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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/29345217/statistical-analysis-of-human-microarray-data-shows-that-dietary-intervention-with-n-3-fatty-acids-flavonoids-and-resveratrol-enriches-for-immune-response-and-disease-pathways
#1
Alix Warburton, Olga Vasieva, Peter Quinn, James P Stewart, John P Quinn
n-3 Fatty acids, flavonoids and resveratrol are well publicised for their beneficial effects on human health and wellbeing. Identifying common, underlying biological mechanisms targeted by these functional foods would therefore be informative for the public health sector for advising on nutritional health and disease, food and drug product development and consumer interest. The aim of this study was to explore the potential effects of gene expression changes associated with n-3 fatty acids EPA and DHA, flavonoids and resveratrol on modifying biological systems and disease pathways...
January 18, 2018: British Journal of Nutrition
https://www.readbyqxmd.com/read/29341157/minimizing-inequality-in-access-to-precision-medicine-in-breast-cancer-by-real-time-population-based-molecular-analysis-in-the-scan-b-initiative
#2
L Rydén, N Loman, C Larsson, C Hegardt, J Vallon-Christersson, M Malmberg, H Lindman, A Ehinger, L H Saal, Å Borg
BACKGROUND: Selection of systemic therapy for primary breast cancer is currently based on clinical biomarkers along with stage. Novel genomic tests are continuously being introduced as more precise tools for guidance of therapy, although they are often developed for specific patient subgroups. The Sweden Cancerome Analysis Network - Breast (SCAN-B) initiative aims to include all patients with breast cancer for tumour genomic analysis, and to deliver molecular subtype and mutational data back to the treating physician...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29339815/mcl-1-is-a-prognostic-indicator-and-drug-target-in-breast-cancer
#3
Kirsteen J Campbell, Sandeep Dhayade, Nicola Ferrari, Andrew H Sims, Emma Johnson, Susan M Mason, Ashley Dickson, Kevin M Ryan, Gabriela Kalna, Joanne Edwards, Stephen G W Tait, Karen Blyth
Analysis of publicly available genomic and gene expression data demonstrates that MCL1 expression is frequently elevated in breast cancer. Distinct from other pro-survival Bcl-2 family members, the short half-life of MCL-1 protein led us to investigate MCL-1 protein expression in a breast cancer tissue microarray and correlate this with clinical data. Here, we report associations between high MCL-1 and poor prognosis in specific subtypes of breast cancer including triple-negative breast cancer, an aggressive form that lacks targeted treatment options...
January 16, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29338072/targeting-her2-in-colorectal-cancer-the-landscape-of-amplification-and-short-variant-mutations-in-erbb2-and-erbb3
#4
Jeffrey S Ross, Marwan Fakih, Siraj M Ali, Julia A Elvin, Alexa B Schrock, James Suh, Jo-Anne Vergilio, Shakti Ramkissoon, Eric Severson, Sugganth Daniel, David Fabrizio, Garrett Frampton, James Sun, Vincent A Miller, Philip J Stephens, Laurie M Gay
BACKGROUND: In contrast to lung cancer, few precision treatments are available for colorectal cancer (CRC). One rapidly emerging treatment target in CRC is ERBB2 (human epidermal growth factor receptor 2 [HER2]). Oncogenic alterations in HER2, or its dimerization partner HER3, can underlie sensitivity to HER2-targeted therapies. METHODS: In this study, 8887 CRC cases were evaluated by comprehensive genomic profiling for genomic alterations in 315 cancer-related genes, tumor mutational burden, and microsatellite instability...
January 16, 2018: Cancer
https://www.readbyqxmd.com/read/29335925/germline-deleterious-mutations-in-genes-other-than-brca2-are-infrequent-in-male-breast-cancer
#5
Florentia Fostira, Emmanouil Saloustros, Paraskevi Apostolou, Andromahi Vagena, Despoina Kalfakakou, Davide Mauri, Dimitrios Tryfonopoulos, Vassileios Georgoulias, Drakoulis Yannoukakos, Georgios Fountzilas, Irene Konstantopoulou
PURPOSE: Male breast cancer (MBC) is a rare cancer entity, with mutations in BRCA1 and BRCA2 genes accounting for ~ 10% of patients. Multiple-gene sequencing has already entered clinical practice for female breast cancer, whereas the performance of panel testing in MBC has not been studied extensively. Therefore, the aim of this study was to evaluate the clinical utility of panel testing for MBC, by the largest gene panel used so far, through investigation of patients deriving from a population with known founder effects...
