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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#1
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28320353/genome-independent-hypoxic-repression-of-estrogen-receptor-alpha-in-breast-cancer-cells
#2
Mercè Padró, Raymond J Louie, Brian V Lananna, Adam J Krieg, Luika A Timmerman, Denise A Chan
BACKGROUND: About 75-80% of breast tumors express the estrogen receptor alpha (ER-α) and are treated with endocrine-target therapeutics, making this the premier therapeutic modality in the breast cancer clinic. However, acquired resistance is common and about 20% of resistant tumors loose ER-α expression via unknown mechanisms. Inhibition of ER-α loss could improve endocrine therapeutic efficacy, benefiting a significant number of patients. Here we test whether tumor hypoxia might commonly produce ER-α loss...
March 20, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28302160/increased-genomic-burden-of-germline-copy-number-variants-is-associated-with-early-onset-breast-cancer-australian-breast-cancer-family-registry
#3
Logan C Walker, John F Pearson, George A R Wiggins, Graham G Giles, John L Hopper, Melissa C Southey
BACKGROUND: Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called "missing heritability"...
March 16, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28302091/development-of-a-test-that-measures-real-time-her2-signaling-function-in-live-breast-cancer-cell-lines-and-primary-cells
#4
Yao Huang, David J Burns, Benjamin E Rich, Ian A MacNeil, Abhijit Dandapat, Sajjad M Soltani, Samantha Myhre, Brian F Sullivan, Carol A Lange, Leo T Furcht, Lance G Laing
BACKGROUND: Approximately 18-20% of all human breast cancers have overexpressed human epidermal growth factor receptor 2 (HER2). Standard clinical practice is to treat only overexpressed HER2 (HER2+) cancers with targeted anti-HER2 therapies. However, recent analyses of clinical trial data have found evidence that HER2-targeted therapies may benefit a sub-group of breast cancer patients with non-overexpressed HER2. This suggests that measurement of other biological factors associated with HER2 cancer, such as HER2 signaling pathway activity, should be considered as an alternative means of identifying patients eligible for HER2 therapies...
March 16, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28300277/breast-cancer-and-genomic-testing
#5
C Liedtke, H-C Kolberg
No abstract text is available yet for this article.
March 16, 2017: British Journal of Surgery
https://www.readbyqxmd.com/read/28299801/bi-allelic-alterations-in-dna-repair-genes-underpin-homologous-recombination-dna-repair-defects-in-breast-cancer
#6
Robert W Mutter, Nadeem Riaz, Charlotte K Y Ng, Rob Delsite, Salvatore Piscuoglio, Marcia Edelweiss, Luciano G Martelotto, Rita A Sakr, Tari A King, Dilip D Giri, Maria Drobnjak, Edi Brogi, Ranjit Bindra, Giana Bernheim, Raymond S Lim, Pedro Blecua, Alexis Desrichard, Dan Higginson, Russell Towers, Ruomu Jiang, William Lee, Britta Weigelt, Jorge S Reis-Filho, Simon N Powell
Homologous recombination (HR) DNA repair deficient (HRD) breast cancers have been shown to be sensitive to DNA repair targeted therapies. Burgeoning evidence suggests that sporadic breast cancers, lacking germline BRCA1/BRCA2 mutations, may also be HRD. We developed a functional ex vivo RAD51-based test to identify HRD primary breast cancers. An integrated approach examining methylation, gene expression and whole-exome sequencing was employed to ascertain the etiology of HRD. Functional HRD breast cancers displayed genomic features of lack of competent HR, including large-scale state transitions and specific mutational signatures...
March 15, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28280929/molecular-mechanisms-of-therapy-resistance-in-solid-tumors-chasing-moving-targets
#7
REVIEW
Laura J Tafe
The goal of personalized cancer therapy is to treat tumors based on genomic aberrations that drive their survival and progression. Most patients who receive targeted therapies typically develop resistance and disease progression within a year's time. This review focuses on the heterogeneous mechanisms of therapy resistance to tyrosine kinase inhibitors, endocrine/hormone therapy and checkpoint blockade using non-small cell lung cancer, breast and castration-resistant prostate cancer, and melanoma as classical examples, respectively...
March 10, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28271309/mutational-studies-on-single-circulating-tumor-cells-isolated-from-the-blood-of-inflammatory-breast-cancer-patients
#8
Catherine Bingham, Sandra V Fernandez, Patricia Fittipaldi, Paul W Dempsey, Karen J Ruth, Massimo Cristofanilli, R Katherine Alpaugh
PURPOSE: The molecular characterization of circulating tumor cells (CTCs) is critical to identify the key drivers of cancer metastasis and devising therapeutic approaches, particularly for inflammatory breast cancer (IBC) which is usually diagnosed at advance stages and progresses rapidly. METHODS: Genomic alterations in tumor tissue samples were studied using Foundation One™. Single CTCs were isolated using CellSearch followed by single-cell isolation by DEPArray™...
