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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28814081/monitoring-genetic-population-biomarkers-with-wastewater-based-epidemiology
#1
Zhugen Yang, Gaolian Xu, Julien Reboud, Barbara Kasprzyk-Hordern, Jonathan Mark Cooper
We report a rapid "sample-to-answer" platform for the quantitative monitoring of genetic biomarkers within communities by analysis of wastewater. The assay is based on the loop-mediated isothermal amplification (LAMP) and shows for the first time the ability to rapidly quantify human-specific mitochondrial DNA (mtDNA) from raw untreated wastewater samples. mtDNA provides a model population biomarker associated with carcinogenesis including breast, renal and gastric cancers. We integrated a filter to remove solid impurities and perform DNA extraction and enrichment in a low cost lateral flow-based test...
August 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28811643/overexpressed-somatic-alleles-are-enriched-in-functional-elements-in-breast-cancer
#2
Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, Anelia Horvath
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28802053/gene-panel-testing-of-breast-and-ovarian-cancer-patients-identifies-a-recurrent-rad51c-duplication
#3
Liisa M Pelttari, Hermela Shimelis, Heidi Toiminen, Anders Kvist, Therese Törngren, Åke Borg, Carl Blomqvist, Ralf Bützow, Fergus Couch, Kristiina Aittomäki, Heli Nevanlinna
Gene-panel sequencing allows comprehensive analysis of multiple genes simultaneously and is now routinely used in clinical mutation testing of high-risk breast and ovarian cancer patients. However, only BRCA1 and BRCA2 are often analyzed also for large genomic changes. Here, we have analyzed 10 clinically relevant susceptibility genes in 95 breast or ovarian cancer patients with gene-panel sequencing including also CNV analysis for genomic changes. We identified 12 different pathogenic BRCA1, BRCA2, TP53, PTEN, CHEK2, or RAD51C mutations in 18/95 patients (19%)...
August 12, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28765858/history-development-and-future-of-cancer-screening-in-australia
#4
Ian N Olver, David Roder
INTRODUCTION: The aim of screening an asymptomatic population for cancer is to achieve better health outcomes, particularly a population survival benefit. Australia has three population screening programs: the National Cervical Screening Program (NCSP), BreastScreen Australia and the National Bowel Cancer Screening Program (NBCSP). METHODS: We reviewed the history and development of the three programs. NCSP: Women have a Pap smear every 2 years from age 18-20, or 2 years after first becoming sexually active, until age 69...
July 26, 2017: Public Health Research & Practice
https://www.readbyqxmd.com/read/28752189/impact-of-tissue-based-genomic-profiling-on-clinical-decision-making-in-the-management-of-patients-with-metastatic-breast-cancer-at-academic-centers
#5
Cesar A Santa-Maria, Megan Kruse, Paola Raska, Mia Weiss, April Swoboda, Martin B Mutonga, Jame Abraham, Sarika Jain, Rita Nanda, Alberto J Montero
BACKGROUND: Genomic profiling can identify targetable mutations; however, the impact of tissue-based genomic profiling on clinical decision making for patients with metastatic breast cancer has not been well characterized. METHODS: Patients with stage IV breast cancer who had undergone genomic profiling between 7/2013 and 3/2015 were identified at three academic cancer centers. Genomic analysis was determined to have impacted clinical decision if (A) a patient was enrolled onto a genotype-matched clinical trial or (B) prescribed off-label an FDA-approved therapy targeting an identified mutation...
July 27, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28750640/impact-of-somatic-pi3k-pathway-and-erbb-family-mutations-on-pathological-complete-response-pcr-in-her2-positive-breast-cancer-patients-who-received-neoadjuvant-her2-targeted-therapies
#6
Sinead Toomey, Alexander J Eustace, Joanna Fay, Katherine M Sheehan, Aoife Carr, Malgorzata Milewska, Stephen F Madden, Ausra Teiserskiene, Elaine W Kay, Norma O'Donovan, William Gallagher, Liam Grogan, Oscar Breathnach, Janice Walshe, Catherine Kelly, Brian Moulton, M John Kennedy, Guiseppe Gullo, Arnold D Hill, Colm Power, Deirdre Duke, Niamh Hambly, John Crown, Bryan T Hennessy
BACKGROUND: The Cancer Genome Atlas analysis revealed that somatic EGFR, receptor tyrosine-protein kinase erbB-2 (ERBB2), Erb-B2 receptor tyrosine kinase 3 (ERBB3) and Erb-B2 receptor tyrosine kinase 4 (ERBB4) gene mutations (ERBB family mutations) occur alone or co-occur with somatic mutations in the gene encoding the phosphatidylinositol 3-kinase (PI3K) catalytic subunit (PIK3CA) in 19% of human epidermal growth factor receptor 2 (HER2)-positive breast cancers. Because ERBB family mutations can activate the PI3K/AKT pathway and likely have similar canonical signalling effects to PI3K pathway mutations, we investigated their combined impact on response to neoadjuvant HER2-targeted therapies...