January 15, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#6
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29322925/subtype-identification-from-heterogeneous-tcga-datasets-on-a-genomic-scale-by-multi-view-clustering-with-enhanced-consensus
#7
Menglan Cai, Limin Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. The problem is challenging when different data types show poor agreement of clustering structure...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29316957/evaluating-the-breast-cancer-predisposition-role-of-rare-variants-in-genes-associated-with-low-penetrance-breast-cancer-risk-snps
#8
Na Li, Simone M Rowley, Ella R Thompson, Simone McInerny, Lisa Devereux, Kaushalya C Amarasinghe, Magnus Zethoven, Richard Lupat, David Goode, Jason Li, Alison H Trainer, Kylie L Gorringe, Paul A James, Ian G Campbell
BACKGROUND: Genome-wide association studies (GWASs) have identified numerous single-nucleotide polymorphisms (SNPs) associated with small increases in breast cancer risk. Studies to date suggest that some SNPs alter the expression of the associated genes, which potentially mediates risk modification. On this basis, we hypothesised that some of these genes may be enriched for rare coding variants associated with a higher breast cancer risk. METHODS: The coding regions and exon-intron boundaries of 56 genes that have either been proposed by GWASs to be the regulatory targets of the SNPs and/or located < 500 kb from the risk SNPs were sequenced in index cases from 1043 familial breast cancer families that previously had negative test results for BRCA1 and BRCA2 mutations and 944 population-matched cancer-free control participants from an Australian population...
January 9, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29313063/using-gene-expression-data-to-direct-breast-cancer-therapy-evidence-from-a-preclinical-trial
#9
REVIEW
Shams Reaz, Deimante Tamkus, Eran R Andrechek
The heterogeneity both within and between breast cancers presents a significant clinical challenge for both diagnosis and therapy. This heterogeneity is present at all levels of analysis in breast cancer, ranging from genomic to metabolomic. A function of this heterogeneity is that numerous signaling networks are activated, and while treatment of one arm may be initially effective, this allows the tumor to be poised to evolve a resistance mechanism. Here we review the classification of breast cancers and discuss therapy of hormone positive, HER2 positive, and triple negative breast cancers...
January 8, 2018: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/29311117/expanded-genomic-profiling-of-circulating-tumor-cells-in-metastatic-breast-cancer-patients-to-assess-biomarker-status-and-biology-over-time
#10
Mark Jesus M Magbanua, Hope S Rugo, Denise M Wolfe, Louai Hauranieh, Ritu Roy, Praveen Pendyala, Eduardo Sosa, Janet H Scott, Jin Sun Lee, Brandelyn N Pitcher, Terry M Hyslop, William T Barry, Steven J Isakoff, Maura N Dickler, Laura J Van't Veer, John W Park
Purpose: We profiled circulating tumor cells (CTCs) patients to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC).Methods: CTCs were isolated from 105 MBC patients using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACs), 28 of whom had serial CTC analysis (74 samples, 2-5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (n=151) and genome-wide copy number analysis by array comparative genomic hybridization (n=49)...
January 8, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29304138/the-use-of-automated-ki67-analysis-to-predict-oncotype-dx-risk-of-recurrence-categories-in-early-stage-breast-cancer
#11
Satbir Singh Thakur, Haocheng Li, Angela M Y Chan, Roxana Tudor, Gilbert Bigras, Don Morris, Emeka K Enwere, Hua Yang
Ki67 is a commonly used marker of cancer cell proliferation, and has significant prognostic value in breast cancer. In spite of its clinical importance, assessment of Ki67 remains a challenge, as current manual scoring methods have high inter- and intra-user variability. A major reason for this variability is selection bias, in that different observers will score different regions of the same tumor. Here, we developed an automated Ki67 scoring method that eliminates selection bias, by using whole-slide analysis to identify and score the tumor regions with the highest proliferative rates...
2018: PloS One
https://www.readbyqxmd.com/read/29301932/a-post-reconstruction-harmonization-method-for-multicenter-radiomic-studies-in-pet
#12
Fanny Orlhac, Sarah Boughdad, Cathy Philippe, Hugo Stalla-Bourdillon, Christophe Nioche, Laurence Champion, Michaël Soussan, Frédérique Frouin, Vincent Frouin, Irène Buvat
Introduction: Several reports have shown that radiomic feature values are affected by the acquisition and reconstruction parameters, thus hampering multicenter studies. We propose a method to standardize features measured from Positron Emission Tomography (PET) images obtained using different imaging protocols to remove the center effect while preserving patient-specific effects. Methods: Pre-treatment 18F-FDG-PET images of patients with breast cancer were included. In Department A, 63 patients were scanned using a Gemini Time-Of-Flight-PET/Computed-Tomography scanner including 16 triple-negative lesions (TN)...
January 4, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29301506/the-exploration-of-contrasting-pathways-in-triple-negative-breast-cancer-tnbc
#13
Shavira Narrandes, Shujun Huang, Leigh Murphy, Wayne Xu
BACKGROUND: Triple Negative Breast Cancers (TNBCs) lack the appropriate targets for currently used breast cancer therapies, conferring an aggressive phenotype, more frequent relapse and poorer survival rates. The biological heterogeneity of TNBC complicates the clinical treatment further. We have explored and compared the biological pathways in TNBC and other subtypes of breast cancers, using an in silico approach and the hypothesis that two opposing effects (Yin and Yang) pathways in cancer cells determine the fate of cancer cells...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29300844/link-synthetic-lethality-to-drug-sensitivity-of-cancer-cells
#14
Ruiping Wang, Yue Han, Zhangxiang Zhao, Fan Yang, Tingting Chen, Wenbin Zhou, Xianlong Wang, Lishuang Qi, Wenyuan Zhao, Zheng Guo, Yunyan Gu
Synthetic lethal (SL) interactions occur when alterations in two genes lead to cell death but alteration in only one of them is not lethal. SL interactions provide a new strategy for molecular-targeted cancer therapy. Currently, there are few drugs targeting SL interactions that entered into clinical trials. Therefore, it is necessary to investigate the link between SL interactions and drug sensitivity of cancer cells systematically for drug development purpose. We identified SL interactions by integrating the high-throughput data from The Cancer Genome Atlas, small hairpin RNA data and genetic interactions of yeast...