March 7, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28252435/-genomic-variability-in-patients-with-ductal-form-of-breast-cancer-and-the-possibility-of-correction-the-peptide-bioregulator-and-metal-ions
#9
T Jokhadze, J Monaselidze, G Nemsadze, T Buadze, M Gaiozishvili, T Lezhava
Level of genome stability (structural aberrations, aneuploidy and fragile sites) was studied in cells of the lymphocyte culture of ductal breast cancer patients (DBC). Was studied the correctional influence of separate and combinative action of peptide bioregulator (Ala-Glu-Asp-Gly) and heavy metal - nickel. It is shown that DBC patients are characterized by high level of genome instability, which is the result of the chromatin changing state. The used tests makes it possible to conclude that in the case of this form of cancer subordinates to specific epigenetic variation as a hetero- also euchromatic regions of genome...
January 2017: Georgian Medical News
https://www.readbyqxmd.com/read/28243898/identification-of-frequent-somatic-mutations-in-inflammatory-breast-cancer
#10
Naoko Matsuda, Bora Lim, Ying Wang, Savitri Krishnamurthy, Wendy Woodward, Ricardo H Alvarez, Anthony Lucci, Vicente Valero, James M Reuben, Funda Meric-Bernstam, Naoto T Ueno
PURPOSE: Inflammatory breast cancer is an aggressive form of breast cancer that shows distinct clinical features from non-inflammatory breast cancer. Genomic understanding of inflammatory breast cancer will shed light on biological targets for this disease. Our objective was to identify targeted hotspot mutations using multiplex genome sequencing in inflammatory breast cancer and compare the findings with those for patients with non-inflammatory breast cancer to further recognize novel targets...
February 27, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28243896/breast-cancer-specific-survival-in-patients-with-lymph-node-positive-hormone-receptor-positive-invasive-breast-cancer-and-oncotype-dx-recurrence-score-results-in-the-seer-database
#11
Megan C Roberts, Dave P Miller, Steven Shak, Valentina I Petkov
PURPOSE: The Oncotype DX(®) Breast Recurrence Score™ (RS) assay is validated to predict breast cancer (BC) recurrence and adjuvant chemotherapy benefit in select patients with lymph node-positive (LN+), hormone receptor-positive (HR+), HER2-negative BC. We assessed 5-year BC-specific survival (BCSS) in LN+ patients with RS results in SEER databases. METHODS: In this population-based study, BC cases in SEER registries (diagnosed 2004-2013) were linked to RS results from assays performed by Genomic Health (2004-2014)...
February 27, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28239551/genome-wide-chromatin-accessibility-dna-methylation-and-gene-expression-analysis-of-histone-deacetylase-inhibition-in-triple-negative-breast-cancer
#12
Matias A Bustos, Matthew P Salomon, Nellie Nelson, Sandy C Hsu, Maggie L DiNome, Dave S B Hoon, Diego M Marzese
Triple-negative breast cancer (TNBC), especially the subset with a basal phenotype, represents the most aggressive subtype of breast cancer. Unlike other solid tumors, TNBCs harbor a low number of driver mutations. Conversely, we and others have demonstrated a significant impact of epigenetic alterations, including DNA methylation and histone post-translational modifications, affecting TNBCs. Due to the promising results in pre-clinical studies, histone deacetylase inhibitors (HDACi) are currently being tested in several clinical trials for breast cancer and other solid tumors...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28235761/high-throughput-genomic-profiling-of-adult-solid-tumors-reveals-novel-insights-into-cancer-pathogenesis
#13
Ryan J Hartmaier, Lee Albacker, Juliann Chmielecki, Mark Bailey, Jie He, Michael E Goldberg, Shakti Ramkissoon, James Suh, Julia A Elvin, Samuel Chiacchia, Garrett M Frampton, Jeffrey S Ross, Vincent Miller, Philip J Stephens, Doron Lipson
Genomic profiling is widely predicted to become a standard of care in clinical oncology, but more effective data sharing to accelerate progress in precision medicine will be required. Here we describe cancer-associated genomic profiles from 18,004 unique adult cancers. The dataset was composed of 162 tumor subtypes including multiple rare and uncommon tumors. Comparison of alteration frequencies to The Cancer Genome Atlas (TCGA) identified some differences and suggested an enrichment of treatment-refractory samples in breast and lung cancer cohorts...
February 24, 2017: Cancer Research
https://www.readbyqxmd.com/read/28224383/oncologist-and-organizational-factors-associated-with-variation-in-breast-cancer-multigene-testing
#14
Tracy A Lieu, G Thomas Ray, Stephanie R Prausnitz, Laurel A Habel, Stacey Alexeeff, Yan Li, Scott D Ramsey, Charles E Phelps, Neetu Chawla, Suzanne C O'Neill, Jeanne S Mandelblatt
PURPOSE: Multigene testing for breast cancer recurrence risk became available in 2007, yet many eligible patients remain untested. This study evaluated variation in testing rates, and oncologist and organizational factors associated with variation, in a setting without financial influences on testing. METHODS: We conducted a retrospective cohort study using electronic data and oncologist surveys within Kaiser Permanente Northern California, a large integrated health care system...
