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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28640531/apparent-diffusion-coefficient-in-estrogen-receptor-positive-and-lymph-node-negative-invasive-breast-cancers-at-3-0t-dw-mri-a-potential-predictor-for-an-oncotype-dx-test-recurrence-score
#1
Sunitha B Thakur, Manuela Durando, Soledad Milans, Gene Y Cho, Lucas Gennaro, Elizabeth J Sutton, Dilip Giri, Elizabeth A Morris
PURPOSE: To measure the apparent diffusion coefficient (ADC) values in estrogen receptor-positive (ER+) and axillary lymph node-negative (LN-) invasive breast cancer and investigate the correlation of ADC with Oncotype Dx test recurrence scores (ODxRS). MATERIALS AND METHODS: This was a Health Insurance Portability and Accountability Act (HIPAA)-compliant single-site retrospective study. Patients underwent preoperative 3.0T MRI scans with additional diffusion-weighted imaging sequential scans (b = 0, 600 and b = 0, 1000 s/mm(2) ) from January 2011 to 2013...
June 22, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28637796/quantifying-the-genetic-correlation-between-multiple-cancer-types
#2
Sara Lindström, Hilary Finucane, Brendan Bulik-Sullivan, Fredrick R Schumacher, Christopher I Amos, Rayjean J Hung, Kristin Rand, Stephen B Gruber, David Conti, Jennifer B Permuth, Hui-Yi Lin, Ellen L Goode, Thomas A Sellers, Laufey T Amundadottir, Rachael Stolzenberg-Solomon, Alison Klein, Gloria Petersen, Harvey Risch, Brian Wolpin, Li Hsu, Jeroen R Huyghe, Jenny Chang Claude, Andrew Chan, Sonja Berndt, Rosalind A Eeles, Douglas Easton, Christopher A Haiman, David J Hunter, Benjamin Neale, Alkes Price, Peter Kraft
Many cancers share specific genetic risk factors including both rare high-penetrance mutations and common single nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS). However, little is known about the overall shared heritability across cancers. Quantifying the extent to which two distinct cancers share genetic origin will give insights to shared biological mechanisms underlying cancer and inform design for future genetic association studies. In this study, we estimated the pair-wise genetic correlation between six cancer types (breast, colorectal, lung, ovarian, pancreatic and prostate) using cancer-specific GWAS summary statistics data based on 66,958 case and 70,665 control subjects of European ancestry...
June 21, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28624696/superimposable-outcomes-for-sequential-and-concomitant-administration-of-adjuvant-trastuzumab-in%C3%A2-her2-positive-breast-cancer-results-from-the-signal-phare-prospective-cohort
#3
Xavier Pivot, Pierre Fumoleau, Jean-Yves Pierga, Suzette Delaloge, Hervé Bonnefoi, Thomas Bachelot, Christelle Jouannaud, Hugues Bourgeois, Maria Rios, Patrick Soulié, Jean-Philippe Jacquin, Sandrine Lavau-Denes, Pierre Kerbrat, David Cox, Céline Faure-Mercier, Iris Pauporte, Joseph Gligorov, Elsa Curtit, Julie Henriques, Sophie Paget-Bailly, Gilles Romieu
AIM: Adjuvant clinical trials in early human epidermal growth factor receptor 2 (HER2)-positive breast cancer have assessed either sequential or concomitant incorporation of trastuzumab with chemotherapy; only the North Central Cancer Treatment Group (NCCTG)-N9831 trial prospectively compared both modalities. In routine trastuzumab has been incorporated into a concurrent regimen with taxane chemotherapy instead of sequential modality on the basis of a positive risk-benefit ratio. This present study assessed sequential versus concomitant administration of adjuvant trastuzumab...
June 15, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28620890/identification-and-characterization-of-a-new-brca2-rearrangement-in-an-italian-family-with-hereditary-breast-and-ovarian-cancer-syndrome
#4
Paola Concolino, Roberta Rizza, Karl Hackmann, Angelo Minucci, Giovanni Luca Scaglione, Maria De Bonis, Alessandra Costella, Cecilia Zuppi, Evelin Schrock, Ettore Capoluongo
INTRODUCTION: Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE: Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication...