December 28, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29295635/real-world-utilization-of-molecular-diagnostic-testing-and-matched-drug-therapies-in-the-treatment-of-metastatic-cancers
#15
Anita Chawla, Miranda Peeples, Nanxin Li, Rachel Anhorn, Jason Ryan, James Signorovitch
AIMS: To assess the frequency of biopsies and molecular diagnostic testing (human DNA/RNA analysis), anti-cancer drug use (genomically-matched targeted therapy [GMTT], unmatched targeted therapy [UTT], endocrine therapy [ET], and chemotherapy [CT]), and medical service costs among adults with metastatic cancer. METHODS: Adults diagnosed with metastatic breast, non-small cell lung (NSCLC), colorectal, head and neck, ovarian, and uterine cancer (2010Q1-2015Q1) were identified in the OptumHealth Care Solutions claims database and followed from first metastatic diagnosis for ≥1 month and until end of data availability...
January 3, 2018: Journal of Medical Economics
https://www.readbyqxmd.com/read/29286618/cancer-detection-in-microarray-data-using-a-modified-cat-swarm-optimization-clustering-approach
#16
Pandi M, Balamurugan R, Sadhasivam N
Objective: A better understanding of functional genomics can be obtained by extracting patterns hidden in gene expression data. This could have paramount implications for cancer diagnosis, gene treatments and other domains. Clustering may reveal natural structures and identify interesting patterns in underlying data. The main objective of this research was to derive a heuristic approach to detection of highly co-expressed genes related to cancer from gene expression data with minimum Mean Squared Error (MSE)...
December 29, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29286226/almost-complete-lack-of-human-cytomegalovirus-and-human-papillomaviruses-genome-in-benign-and-malignant-breast-lesions-in-shiraz-southwest-of-iran
#17
Sahar Bakhtiyrizadeh, Seyed Younes Hosseini, Ramin Yaghobi, Aliakbar Safaei, Jamal Sarvari
Breast cancer ranks as the most common cancer among women worldwide. There have been controversial reports regarding contributions of human papillomaviruses (HPVs) and human cytomegalovirus (HCMV) to its development. The aim of this study was to determine the frequency of HPV and HCMV positivity in benign and malignant breast tumors. Materials and Methods: Formalin fixed paraffin-embedded tissue specimens of 150 breast cancers (invasive ductal and lobular carcinomas) and 150 non-malignant breast lesions (fibroadenomas, fibrocystic disease and adenosis) were examined...
December 29, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29282678/biomarker-studies-in-early-detection-and-prognosis-of-breast-cancer
#18
Gang Li, Jing Hu, Guohong Hu
Breast cancer is characterized with enormous heterogeneity, which represents the major hurdle for accurate diagnosis and curative therapy. It is generally believed that genome unstability and molecular evolvability underlie the robustness of cancer cells in hostile microenvironment and their resilience to therapeutic intervention. Conventional histopathological classification of breast cancer falls short of providing sufficient prognostic and predictive power, and thus biomarkers indicative of tumor intrinsic features at molecular levels have been actively pursued in biomedical researches...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29281680/characteristics-of-percutaneous-core-biopsies-adequate-for-next-generation-genomic-sequencing
#19
Sharjeel H Sabir, Savitri Krishnamurthy, Sanjay Gupta, Gordon B Mills, Wei Wei, Andrea C Cortes, Kenna R Mills Shaw, Rajyalakshmi Luthra, Michael J Wallace
PURPOSE: Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. MATERIALS AND METHODS: All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion...
2017: PloS One
https://www.readbyqxmd.com/read/29261249/real-world-economic-value-of-a-21-gene-assay-in-early-stage-breast-cancer
#20
Stanley E Waintraub, Donna McNamara, Deena Mary Atieh Graham, Andrew L Pecora, John Min, Tommy Wu, Hyun Gi Noh, Jacqueline Connors, Ruth Pe Benito, Kelly Choi, Eric Schultz, Stuart L Goldberg
OBJECTIVES: Value-based payment reforms shift cost-containment responsibilities to the physician. Although gene expression profiling (GEP) utilizing a 21-gene panel among patients with early-stage, axillary lymph node-negative, hormone receptor-positive, HER2/neu oncogene-negative breast cancer is able to identify a cohort that may achieve excellent outcomes without adjuvant chemotherapy, high up-front costs (list price, $4175) could dissuade usage. STUDY DESIGN: Retrospective review of consecutive patients with breast cancer treated at a single cancer center...
December 1, 2017: American Journal of Managed Care
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