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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28087099/prognostic-and-predictive-indicators-in-early-stage-breast-cancer-and-the-role-of-genomic-profiling-focus-on-the-oncotype-dx-%C3%A2-breast-recurrence-score-assay
#1
E Curtit, L Mansi, Y Maisonnette-Escot, J-L Sautière, X Pivot
Although useful prognostic and predictive insights can be gained from patient and tumour characteristics in early-stage breast cancer, it is not always straightforward to predict the likely risk of recurrence for each individual patient following breast surgery. One of the most difficult challenges faced by clinicians is identifying patients who may benefit most from adjuvant chemotherapy, and distinguishing these cases from those where endocrine therapy may be sufficient for cure. Genomic tests such as the Oncotype DX(®) Breast Recurrence Score(®) Assay have been developed to provide a robust and clinically validated assessment of a patient's individual tumour signature...
December 14, 2016: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28075351/circulating-nucleosomes-and-nucleosome-modifications-as-biomarkers-in-cancer
#2
REVIEW
Peter McAnena, James A L Brown, Michael J Kerin
Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment...
January 8, 2017: Cancers
https://www.readbyqxmd.com/read/28068660/direct-to-consumer-genetic-testing-user-motivations-decision-making-and-perceived-utility-of-results
#3
J Scott Roberts, Michele C Gornick, Deanna Alexis Carere, Wendy R Uhlmann, Mack T Ruffin, Robert C Green
BACKGROUND/AIMS: To describe the interests, decision making, and responses of consumers of direct-to-consumer personal genomic testing (DTC-PGT) services. METHODS: Prior to 2013 regulatory restrictions on DTC-PGT services, 1,648 consumers from 2 leading companies completed Web surveys before and after receiving test results. RESULTS: Prior to testing, DTC-PGT consumers were as interested in ancestry (74% very interested) and trait information (72%) as they were in disease risks (72%)...
January 10, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28061482/genomic-mutation-driven-metastatic-breast-cancer-therapy-a-single-center-experience
#4
Yuan Yuan, Susan E Yost, Yate-Ching Yuan, Nicola M Solomon, Isa Mambetsariev, Sumanta Pal, Paul Frankel, Ravi Salgia, Susan L Neuhausen, Joanne Mortimer
BACKGROUND: Next-Generation Sequencing (NGS) has made genomic mutation-driven therapy feasible for metastatic breast cancer (MBC) patients. We frequently submit tumor tissue from MBC patients for targeted NGS of tumor using the Illumina HiSeq 2000 platform (FoundationOne®, Foundation Medicine, MA). Herein, we report the results and clinical impact of this test in MBC patients. PATIENTS AND METHODS: We identified patients with MBC treated at City of Hope from January 2014 to May 2016 who underwent NGS...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28035408/identification-of-antibiotic-resistance-genes-in-the-multidrug-resistant-acinetobacter-baumannii-strain-mdr-shh02-using-whole-genome-sequencing
#5
Hualiang Wang, Jinghua Wang, Peijuan Yu, Ping Ge, Yanqun Jiang, Rong Xu, Rong Chen, Xuejie Liu
This study aimed to investigate antibiotic resistance genes in the multidrug-resistant (MDR) Acinetobacter baumannii (A. baumanii) strain, MDR-SHH02, using whole‑genome sequencing (WGS). The antibiotic resistance of MDR-SHH02 isolated from a patient with breast cancer to 19 types of antibiotics was determined using the Kirby‑Bauer method. WGS of MDR-SHH02 was then performed. Following quality control and transcriptome assembly, functional annotation of genes was conducted, and the phylogenetic tree of MDR-SHH02, along with another 5 A...
