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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28537877/clinical-validation-of-genetic-variants-associated-with-in-vitro-chemotherapy-related-lymphoblastoid-cell-toxicity
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28515241/use-of-biomarkers-and-multigene-assays-in-breast-cancer
#4
Lee S Schwartzberg
All patients with early breast cancer should be classified by subgroup through testing estrogen receptor, progesterone receptor, and HER2 status, with or without Ki-67 proliferation percentage. Genomic expression profiling aids clinical decision-making in most patients, because most are estrogen receptor-positive. The commercially available classifiers are prognostic for distant recurrence in node-negative and also node-positive patients. Patients at genomically low risk have excellent 5-year outcomes with endocrine therapy alone...
May 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/28513873/myxoid-fibroadenomas-differ-from-conventional-fibroadenomas-a-hypothesis-generating-study
#5
John R Lozada, Kathleen A Burke, Aoife Maguire, Fresia Pareja, Raymond S Lim, Jisun Kim, Rodrigo Gularte-Merida, Melissa P Murray, Edi Brogi, Britta Weigelt, Jorge S Reis-Filho, Felipe C Geyer
AIMS: Breast myxoid fibroadenomas (MFAs) are characterized by a distinctive hypocellular myxoid stroma, and occur sporadically or in the context of Carney Complex, an inheritable condition caused by PRKAR1A inactivating germline mutations. Conventional fibroadenomas (FAs) are underpinned by recurrent MED12 mutations in the stromal components of the lesions. We sought to investigate the genomic landscape of MFAs and compare it to that of conventional FAs. METHODS AND RESULTS: Eleven MFAs from patients without clinical and/or genetic evidence of Carney Complex were retrieved...
May 17, 2017: Histopathology
https://www.readbyqxmd.com/read/28504904/application-of-panel-based-tests-for-inherited-risk-of-cancer
#6
Payal D Shah, Katherine L Nathanson
Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases...
May 15, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28503721/limited-influence-of-germline-genetic-variation-on-all-cause-mortality-in-women-with-early-onset-breast-cancer-evidence-from-gene-based-tests-single-marker-regression-and-whole-genome-prediction
#7
Molly Scannell Bryan, Maria Argos, Irene L Andrulis, John L Hopper, Jenny Chang-Claude, Kathleen Malone, Esther M John, Marilie D Gammon, Mary Daly, Mary Beth Terry, Saundra S Buys, Dezheng Huo, Olofunmilayo Olopade, Jeanine M Genkinger, Farzana Jasmine, Muhammad G Kibriya, Lin Chen, Habibul Ahsan
PURPOSE: Women diagnosed with breast cancer have heterogeneous survival outcomes that cannot be fully explained by known prognostic factors, and germline variation is a plausible but unconfirmed risk factor. METHODS: We used three approaches to test the hypothesis that germline variation drives some differences in survival: mortality loci identification, tumor aggressiveness loci identification, and whole-genome prediction. The 2954 study participants were women diagnosed with breast cancer before age 50, with a median follow-up of 15 years who were genotyped on an exome array...
May 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28502100/her2-fish-results-in-breast-cancers-with-increased-cen17-signals-using-alternative-chromosome-17-probes-reclassifying-cases-in-the-equivocal-category
#8
Maria-Anna Holzschuh, Zbigniew Czyz, Sven Hauke, Elisabeth Christine Inwald, Bernhard Polzer, Gero Brockhoff
AIMS: HER2 testing of invasive breast cancer by in-situ hybridisation guides therapy decisions. Probing HER2 and cen17 simultaneously is supposed to reveal both a potential HER2 gene amplification and polysomy 17. However, a considerable number of breast cancer patients with quasi polysomy 17 are considered "equivocal" which is diagnostically meaningless. Moreover, patients with equivocal / false polysomic tumours are prevented from a potentially beneficial anti-HER2 treatment. Here we evaluated the RAI1, D17S122, and TP53 hybridisation markers to reliably indicate true polysomy and to accurately reclassify equivocal samples as HER2-positive...
May 14, 2017: Histopathology
https://www.readbyqxmd.com/read/28500398/comparative-clinical-utility-of-tumor-genomic-testing-and-cell-free-dna-in-metastatic-breast-cancer
#9
Kara N Maxwell, Danielle Soucier-Ernst, Emin Tahirovic, Andrea B Troxel, Candace Clark, Michael Feldman, Christopher Colameco, Bijal Kakrecha, Melissa Langer, David Lieberman, Jennifer J D Morrissette, Matt R Paul, Tien-Chi Pan, Stephanie Yee, Natalie Shih, Erica Carpenter, Lewis A Chodosh, Angela DeMichele
PURPOSE: Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS: Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment...
