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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28724549/identification-of-new-tumor-suppressor-genes-in-triple-negative-breast-cancer
#1
Roberto Rangel, Liliana Guzman-Rojas, Takahiro Kodama, Michiko Kodama, Justin Y Newberg, Neal G Copeland, Nancy A Jenkins
Although genomic sequencing has provided a better understating of the genetic landmarks in triple-negative breast cancer (TNBC), functional validation of candidate cancer genes (CCG) remains unsolved. In this study, we used a transposon mutagenesis strategy based on a two-step Sleeping Beauty (SB) forward genetic screen to identify and validate new tumor suppressors (TS) in this disease. We generated 120 siRNAs targeting 40 SB-identified candidate breast cancer TS genes and used them to downregulate expression of these genes in four human TNBC cell lines...
July 19, 2017: Cancer Research
https://www.readbyqxmd.com/read/28717669/pitfalls-in-genetic-testing-a-case-of-a-snp-in-primer-annealing-region-leading-to-allele-dropout-in-brca1
#2
Felipe Carneiro Silva, Giovana Tardin Torrezan, Rafael Canfield Brianese, Raquel Stabellini, Dirce Maria Carraro
BACKGROUND: Hereditary breast and ovarian cancer is characterized by mutations in BRCA1 or BRCA2 genes and PCR-based screening techniques, such as capillary sequencing and next-generation sequencing (NGS), are considered gold standard methods for detection of pathogenic mutations in these genes. Single-nucleotide polymorphisms (SNPs) constitute a vast source of variation in the human genome and represent a risk for misdiagnosis in genetic testing, since the presence of a SNP in primer-annealing sites may cause false negative results due to allele dropout...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717660/a-novel-molecular-diagnostics-platform-for-somatic-and-germline-precision-oncology
#3
Rubén Cabanillas, Marta Diñeiro, David Castillo, Patricia C Pruneda, Cristina Penas, Guadalupe A Cifuentes, Álvaro de Vicente, Noelia S Durán, Rebeca Álvarez, Gonzalo R Ordóñez, Juan Cadiñanos
BACKGROUND: Next-generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28710396/the-cinsarc-signature-as-a-prognostic-marker-for-clinical-outcome-in-multiple-neoplasms
#4
Tom Lesluyes, Lucile Delespaul, Jean-Michel Coindre, Frédéric Chibon
We previously reported the CINSARC signature as a prognostic marker for metastatic events in soft tissue sarcomas, breast carcinomas and lymphomas through genomic instability, acting as a major factor for tumor aggressiveness. In this study, we used a published resource to investigate CINSARC enrichment in poor outcome-associated genes at pan-cancer level and in 39 cancer types. CINSARC outperformed more than 15,000 defined signatures (including cancer-related), being enriched in top-ranked poor outcome-associated genes of 21 cancer types, widest coverage reached among all tested signatures...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28699911/a-six-long-non-coding-rnas-signature-as-a-potential-prognostic-marker-for-survival-prediction-of-er-positive-breast-cancer-patients
#5
Lei Zhong, Ge Lou, Xinglu Zhou, Youyou Qin, Lin Liu, Wenqian Jiang
Dysregulated expression of lncRNAs has been observed in various human complex diseases (including cancers) by recent transcriptional profiling studies, highlighting potentials of lncRNAs as biomarkers for cancer diagnosis and prognosis. Despite some efforts have been made to search for novel lncRNA signature in breast cancer, the prognostic value of lncRNAs for ER-positive breast cancer patients still needs to be systematically investigated. In this study, we analyzed lncRNA expression profiles in a large of more than 600 breast cancer patients with ER-positive status from The Cancer Genome Atlas (TCGA) and identified six lncRNAs that are significantly associated with survival...