December 30, 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28034454/comprehensive-genomic-sequencing-and-the-molecular-profiles-of-clinically-advanced-breast-cancer
#6
Jeffrey S Ross, Laurie M Gay
Targeting specific mutations that have arisen within a tumour is a promising means of increasing the efficacy of treatments, and breast cancer is no exception to this new paradigm of personalised medicine. Traditional DNA sequencing methods used to characterise clinical cancer specimens and impact treatment decisions are highly sensitive, but are often limited in their scope to known mutational hot spots. Next-generation sequencing (NGS) technologies can also test for these well-known hot spots, as well as identifying insertions and deletions, copy number changes such as ERBB2 (HER2) gene amplification, and a wide array of fusion or rearrangement events...
December 26, 2016: Pathology
https://www.readbyqxmd.com/read/28033448/second-opinions-from-medical-oncologists-for-early-stage-breast-cancer-prevalence-correlates-and-consequences
#7
Allison W Kurian, Christopher R Friese, Irina Bondarenko, Reshma Jagsi, Yun Li, Ann S Hamilton, Kevin C Ward, Steven J Katz
Importance: Advances in the evaluation and treatment of breast cancer have made the clinical decision-making context much more complex. A second opinion from a medical oncologist may facilitate decision making for women with breast cancer, yet little is known about second opinion use. Objective: To investigate the patterns and correlates of second opinion use and the effect on chemotherapy decisions. Design, Setting, and Participants: A total of 1901 women newly diagnosed with stages 0 to II breast cancer between July 2013 and September 2014 (response rate, 71...
December 29, 2016: JAMA Oncology
https://www.readbyqxmd.com/read/28027945/next-generation-assessment-of-erbb2-human%C3%A2-epidermal-growth-factor-receptor-2-amplification-status-clinical-validation-in-the-context-of-a-hybrid-capture-based-comprehensive-solid-tumor-genomic-profiling-assay
#8
Dara S Ross, Ahmet Zehir, Donavan T Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F Hechtman, Yelena Y Janjigian, Britta Weigelt, Pedram Razavi, David M Hyman, José Baselga, Michael F Berger, Marc Ladanyi, Maria E Arcila
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to patients' treatment plans. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling...
December 24, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28008224/centrosome-a-promising-anti-cancer-target
#9
REVIEW
Yainyrette Rivera-Rivera, Harold I Saavedra
The centrosome, an organelle discovered >100 years ago, is the main microtubule-organizing center in mammalian organisms. The centrosome is composed of a pair of centrioles surrounded by the pericentriolar material (PMC) and plays a major role in the regulation of cell cycle transitions (G1-S, G2-M, and metaphase-anaphase), ensuring the normality of cell division. Hundreds of proteins found in the centrosome exert a variety of roles, including microtubule dynamics, nucleation, and kinetochore-microtubule attachments that allow correct chromosome alignment and segregation...
2016: Biologics: Targets & Therapy
https://www.readbyqxmd.com/read/27995640/genotoxic-risk-of-ethyl-paraben-could-be-related-to-telomere-shortening
#10
F Finot, A Kaddour, L Morat, I Mouche, N Zaguia, C Cuceu, D Souverville, S Négrault, O Cariou, A Essahli, N Prigent, J Saul, F Paillard, L Heidingsfelder, P Lafouge, M Al Jawhari, W M Hempel, M El May, B Colicchio, A Dieterlen, E Jeandidier, L Sabatier, J Clements, R M'Kacher
The ability of parabens to promote the appearance of multiple cancer hallmarks in breast epithelium cells provides grounds for regulatory review of the implication of the presence of parabens in human breast tissue. It is well documented that telomere dysfunction plays a significant role in the initiation of genomic instability during carcinogenesis in human breast cancer. In the present study, we evaluated the genotoxic effect of ethyl 4-hydroxybenzoate (ethyl-paraben), with and without metabolic activation (S9), in studies following OECD guidelines...