May 12, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28487443/her2-reactivation-through-acquisition-of-the-her2-l755s-mutation-as-a-mechanism-of-acquired-resistance-to-her2-targeted-therapy-in-her2-breast-cancer
#10
Xiaowei Xu, Carmine De Angelis, Kathleen A Burke, Agostina Nardone, Huizhong Hu, Lanfang Qin, Jamunarani Veeraraghavan, Vidyalakshmi Sethunath, Laura M Heiser, Nicholas J Wang, Charlotte K Y Ng, Edward Chen, Alexander Renwick, Tao Wang, Sarmistha Nanda, Martin Shea, Tamika Mitchell, Mahitha Rajendran, Ian Waters, Daniel J Zabransky, Kenneth L Scott, Carolina Gutierrez, Chandandeep Nagi, Felipe C Geyer, Gary C Chamness, Ben Ho Park, Chad Shaw, Susan G Hilsenbeck, Mothaffar F Rimawi, Joe W Gray, Britta Weigelt, Jorge S Reis-Filho, C Kent Osborne, Rachel Schiff
Purpose: Resistance to anti-HER2 therapies in HER2+ breast cancer can occur through activation of alternative survival pathways or reactivation of the HER signaling network. Here we employed BT474 parental and treatment-resistant cell line models to investigate a mechanism by which HER2+ breast cancer can reactivate the HER network under potent HER2-targeted therapies. <p>Experimental Design: Resistant derivatives to lapatinib (L), trastuzumab (T), or the combination (LR/TR/LTR) were developed independently from two independent estrogen receptor ER+/HER2+ BT474 cell lines (AZ/ATCC)...
May 9, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28481952/identification-of-potential-new-treatment-response-markers-and-therapeutic-targets-using-a-gaussian-process-based-method-in-lapatinib-insensitive-breast-cancer-models
#11
Tapesh Santra, Sandra Roche, Neil Conlon, Norma O'Donovan, John Crown, Robert O'Connor, Walter Kolch
Molecularly targeted therapeutics hold promise of revolutionizing treatments of advanced malignancies. However, a large number of patients do not respond to these treatments. Here, we take a systems biology approach to understand the molecular mechanisms that prevent breast cancer (BC) cells from responding to lapatinib, a dual kinase inhibitor that targets human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR). To this end, we analysed temporal gene expression profiles of four BC cell lines, two of which respond and the remaining two do not respond to lapatinib...
2017: PloS One
https://www.readbyqxmd.com/read/28472036/accurate-detection-of-low-prevalence-akt1-e17k-mutation-in-tissue-or-plasma-from-advanced-cancer-patients
#12
Elza C de Bruin, Jessica L Whiteley, Claire Corcoran, Pauline M Kirk, Jayne C Fox, Javier Armisen, Justin P O Lindemann, Gaia Schiavon, Helen J Ambrose, Alexander Kohlmann
Personalized healthcare relies on accurate companion diagnostic assays that enable the most appropriate treatment decision for cancer patients. Extensive assay validation prior to use in a clinical setting is essential for providing a reliable test result. This poses a challenge for low prevalence mutations with limited availability of appropriate clinical samples harboring the mutation. To enable prospective screening for the low prevalence AKT1 E17K mutation, we have developed and validated a competitive allele-specific TaqMan® PCR (castPCR™) assay for mutation detection in formalin-fixed paraffin-embedded (FFPE) tumor tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28465148/competitive-pcr-high-resolution-melting-analysis-c-pcr-hrma-for-large-genomic-rearrangements-lgrs-detection-a-new-approach-to-assess-quantitative-status-of-brca1-gene-in-a-reference-laboratory
#13
Angelo Minucci, Elisa De Paolis, Paola Concolino, Maria De Bonis, Roberta Rizza, Giulia Canu, Giovanni Luca Scaglione, Flavio Mignone, Giovanni Scambia, Cecilia Zuppi, Ettore Capoluongo
AIM OF THE STUDY: Evaluation of copy number variation (CNV) in BRCA1/2 genes, due to large genomic rearrangements (LGRs), is a mandatory analysis in hereditary breast and ovarian cancers families, if no pathogenic variants are found by sequencing. LGRs cannot be detected by conventional methods and several alternative methods have been developed. Since these approaches are expensive and time consuming, identification of alternative screening methods for LGRs detection is needed in order to reduce and optimize the diagnostic procedure...
April 30, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28453507/genetic-cancer-risk-assessment-for-breast-cancer-in-latin-america
#14
Yanin Chavarri-Guerra, Kathleen Reilly Blazer, Jeffrey Nelson Weitzel
In Latin America, breast cancer is the most common malignancy in women, and limited available data suggest that up to 15% of all breast cancer cases in the region are hereditary. Genetic cancer risk assessment and counseling is a critical component of the appropriate clinical care of patients with hereditary breast cancer and their families. Unfortunately, genetic services are underdeveloped across Latin America, and access to genetic testing and counseling is very scarce in the region. Barriers contributing to the access to genetic care are high cost and lack of insurance coverage for genetic tests, insufficient oncogenetics training or expertise, nonexistence of genetic counseling as a clinical discipline, and lack of supportive healthcare policies...