July 27, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28743680/internet-based-assessment-of-oncology-health-care-professional-learning-style-and-optimization-of-materials-for-web-based-learning-controlled-trial-with-concealed-allocation
#7
Christine M Micheel, Ingrid A Anderson, Patricia Lee, Sheau-Chiann Chen, Katy Justiss, Nunzia B Giuse, Fei Ye, Sheila V Kusnoor, Mia A Levy
BACKGROUND: Precision medicine has resulted in increasing complexity in the treatment of cancer. Web-based educational materials can help address the needs of oncology health care professionals seeking to understand up-to-date treatment strategies. OBJECTIVE: This study aimed to assess learning styles of oncology health care professionals and to determine whether learning style-tailored educational materials lead to enhanced learning. METHODS: In all, 21,465 oncology health care professionals were invited by email to participate in the fully automated, parallel group study...
July 25, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28736464/the-generalized-higher-criticism-for-testing-snp-set-effects-in-genetic-association-studies
#8
Ian Barnett, Rajarshi Mukherjee, Xihong Lin
It is of substantial interest to study the effects of genes, genetic pathways, and networks on the risk of complex diseases. These genetic constructs each contain multiple SNPs, which are often correlated and function jointly, and might be large in number. However, only a sparse subset of SNPs in a genetic construct is generally associated with the disease of interest. In this article, we propose the generalized higher criticism (GHC) to test for the association between an SNP set and a disease outcome. The higher criticism is a test traditionally used in high-dimensional signal detection settings when marginal test statistics are independent and the number of parameters is very large...
2017: Journal of the American Statistical Association
https://www.readbyqxmd.com/read/28734953/estimating-relative-mitochondrial-dna-copy-number-using-high-throughput-sequencing-data
#9
Pan Zhang, Brian D Lehmann, David C Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo
We hypothesize that the relative mitochondria copy number (MTCN) can be estimated by comparing the abundance of mitochondrial DNA to nuclear DNA reads using high throughput sequencing data. To test this hypothesis, we examined relative MTCN across 13 breast cancer cell lines using the RT-PCR based NovaQUANT Human Mitochondrial to Nuclear DNA Ratio Kit as the gold standard. Six distinct computational approaches were used to estimate the relative MTCN in order to compare to the RT-PCR measurements. The results demonstrate that relative MTCN correlates well with the RT-PCR measurements using exome sequencing data, but not RNA-seq data...
July 19, 2017: Genomics
https://www.readbyqxmd.com/read/28730229/molecular-analysis-of-brca1-and-brca2-genes-by-next-generation-sequencing-and-ultrastructural-aspects-of-breast-tumor-tissue
#10
Corina Elena Mihalcea, Ana Maria Moroşanu, Daniela Murăraşu, Liliana Puiu, Sabin Aurel Cinca, Silviu Cristian Voinea, Nicolae Mirancea
In this paper, we focus our interest on the dynamics alterations of the tumor-stroma interface at the ultrastructural level and to detect BRCA1 and BRCA2 mutations using next generation sequencing (NGS) of breast tumor tissue. Electron microscopic investigation revealed some peculiar infrastructural alterations of the tumor cells per se as well as of the tumor-stroma interface: invadopodia, shedding microvesicles, altered morphology and reduced number of telocytes, different abnormalities of the microvasculature...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28724549/identification-of-new-tumor-suppressor-genes-in-triple-negative-breast-cancer
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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/28669927/evaluation-of-genetic-variants-in-autophagy-pathway-genes-as-prognostic-biomarkers-for-breast-cancer
#19
Jing Zhou, Dong Hang, Yue Jiang, Jiaping Chen, Jing Han, Wen Zhou, Guangfu Jin, Hongxia Ma, Juncheng Dai
Autophagy-related genes (ATGs) play a critical role in the development of various diseases including cancer. However, the role of ATGs in breast cancer survival remains unclear. This study aims to investigate whether genetic variants in core ATGs are correlated with the prognosis of breast cancer. A total of 14 potentially functional variants in core ATGs were genotyped in 790 breast cancer patients. The association of each variant with breast cancer-specific survival was evaluated by log-rank test and Cox regression model...
June 29, 2017: Gene
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
#20
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
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