July 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28693600/normal-breast-tissue-dna-methylation-differences-at-regulatory-elements-are-associated-with-the-cancer-risk-factor-age
#6
Kevin C Johnson, E Andres Houseman, Jessica E King, Brock C Christensen
BACKGROUND: The underlying biological mechanisms through which epidemiologically defined breast cancer risk factors contribute to disease risk remain poorly understood. Identification of the molecular changes associated with cancer risk factors in normal tissues may aid in determining the earliest events of carcinogenesis and informing cancer prevention strategies. METHODS: Here we investigated the impact cancer risk factors have on the normal breast epigenome by analyzing DNA methylation genome-wide (Infinium 450 K array) in cancer-free women from the Susan G...
July 10, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28680148/prevalence-and-penetrance-of-brca1-and-brca2-germline-mutations-in-colombian-breast-cancer-patients
#7
D Torres, J Lorenzo Bermejo, M U Rashid, I Briceño, F Gil, A Beltran, V Ariza, U Hamann
Pathogenic BRCA1/2 germline mutations confer high risks of breast and ovarian cancer to women of European ancestry. Characterization of BRCA1/2 mutations in other ethnic groups is also medically important. We comprehensively screened 68 Colombian breast/ovarian cancer families for small-range mutations, 221 families for large-genomic rearrangements, and 1,022 unselected breast cancer cases for Colombian founder mutations in BRCA1/2. The risk of cancer among relatives of mutation carriers and the mutation penetrance were estimated by survival analysis...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28671019/identification-and-prognostic-value-of-anterior-gradient-protein-2-expression-in-breast-cancer-based-on-tissue-microarray
#8
Jilong Guo, Guohua Gong, Bin Zhang
Breast cancer has attracted substantial attention as one of the major cancers causing death in women. It is crucial to find potential biomarkers of prognostic value in breast cancer. In this study, the expression pattern of anterior gradient protein 2 in breast cancer was identified based on the main molecular subgroups. Through analysis of 69 samples from the Gene Expression Omnibus database, we found that anterior gradient protein 2 expression was significantly higher in non-triple-negative breast cancer tissues compared with normal tissues and triple-negative breast cancer tissues (p < 0...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28664507/reducing-chemotherapy-use-in-clinically-high-risk-genomically-low-risk-pn0-and-pn1-early-breast-cancer-patients-five-year-data-from-the-prospective-randomised-phase-3-west-german-study-group-wsg-planb-trial
#9
Ulrike Nitz, Oleg Gluz, Matthias Christgen, Ronald E Kates, Michael Clemens, Wolfram Malter, Benno Nuding, Bahriye Aktas, Sherko Kuemmel, Toralf Reimer, Andrea Stefek, Fatemeh Lorenz-Salehi, Petra Krabisch, Marianne Just, Doris Augustin, Cornelia Liedtke, Calvin Chao, Steven Shak, Rachel Wuerstlein, Hans H Kreipe, Nadia Harbeck
BACKGROUND: The prospective phase 3 PlanB trial used the Oncotype DX(®) Recurrence Score(®) (RS) to define a genomically low-risk subset of clinically high-risk pN0-1 early breast cancer (EBC) patients for treatment with adjuvant endocrine therapy (ET) alone. Here, we report five-year data evaluating the prognostic value of RS, Ki-67, and other traditional clinicopathological parameters. METHODS: A central tumour bank was prospectively established within PlanB...
June 29, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28656489/detection-of-brca1-gross-rearrangements-by-droplet-digital-pcr
#10
Elena V Preobrazhenskaya, Ilya V Bizin, Ekatherina Sh Kuligina, Alla Yu Shleykina, Evgeny N Suspitsin, Olga A Zaytseva, Elena I Anisimova, Sergey A Laptiev, Tatiana V Gorodnova, Alexey M Belyaev, Evgeny N Imyanitov, Anna P Sokolenko
PURPOSE: Large genomic rearrangements (LGRs) constitute a significant share of pathogenic BRCA1 mutations. Multiplex ligation-dependent probe amplification (MLPA) is a leading method for LGR detection; however, it is entirely based on the use of commercial kits, includes relatively time-consuming hybridization step, and is not convenient for large-scale screening of recurrent LGRs. MATERIALS AND METHODS: We developed and validated the droplet digital PCR (ddPCR) assay, which covers the entire coding region of BRCA1 gene and is capable to precisely quantitate the copy number for each exon...