December 20, 2016: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/27993963/genome-wide-association-study-for-anthracycline-induced-congestive-heart-failure
#11
Bryan P Schneider, Fei Shen, Laura Gardner, Milan Radovich, Lang Li, Kathy D Miller, Guanglong Jiang, Dongbing Lai, Anne O'Neill, Joseph A Sparano, Nancy E Davidson, David Cameron, Irmina Gradus-Pizlo, Ronald A Mastouri, Thomas M Suter, Tatiana Foroud, George W Sledge
PURPOSE: Anthracycline-induced congestive heart failure (CHF) is a rare but serious toxicity associated with this commonly employed anticancer therapy. The ability to predict which patients might be at increased risk prior to exposure would be valuable to optimally counsel risk-to-benefit ratio for each patient. Herein, we present a genome-wide approach for biomarker discovery with two validation cohorts to predict CHF from adult patients planning to receive anthracycline. EXPERIMENTAL DESIGN: We performed a genome-wide association study in 3,431 patients from the randomized phase III adjuvant breast cancer trial E5103 to identify single nucleotide polymorphism (SNP) genotypes associated with an increased risk of anthracycline-induced CHF...
January 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27992319/therapeutics-targeting-fgf-signaling-network-in-human-diseases
#12
REVIEW
Masaru Katoh
Fibroblast growth factor (FGF) signaling through its receptors, FGFR1, FGFR2, FGFR3, or FGFR4, regulates cell fate, angiogenesis, immunity, and metabolism. Dysregulated FGF signaling causes human diseases, such as breast cancer, chondrodysplasia, gastric cancer, lung cancer, and X-linked hypophosphatemic rickets. Recombinant FGFs are pro-FGF signaling therapeutics for tissue and/or wound repair, whereas FGF analogs and gene therapy are under development for the treatment of cardiovascular disease, diabetes, and osteoarthritis...
December 2016: Trends in Pharmacological Sciences
https://www.readbyqxmd.com/read/27974384/brca-testing-by-single-molecule-molecular-inversion-probes
#13
Kornelia Neveling, Arjen R Mensenkamp, Ronny Derks, Michael Kwint, Hicham Ouchene, Marloes Steehouwer, Bart van Lier, Ermanno Bosgoed, Alwin Rikken, Marloes Tychon, Dimitra Zafeiropoulou, Steven Castelein, Jayne Hehir-Kwa, Djie Tjwan Thung, Tom Hofste, Stefan H Lelieveld, Stijn M M Bertens, Ivo B J F Adan, Astrid Eijkelenboom, Bastiaan B Tops, Helger Yntema, Tomasz Stokowy, Per M Knappskog, Hildegunn Høberg-Vetti, Vidar M Steen, Evan Boyle, Beth Martin, Marjolijn J L Ligtenberg, Jay Shendure, Marcel R Nelen, Alexander Hoischen
BACKGROUND: Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested single gene tests, those for breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2), and developed an automated work flow based on smMIPs...
December 14, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27959926/predictors-of-chemosensitivity-in-triple-negative-breast-cancer-an-integrated-genomic-analysis
#14
Tingting Jiang, Weiwei Shi, Vikram B Wali, Lőrinc S Pongor, Charles Li, Rosanna Lau, Balázs Győrffy, Richard P Lifton, William F Symmans, Lajos Pusztai, Christos Hatzis
BACKGROUND: Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive disease, and although no effective targeted therapies are available to date, about one-third of patients with TNBC achieve pathologic complete response (pCR) from standard-of-care anthracycline/taxane (ACT) chemotherapy. The heterogeneity of these tumors, however, has hindered the discovery of effective biomarkers to identify such patients. METHODS AND FINDINGS: We performed whole exome sequencing on 29 TNBC cases from the MD Anderson Cancer Center (MDACC) selected because they had either pCR (n = 18) or extensive residual disease (n = 11) after neoadjuvant chemotherapy, with cases from The Cancer Genome Atlas (TCGA; n = 144) and METABRIC (n = 278) cohorts serving as validation cohorts...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27942580/genetic-variation-in-the-insulin-insulin-like-growth-factor-growth-hormone-and-leptin-pathways-in-relation-to-breast-cancer-in-african-american-women-the-amber-consortium
#15
Edward A Ruiz-Narváez, Kathryn L Lunetta, Chi-Chen Hong, Stephen Haddad, Song Yao, Ting-Yuan David Cheng, Jeannette T Bensen, Elisa V Bandera, Christopher A Haiman, Melissa A Troester, Christine B Ambrosone, Lynn Rosenberg, Julie R Palmer
The insulin/insulin-like growth factor (IGF) system and related pathways such as growth hormone, and leptin signaling have a key role in cancer development. It is unclear how germline variation in these pathways affects breast cancer risk. We conducted gene-based analyses of 184 genes in the insulin/IGF, growth hormone, and leptin pathways to identify genetic variation associated with risk of breast cancer overall, and for estrogen receptor (ER) subtypes. Tag single-nucleotide polymorphisms (SNPs) for each gene were selected and genotyped on a customized Illumina SNP array...