March 2017: Revista de Investigación Clínica; Organo del Hospital de Enfermedades de la Nutrición
https://www.readbyqxmd.com/read/28446149/effect-of-genetic-variants-and-traits-related-to-glucose-metabolism-and-their-interaction-with-obesity-on-breast-and-colorectal-cancer-risk-among-postmenopausal-women
#15
Su Yon Jung, Eric M Sobel, Jeanette C Papp, Zuo-Feng Zhang
BACKGROUND: Impaired glucose metabolism-related genetic variants and traits likely interact with obesity and related lifestyle factors, influencing postmenopausal breast and colorectal cancer (CRC), but their interconnected pathways are not fully understood. By stratifying via obesity and lifestyles, we partitioned the total effect of glucose metabolism genetic variants on cancer risk into two putative mechanisms: 1) indirect (risk-associated glucose metabolism genetic variants mediated by glucose metabolism traits) and 2) direct (risk-associated glucose metabolism genetic variants through pathways other than glucose metabolism traits) effects...
April 26, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28440475/a-nine-mirna-signature-as-a-potential-diagnostic-marker-for-breast-carcinoma-an-integrated-study-of-1-110-cases
#16
Dan-Dan Xiong, Jun Lv, Kang-Lai Wei, Zhen-Bo Feng, Ji-Tian Chen, Ke-Cheng Liu, Gang Chen, Dian-Zhong Luo
Growing evidence indicates that microRNAs (miRNAs) play critical roles in the initiation and progression of breast carcinoma (BC) and are promising diagnostic biomarkers. In the present study, we aimed to identify a multi-marker miRNA pool with high diagnostic performance for BC. We collected miRNA expression profiles of BC samples and normal breast tissues from The Cancer Genome Atlas (TCGA) and screened differentially expressed miRNAs by conducting two‑sample t-tests and by calculating log2 fold-change (log2FC) ratios...
April 25, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28428927/limitations-of-personalized-medicine-and-gene-assays-for-breast-cancer
#17
David Tiberi, Laura Masucci, Daniel Shedid, Isabelle Roy, Toni Vu, Erica Patocskai, André Robidoux, Philip Wong
Adjuvant systemic treatments reduce the risk of breast cancer recurrence following the local treatment of primary stage I-III breast cancers. For patients with hormone-positive breast cancers receiving hormonal therapy, the risk of distant recurrence is under 20% and therefore, many patients may potentially be spared of chemotherapy. Consequently, several molecular signatures based on gene expression were developed to better determine which breast cancer patients would benefit from chemotherapy. We present the case of a 62-year-old woman diagnosed with an early stage hormone receptor-positive breast cancer that was treated with a partial mastectomy...
March 17, 2017: Curēus
https://www.readbyqxmd.com/read/28428277/immune-gene-expression-is-associated-with-genomic-aberrations-in-breast-cancer
#18
Anton Safonov, Tingting Jiang, Giampaolo Bianchini, Balázs Győrffy, Thomas Karn, Christos Hatzis, Lajos Pusztai
The presence of tumor-infiltrating lymphocytes (TIL) is a favorable prognostic factor in breast cancer, but what drives immune infiltration remains unknown. Here we examine if clonal heterogeneity, total mutation load, neoantigen load, copy number variations (CNV), gene- or pathway-level somatic mutations, or germline polymorphisms (SNP) are associated with immune metagene expression in breast cancer subtypes. Thirteen published immune metagenes correlated separately with genomic metrics in the 3 major breast cancer subtypes...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28423538/gene-regulatory-pattern-analysis-reveals-essential-role-of-core-transcriptional-factors-activation-in-triple-negative-breast-cancer
#19
Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo-Cheng Yuan, Chengchao Shou
BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype. Genome-scale molecular characteristics and regulatory mechanisms that distinguish TNBC from other subtypes remain incompletely characterized. RESULTS: By combining gene expression analysis and PANDA network, we defined three different TF regulatory patterns. A core TNBC-Specific TF Activation Driven Pattern (TNBCac) was specifically identified in TNBC by computational analysis...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422318/computational-analysis-of-breast-cancer-gwas-loci-identifies-the-putative-deleterious-effect-of-stxbp4-and-znf404-gene-variants
#20
Tariq Ahmad Masoodi, Babajan Banaganapalli, Venkatesh Vaidyanathan, Venkateswar R Talluri, Noor A Shaik
The genome-wide association studies (GWAS) have enabled us in identifying different breast cancer (BC) susceptibility loci. However, majority of these are non-coding variants with no annotated biological function. We investigated such 78 noncoding genome wide associated SNPs of BC and further expanded the list to 2,162 variants with strong linkage-disequilibrium (LD, r(2) ≥0.8). Using multiple publically available algorithms such as CADD, GWAVA, and FATHAMM, we classified all these variants into deleterious, damaging, or benign categories...
April 19, 2017: Journal of Cellular Biochemistry
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