June 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28615971/clinical-use-of-the-oncotype-dx-genomic-test-to-guide-treatment-decisions-for-patients-with-invasive-breast-cancer
#5
REVIEW
Terri P McVeigh, Michael J Kerin
Implementation of the Oncotype DX assay has led to a change in the manner in which chemotherapy is utilized in patients with early stage, estrogen receptor (ER)-positive, node-negative breast cancer; ensuring that patients at highest risk of recurrence are prescribed systemic treatment, while at the same time sparing low-risk patients potential adverse events from therapy unlikely to influence their survival. This test generates a recurrence score between 0 and 100, which correlates with probability of distant disease recurrence...
2017: Breast Cancer: Targets and Therapy
https://www.readbyqxmd.com/read/28615668/improving-the-detection-of-pathways-in-genome-wide-association-studies-by-combined-effects-of-snps-from-linkage-disequilibrium-blocks
#6
Huiying Zhao, Dale R Nyholt, Yuanhao Yang, Jihua Wang, Yuedong Yang
Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607444/identification-of-novel-dysregulated-key-genes-in-breast-cancer-through-high-throughput-chip-seq-data-analysis
#7
Utkarsh Raj, Imlimaong Aier, Rahul Semwal, Pritish Kumar Varadwaj
Breast cancer is the most common cancer in women both in the developed and less developed countries, and it imposes a considerable threat to human health. Therefore, in order to develop effective targeted therapies against Breast cancer, a deep understanding of its underlying molecular mechanisms is required. The application of deep transcriptional sequencing has been found to be reported to provide an efficient genomic assay to delve into the insights of the diseases and may prove to be useful in the study of Breast cancer...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606152/heterologous-expression-of-cytotoxic-sesquiterpenoids-from-the-medicinal-mushroom-lignosus-rhinocerotis-in-yeast
#8
Hui-Yeng Yeannie Yap, Mariano Jordi Muria-Gonzalez, Boon-Hong Kong, Keith A Stubbs, Chon-Seng Tan, Szu-Ting Ng, Nget-Hong Tan, Peter S Solomon, Shin-Yee Fung, Yit-Heng Chooi
BACKGROUND: Genome mining facilitated by heterologous systems is an emerging approach to access the chemical diversity encoded in basidiomycete genomes. In this study, three sesquiterpene synthase genes, GME3634, GME3638, and GME9210, which were highly expressed in the sclerotium of the medicinal mushroom Lignosus rhinocerotis, were cloned and heterologously expressed in a yeast system. RESULTS: Metabolite profile analysis of the yeast culture extracts by GC-MS showed the production of several sesquiterpene alcohols (C15H26O), including cadinols and germacrene D-4-ol as major products...
June 12, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28601027/a-semantic-interoperability-approach-to-support-integration-of-gene-expression-and-clinical-data-in-breast-cancer
#9
Raul Alonso-Calvo, Sergio Paraiso-Medina, David Perez-Rey, Enrique Alonso-Oset, Ruud van Stiphout, Sheng Yu, Marian Taylor, Francesca Buffa, Carlos Fernandez-Lozano, Alejandro Pazos, Victor Maojo
INTRODUCTION: The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. METHODS: This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials...