2016: NPJ Breast Cancer
https://www.readbyqxmd.com/read/27937091/personal-genomic-testing-for-cancer-risk-results-from-the-impact-of-personal-genomics-study
#16
Stacy W Gray, Sarah E Gollust, Deanna Alexis Carere, Clara A Chen, Angel Cronin, Sarah S Kalia, Huma Q Rana, Mack T Ruffin, Catharine Wang, J Scott Roberts, Robert C Green
Purpose Significant concerns exist regarding the potential for unwarranted behavior changes and the overuse of health care resources in response to direct-to-consumer personal genomic testing (PGT). However, little is known about customers' behaviors after PGT. Methods Longitudinal surveys were given to new customers of 23andMe (Mountain View, CA) and Pathway Genomics (San Diego, CA). Survey data were linked to individual-level PGT results through a secure data transfer process. Results Of the 1,042 customers who completed baseline and 6-month surveys (response rate, 71...
December 12, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/27903675/a-pam50-based-chemo-endocrine-score-for-hormone-receptor-positive-breast-cancer-with-an-intermediate-risk-of-relapse
#17
Aleix Prat, Ana Lluch, Arran K Turnbull, Anita K Dunbier, Lourdes Calvo, Joan Albanell, Juan de la Haba-Rodríguez, Angels Arcusa, Ignacio Chacón, Pedro Sánchez-Rovira, Arrate Plazaola, Montse Muñoz, Laia Paré, Joel S Parker, Nuria Ribelles, Begona Jimenez, Abdul Aziz Bin Aiderus, Rosalía Caballero, Barbara Adamo, Mitch Dowsett, Eva M Carrasco, Miguel Martín, J Michael Dixon, Charles M Perou, Emilio Alba
PURPOSE: Hormone receptor-positive (HR+) breast cancer is clinically and biologically heterogeneous and subgroups with different prognostic and treatment sensitivities need to be identified. EXPERIMENTAL DESIGN: Research-based PAM50 subtyping and expression of additional genes was performed on 63 patients with HR+/HER2- disease randomized to neoadjuvant multi-agent chemotherapy versus endocrine therapy in a phase II trial. The biology associated with treatment response was used to derive a PAM50-based Chemo-Endocrine Score (CES)...
November 30, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27899188/familial-prostate-cancer
#18
Veda N Giri, Jennifer L Beebe-Dimmer
Prostate cancer is the most commonly diagnosed cancer among men in the United States as well as most Western countries. A significant proportion of men report having a positive family history of prostate cancer in a first-degree relative (father, brother, son), which is important in that family history is one of the only established risk factors for the disease and plays a role in decision-making for prostate cancer screening. Familial aggregation of prostate cancer is considered a surrogate marker of genetic susceptibility to developing the disease, but shared environment cannot be excluded as an explanation for clustering of cases among family members...
October 2016: Seminars in Oncology
https://www.readbyqxmd.com/read/27895805/blood-based-dna-methylation-as-biomarker-for-breast-cancer-a-systematic-review
#19
REVIEW
Qiuqiong Tang, Jie Cheng, Xue Cao, Harald Surowy, Barbara Burwinkel
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#20
Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Pietro Liò, Ivan Merelli
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level...
2016: Frontiers in Genetics
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