardly any recent work can be found on paired data with incompleteness in single arm. This paper aims to fill this gap by proposing some new methods, namely, P-value pooling methods and a nonparametric combination test. Simulation studies are conducted to investigate the performance of the proposed methods in terms of type I error and power at small to moderate sample sizes...
January 1, 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29614442/the-role-of-genomic-profiling-in-adolescents-and-young-adults-ayas-with-advanced-cancer-participating-in-phase-i-clinical-trials
#18
Terri Patricia McVeigh, Raghav Sundar, Nikolaos Diamantis, Stan B Kaye, Udai Banerji, Juanita S Lopez, Johann de Bono, Winette T A van der Graaf, Angela J George
INTRODUCTION: Adolescents and young adults (AYAs) diagnosed with cancer between ages 15-39 years may harbour germline variants associated with cancer predisposition. Such variants represent putative therapeutic targets, as may somatic variants in the tumour. Germline and tumour molecular profiling is increasingly utilised to facilitate personalisation of cancer treatment in such individuals. AIM: Considering AYAs with advanced solid tumours managed in a specialist drug development unit (DDU), the aims of this study were to investigate the use and impact of: 1...
March 31, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29593426/clinical-and-economic-impact-of-the-21-gene-recurrence-score-assay-in-adjuvant-therapy-decision-making-in-patients-with-early-stage-breast-cancer-pooled-analysis-in-4-basque-country-university-hospitals
#19
Purificación Martínez Del Prado, Isabel Alvarez-López, Severina Domínguez-Fernández, Arrate Plazaola, Oliver Ibarrondo, Elena Galve-Calvo, Nerea Ancizar-Lizarraga, María Gutierrez-Toribio, Ainhara Lahuerta-Martínez, Javier Mar
Purpose: The 21-gene recurrence score (RS) is a genomic test developed as a prognostic and predictive tool to improve the treatment decision making in cases of estrogen receptor-positive and human epidermal growth factor receptor 2-negative early-stage breast cancer. This study examined the clinical and economic impact of its use in 4 Basque Country university hospitals. Methods: Taking into consideration the RS result, we recorded the recommended initial systemic adjuvant therapy (endocrine therapy with or without chemotherapy) according to standard clinicopathologic factors and the final decision about chemotherapy...
2018: ClinicoEconomics and Outcomes Research: CEOR
https://www.readbyqxmd.com/read/29582426/prevalence-of-brca1-2-large-genomic-rearrangements-in-chinese-women-with-sporadic-triple-negative-or-familial-breast-cancer
#20
L Su, J Zhang, H Meng, T Ouyang, J Li, T Wang, Z Fan, T Fan, B Lin, Y Xie
The prevalence of BRCA1/2 large genomic rearrangements (LGRs) and their underlying mechanisms have not been fully evaluated in Chinese women with breast cancer. In this study, we determined the prevalence of BRCA1/2 LGRs in 834 patients with familial breast cancer and 660 patients with sporadic triple-negative breast cancer who were negative for BRCA1/2 small-range mutations using the multiplex ligation-dependent probe amplification method. We found that twenty index patients (2.4%) in the familial breast cancer group carried a BRCA1 or BRCA2 LGR, and the frequencies of BRCA1 and BRCA2 LGRs were 1...
March 27, 2018: Clinical Genetics
keyword
keyword
53823
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"