June 5, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28595730/recurrent-large-genomic-rearrangements-in-brca1-and-brca2-in-an-irish-case-series
#10
Terri P McVeigh, Nuala Cody, Cliona Carroll, Marie Duff, Michael Farrell, Lisa Bradley, David Gallagher, Trudi McDevitt, Andrew J Green
Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Comprehensive mutation testing using these two methods has been facilitated via our centre since 2005...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28591191/reanalysis-of-brca1-2-negative-high-risk-ovarian-cancer-patients-reveals-novel-germline-risk-loci-and-insights-into-missing-heritability
#11
Jaime L Stafford, Gregory Dyson, Nancy K Levin, Sophia Chaudhry, Rita Rosati, Hasini Kalpage, Courtney Wernette, Nancie Petrucelli, Michael S Simon, Michael A Tainsky
While up to 25% of ovarian cancer (OVCA) cases are thought to be due to inherited factors, the majority of genetic risk remains unexplained. To address this gap, we sought to identify previously undescribed OVCA risk variants through the whole exome sequencing (WES) and candidate gene analysis of 48 women with ovarian cancer and selected for high risk of genetic inheritance, yet negative for any known pathogenic variants in either BRCA1 or BRCA2. In silico SNP analysis was employed to identify suspect variants followed by validation using Sanger DNA sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28589855/identifying-subtype-specific-associations-between-gene-expression-and-dna-methylation-profiles-in-breast-cancer
#12
Garam Lee, Lisa Bang, So Yeon Kim, Dokyoon Kim, Kyung-Ah Sohn
BACKGROUND: Breast cancer is a complex disease in which different genomic patterns exists depending on different subtypes. Recent researches present that multiple subtypes of breast cancer occur at different rates, and play a crucial role in planning treatment. To better understand underlying biological mechanisms on breast cancer subtypes, investigating the specific gene regulatory system via different subtypes is desirable. METHODS: Gene expression, as an intermediate phenotype, is estimated based on methylation profiles to identify the impact of epigenomic features on transcriptomic changes in breast cancer...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28582508/association-of-breast-cancer-risk-and-the-mtor-pathway-in-women-of-african-ancestry-in-the-root-consortium
#13
Shengfeng Wang, Dezheng Huo, Temidayo O Ogundiran, Oladosu Ojengbede, Wei Zheng, Katherine L Nathanson, Barbara Nemesure, Stefan Ambs, Olufunmilayo I Olopade, Yonglan Zheng
Functional studies have elucidated the role of the mammalian target of rapamycin (mTOR) pathway in breast carcinogenesis, but to date, there is a paucity of data on its contribution to breast cancer risk in women of African ancestry. We examined 47,628 SNPs in 61 mTOR pathway genes in the genome wide association study of breast cancer in the African Diaspora study (The Root consortium), which included 3,686 participants (1,657 cases). Pathway- and gene-level analyses were conducted using the adaptive rank truncated product (ARTP) test for 10,994 SNPs that were not highly correlated (r2 < 0...
June 5, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28572255/unmet-needs-in-clinical-research-in-breast-cancer-where-do-we-need-to-go
#14
EDITORIAL
Ann H Partridge, Lisa A Carey
This CCR Focus highlights areas in breast cancer research with the greatest potential for clinical and therapeutic application. The articles in this CCR Focus address the state of the science in a broad range of areas with a focus on "hot" although sometimes controversial topics, unanswered questions, and unmet need. From mutational signatures, the cancer genomic revolution, and new inroads in immunotherapy for breast cancer to unique concerns of vulnerable populations as well as national and global health disparities, these works represent much of the promise of breast cancer research as well as the challenges in the coming years...
June 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28558674/learning-rule-sets-from-survival-data
#15
Łukasz Wróbel, Adam Gudyś, Marek Sikora
BACKGROUND: Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their condition, examination results, and undergoing treatment. The recent developments in the next generation sequencing open new opportunities in survival study as they allow vast amount of genome-, transcriptome-, and proteome-related features to be investigated. These include single nucleotide and structural variants, expressions of genes and microRNAs, DNA methylation, and many others...
May 30, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28557251/evidence-for-the-association-of-epstein-barr-virus-in-breast-cancer-in-indian-patients-using-in-situ-hybridization-technique
#16
Trupti Pai, Sudeep Gupta, Mamta Gurav, Shona Nag, Tanuja Shet, Asawari Patil, Sangeeta Desai
Epstein-Barr Virus (EBV) is etiologically linked to Burkitt lymphoma (BL), nasopharyngeal carcinoma, post-transplant lymphomas, Hodgkin disease, and possibly other tumors. However, the association of oncogenic EBV with breast carcinoma (BC) is still controversial and a matter of debate. We aimed to study the presence of EBV genome in BC cases in Indian patients and its association with the clinicopathological features. The formalin fixed paraffin embedded tissues from 83 women with primary invasive BC were studied for the presence of EBV by in-situ hybridization (ISH) technique for Epstein-Barr Virus Encoded RNA (EBER) with appropriate controls...