June 27, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28653249/erratum-to-comparative-clinical-utility-of-tumor-genomic-testing-and-cell-free-dna-in-metastatic-breast-cancer
#11
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
No abstract text is available yet for this article.
June 26, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28651004/a-human-endogenous-retrovirus-derived-gene-that-can-contribute-to-oncogenesis-by-activating-the-erk-pathway-and-inducing-migration-and-invasion
#12
Cécile Lemaître, Jhen Tsang, Caroline Bireau, Thierry Heidmann, Marie Dewannieux
Endogenous retroviruses are cellular genes of retroviral origin captured by their host during the course of evolution and represent around 8% of the human genome. Although most are defective and transcriptionally silenced, some are still able to generate retroviral-like particles and proteins. Among these, the HERV-K(HML2) family is remarkable since its members have amplified relatively recently and many of them still have full length coding genes. Furthermore, they are induced in cancers, especially in melanoma, breast cancer and germ cell tumours, where viral particles, as well as the envelope protein (Env), can be detected...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28649657/dual-pi3k-and-wnt-pathway-inhibition-is-a-synergistic-combination-against-triple-negative-breast-cancer
#13
Jeffrey P Solzak, Rutuja V Atale, Bradley A Hancock, Anthony L Sinn, Karen E Pollok, David R Jones, Milan Radovich
Triple negative breast cancer accounts for 15-20% of all breast cancer cases, but despite its lower incidence, contributes to a disproportionately higher rate of mortality. As there are currently no Food and Drug Administration-approved targeted agents for triple negative breast cancer, we embarked on a genomic-guided effort to identify novel targeted modalities. Analyses by our group and The Cancer Genome Atlas have identified activation of the PI3K-pathway in the majority of triple negative breast cancers...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649644/constitutional-variants-are-not-associated-with-her2-positive-breast-cancer-results-from-the-signal-phare-clinical-cohort
#14
Xavier Pivot, Gilles Romieu, Pierre Fumoleau, Maria Rios, Hervé Bonnefoi, Thomas Bachelot, Patrick Soulié, Christelle Jouannaud, Hugues Bourgeois, Thierry Petit, Isabelle Tennevet, David Assouline, Marie-Christine Mathieu, Jean-Philippe Jacquin, Sandrine Lavau-Denes, Ariane Darut-Jouve, Jean-Marc Ferrero, Carole Tarpin, Christelle Lévy, Valérie Delecroix, Véronique Trillet-Lenoir, Oana Cojocarasu, Jérôme Meunier, Jean-Yves Pierga, Cécile Agostini, Pierre Kerbrat, Céline Faure-Mercier, Hélène Blanché, Mourad Sahbatou, Anne Boland, Delphine Bacq, Céline Besse, Fabien Calvo, Alexia Renaud, Jean-François Deleuze, Iris Pauporté, Gilles Thomas, David G Cox
Human epidermal growth factor receptor 2-positive breast cancer is a subtype of interest regarding its outcome and the impressive impact of human epidermal growth factor receptor 2 targeted therapy. Constitutional variants may be involved in the aetiology of human epidermal growth factor receptor 2-positive breast cancer, and we propose a case-case study to test the hypothesis that single nucleotide polymorphisms may be associated with human epidermal growth factor receptor 2 status. A Genome-Wide Association Study was used in a cohort of 9836 patients from the SIGNAL/PHARE study (NCT00381901-RECF1098)...
2017: NPJ Breast Cancer
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
#15
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
#16
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
#17
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...
August 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
#18
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
#19
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
#20
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
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