February 21, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28224382/retrospective-review-of-genomic-testing-in-breast-cancer-does-it-improve-outcome
#15
Grady M Gastelum, Cyrus Iqbal, Susan G Hilsenbeck, Mothaffar F Rimawi, Polly Niravath
PURPOSE: Tumor genomic testing has become widely available in many clinical settings. However, we do not yet understand how to best harness the information yielded from this testing. We retrospectively investigated the clinical courses of 24 patients who underwent tumor genomic testing to determine whether targeted therapy is associated with improved progression free survival (PFS) compared to standard therapy. METHODS: The patient population comprised metastatic breast cancer patients who underwent tumor genomic testing (testing biopsy specimens of primary or metastatic lesions for 50 commonly mutated genes) at our institution between September 1, 2010 and June 1, 2015...
February 21, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28212807/prevalence-of-brca1-and-brca2-large-genomic-rearrangements-in-tunisian-high-risk-breast-ovarian-cancer-families-implications-for-genetic-testing
#16
Aouatef Riahi, Habiba Chabouni-Bouhamed, Maher Kharrat
Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28210550/evaluating-the-performance-of-national-comprehensive-cancer-network-nccn-breast-and-ovarian-genetic-familial-high-risk-assessment-referral-criteria-for-breast-cancer-women-in-an-asian-surgical-breast-clinic
#17
Geok-Hoon Lim, Eillen Borje, John C Allen
BACKGROUND: Globally, resources for genomic services vary. Current National Comprehensive Cancer Network (NCCN) breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation are useful, but lack specificity for reliably excluding patients with low a priori risk. This may result in patient overload in lesser-equipped genetics clinics. Since we use Manchester and the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk assessment models in our genetics clinic to determine whether genetic testing is warranted, we chose Manchester and BOADICEA as the reference standard to compare how the NCCN breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation performs against these two risk assessment models in referring breast cancer patients for genetic evaluation...
February 2017: Gland Surgery
https://www.readbyqxmd.com/read/28205193/new-therapeutic-strategies-for-triple-negative-breast-cancer
#18
REVIEW
Borbála Székely, Andrea L M Silber, Lajos Pusztai
Relatively few clinically important therapeutic advances have occurred in the treatment of triple-negative breast cancer (TNBC) since the introduction of taxanes as adjuvant therapy over 20 years ago. However, this is rapidly changing due to a variety of conceptually important clinical trials and emerging new options such as immune checkpoint inhibitors and antibody-drug conjugates. Evidence also increasingly supports that platinum drugs and inhibitors of poly (ADP-ribose) polymerase, or PARP, are particularly effective in the treatment of germline BRCA-mutant cancers, including TNBC...
February 15, 2017: Oncology (Williston Park, NY)
https://www.readbyqxmd.com/read/28205045/characteristics-of-brca1-2-mutations-carriers-including-large-genomic-rearrangements-in-high-risk-breast-cancer-patients
#19
Boyoung Park, Ji Yeon Sohn, Kyong-Ah Yoon, Keun Seok Lee, Eun Hae Cho, Myong Cheol Lim, Moon Jung Yang, Soo Jin Park, Moo Hyun Lee, See Youn Lee, Yoon Jung Chang, Dong Ock Lee, Sun-Young Kong, Eun Sook Lee
PURPOSE: We investigated the prevalence of BRCA1/2 small mutations and large genomic rearrangements in high risk breast cancer patients who attended a genetic counseling clinic. METHODS: In total 478 patients were assessed for BRCA1/2 mutations by direct sequencing, of whom, 306 were identified as non-carriers of BRCA1/2 mutation and assessed for large rearrangement mutations by multiplex ligation-dependent probe amplification. Family history and clinicopathological characteristics of patients were evaluated...
February 15, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28205043/a-polygenic-risk-score-for-breast-cancer-risk-in-a-taiwanese-population
#20
Yi-Chen Hsieh, Shih-Hsin Tu, Chien-Tien Su, Er-Chieh Cho, Chih-Hsiung Wu, Mao-Chih Hsieh, Shiyng-Yu Lin, Yun-Ru Liu, Chin-Sheng Hung, Hung-Yi Chiou
BACKGROUND: Multiple common variants identified by genome-wide association studies showed limited evidence of the risk of breast cancer in Taiwan. In this study, we analyzed the breast cancer risk in relation to 13 individual single-nucleotide polymorphisms (SNPs) identified by a GWAS in an Asian population. METHODS: In total, 446 breast cancer patients and 514 healthy controls were recruited for this case-control study. In addition, we developed a polygenic risk score (PRS) including those variants significantly associated with breast cancer risk, and also evaluated the contribution of PRS and clinical risk factors to breast cancer using receiver operating characteristic curve (AUC)...
February 15, 2017: Breast Cancer Research and Treatment
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