May 30, 2017: Breast Journal
https://www.readbyqxmd.com/read/28554120/genome-wide-predicting-disease-related-protein-complexes-by-walking-on-the-heterogeneous-network-based-on-data-integration-and-laplacian-normalization
#17
Zhiming Liu, Jiawei Luo
BACKGROUND: Associating protein complexes to human inherited diseases is critical for better understanding of biological processes and functional mechanisms of the disease. Many protein complexes have been identified and functionally annotated by computational and purification methods so far, however, the particular roles they were playing in causing disease have not yet been well determined. RESULTS: In this study, we present a novel method to identify associations between protein complexes and diseases...
April 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28537877/clinical-validation-of-genetic-variants-associated-with-in-vitro-chemotherapy-related-lymphoblastoid-cell-toxicity
#18
Peter A Fasching, Lothar Häberle, Brigitte Rack, Liang Li, Alexander Hein, Arif B Ekici, Andre Reis, Michael P Lux, Julie M Cunningham, Matthias Ruebner, Gergory Jenkins, Brooke Fridley, Andreas Schneeweiss, Hans Tesch, Werner Lichtenegger, Tanja Fehm, Georg Heinrich, Mahdi Rezai, Matthias W Beckmann, Wolfgang Janni, Richard M Weinshilboum, Liewei Wang
Hematotoxicity is one of the major side effects of chemotherapy. The aim of this study was to examine the association between single nucleotide polymorphisms (SNPs) and hematotoxicity in breast cancer patients in a subset of patients of the SUCCESS prospective phase III chemotherapy study. All patients (n = 1678) received three cycles of 5-fluorouracil, epirubicin, and cyclophosphamide (FEC) followed by three cycles of docetaxel or docetaxel/gemcitabine, depending on randomization. Germline DNA was genotyped for 246 SNPs selected from a previous genome-wide association study (GWAS) in a panel of lymphoblastoid cell lines, with gemcitabine toxicity as the phenotype...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28536279/the-damaging-effect-of-passenger-mutations-on-cancer-progression
#19
Christopher McFarland, Julia A Yaglom, Jonathan W Wojtkowiak, Jacob Scott, David L Morse, Michael Y Sherman, Leonid Mirny
Genomic instability and high mutation rates cause cancer to acquire numerous mutations and chromosomal alterations during its somatic evolution, most are termed passengers because they do not confer cancer phenotypes. Evolutionary simulations and cancer genomic studies suggest that mildly deleterious passengers accumulate and can collectively slow cancer progression. Clinical data also suggest an association between passenger load and response to therapeutics, yet no causal link between the effects of passengers and cancer progression has been established...
May 23, 2017: Cancer Research
https://www.readbyqxmd.com/read/28535794/mutation-site-and-context-dependent-effects-of-esr1-mutation-in-genome-edited-breast-cancer-cell-models
#20
Amir Bahreini, Zheqi Li, Peilu Wang, Kevin M Levine, Nilgun Tasdemir, Lan Cao, Hazel M Weir, Shannon L Puhalla, Nancy E Davidson, Andrew M Stern, David Chu, Ben Ho Park, Adrian V Lee, Steffi Oesterreich
BACKGROUND: Mutations in the estrogen receptor alpha (ERα) 1 gene (ESR1) are frequently detected in ER+ metastatic breast cancer, and there is increasing evidence that these mutations confer endocrine resistance in breast cancer patients with advanced disease. However, their functional role is not well-understood, at least in part due to a lack of ESR1 mutant models. Here, we describe the generation and characterization of genome-edited T47D and MCF7 breast cancer cell lines with the two most common ESR1 mutations, Y537S and D538G...
May 23, 2017: Breast Cancer Research: BCR
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