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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/28934488/de-novo-pathway-based-biomarker-identification
#1
Nicolas Alcaraz, Markus List, Richa Batra, Fabio Vandin, Henrik J Ditzel, Jan Baumbach
Gene expression profiles have been extensively discussed as an aid to guide the therapy by predicting disease outcome for the patients suffering from complex diseases, such as cancer. However, prediction models built upon single-gene (SG) features show poor stability and performance on independent datasets. Attempts to mitigate these drawbacks have led to the development of network-based approaches that integrate pathway information to produce meta-gene (MG) features. Also, MG approaches have only dealt with the two-class problem of good versus poor outcome prediction...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28914717/the-relationship-between-mismatch-repair-deficiency-and-pd-l1-expression-in-breast-carcinoma
#2
Anne M Mills, Erik A Dill, Christopher A Moskaluk, Jaroslaw Dziegielewski, Tim N Bullock, Patrick M Dillon
Mismatch repair (MMR) deficiency in solid tumors has recently been linked to susceptibility to immunotherapies targeting the programmed cell death-1 (PD-1)/programmed cell death-1 ligand (PD-L1) axis. Loss of MMR proteins has been shown to correlate with tumoral PD-L1 expression in colorectal and endometrial carcinomas, but the association between expression of MMR proteins and PD-L1 has not previously been studied in breast carcinoma, where MMR deficiency is less common. We assessed the relationship between PD-L1 and MMR protein expression by immunohistochemistry in 245 primary and 40 metastatic breast carcinomas...
September 13, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28912897/genomic-analysis-of-tumor-microenvironment-immune-types-across-14-solid-cancer-types-immunotherapeutic-implications
#3
Yu-Pei Chen, Yu Zhang, Jia-Wei Lv, Ying-Qin Li, Ya-Qin Wang, Qing-Mei He, Xiao-Jing Yang, Ying Sun, Yan-Ping Mao, Jing-Ping Yun, Na Liu, Jun Ma
We performed a comprehensive immuno-genomic analysis of tumor microenvironment immune types (TMITs), which is classified into four groups based on PD-L1+CD8A or PD-L1+cytolytic activity (CYT) expression, across a broad spectrum of solid tumors in order to help identify patients who will benefit from anti- PD-1/PD-L1 therapy. The mRNA sequencing data from The Cancer Genome Atlas (TCGA) of 14 solid cancer types representing 6,685 tumor samples was analyzed. TMIT was classified only for those tumor types that both PD-L1 and CD8A/CYT could prefict mutation and/or neoantigen number...
2017: Theranostics
https://www.readbyqxmd.com/read/28905250/tumour-infiltrating-lymphocytes-tils-related-genomic-signature-predicts-chemotherapy-response-in-breast-cancer
#4
Mariko Kochi, Takayuki Iwamoto, Naoki Niikura, Giampaolo Bianchini, Shinobu Masuda, Taeko Mizoo, Tomohiro Nogami, Tadahiko Shien, Takayuki Motoki, Naruto Taira, Yutaka Tokuda, Hiroyoshi Doihara, Junji Matsuoka, Toshiyoshi Fujiwara
PURPOSE: The present study evaluated whether morphological-measured stromal and intra-tumour tumour-infiltrating lymphocytes (TILs) levels were associated with gene expression profiles, and whether TILs-associated genomic signature (GS) could be used to predict clinical outcomes and response to therapies in several breast cancer subtypes. METHODS: We retrospectively evaluated haematoxylin eosin (HE)-TILs levels and gene expression profiling data from 40 patients with primary breast cancer and extracted the 22 overexpressed genes in cases with high TILs scores as the TILs-GS...
September 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28904067/whole-genome-sequencing-reveals-breast-cancers-with-mismatch-repair-deficiency
#5
Helen Davies, Sandro Morganella, Colin A Purdie, Se Jin Jang, Elin Borgen, Hege Russnes, Dominik Glodzik, Xueqing Zou, Alain Viari, Andrea L Richardson, Anne-Lise Børresen-Dale, Alastair Thompson, Jorunn E Eyfjord, Gu Kong, Michael R Stratton, Serena Nik-Zainal
Mismatch repair (MMR)-deficient cancers have been discovered to be highly responsive to immune therapies such as PD-1 checkpoint blockade, making their definition in patients, where they may be relatively rare, paramount for treatment decisions. In this study, we utilized patterns of mutagenesis known as mutational signatures, which are imprints of the mutagenic processes associated with MMR deficiency, to identify MMR-deficient breast tumors from a whole-genome sequencing dataset comprising a cohort of 640 patients...
September 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28891071/genetic-variation-in-the-vitamin-d-related-pathway-and-breast-cancer-risk-in-women-of-african-ancestry-in-the-root-consortium
#6
Shengfeng Wang, Dezheng Huo, Sonia Kupfer, Dereck Alleyne, Temidayo O Ogundiran, Oladosu Ojengbede, Wei Zheng, Katherine L Nathanson, Barbara Nemesure, Stefan Ambs, Olufunmilayo I Olopade, Yonglan Zheng
The vitamin D related pathway has been evaluated in carcinogenesis but its genetic contribution remains poorly understood. We examined single-nucleotide polymorphisms (SNPs) in the vitamin D related pathway genes using data from a genome-wide association study (GWAS) of breast cancer in the African Diaspora that included 3,686 participants (1,657 cases). Pathway- and gene-level analyses were conducted using the adaptive rank truncated product test. Odds ratios (OR) and 95% confidence intervals (CI) were estimated at SNP-level...
September 10, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28873162/mutation-detection-in-patients-with-advanced-cancer-by-universal-sequencing-of-cancer-related-genes-in-tumor-and-normal-dna-vs-guideline-based-germline-testing
#7
Diana Mandelker, Liying Zhang, Yelena Kemel, Zsofia K Stadler, Vijai Joseph, Ahmet Zehir, Nisha Pradhan, Angela Arnold, Michael F Walsh, Yirong Li, Anoop R Balakrishnan, Aijazuddin Syed, Meera Prasad, Khedoudja Nafa, Maria I Carlo, Karen A Cadoo, Meg Sheehan, Megan H Fleischut, Erin Salo-Mullen, Magan Trottier, Steven M Lipkin, Anne Lincoln, Semanti Mukherjee, Vignesh Ravichandran, Roy Cambria, Jesse Galle, Wassim Abida, Marcia E Arcila, Ryma Benayed, Ronak Shah, Kenneth Yu, Dean F Bajorin, Jonathan A Coleman, Steven D Leach, Maeve A Lowery, Julio Garcia-Aguilar, Philip W Kantoff, Charles L Sawyers, Maura N Dickler, Leonard Saltz, Robert J Motzer, Eileen M O'Reilly, Howard I Scher, Jose Baselga, David S Klimstra, David B Solit, David M Hyman, Michael F Berger, Marc Ladanyi, Mark E Robson, Kenneth Offit
Importance: Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. Objective: To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. Design, Setting, and Participants: From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing...
September 5, 2017: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/28864454/genome-wide-testing-of-exonic-variants-and-breast-cancer-risk-in-the-california-teachers-study
#8
John Charles A Lacson, Huiyan Ma, Eunjung Lee, Susan L Neuhausen, Hoda Anton-Culver, Peggy Reynolds, David O Nelson, Argyrios Ziogas, David Van Den Berg, Dennis M Deapen, Leslie Bernstein, Fredrick R Schumacher
Background: Few studies have focused on the relationship of exonic variation with breast cancer and subtypes defined by tumor markers: estrogen receptor (ER), progesterone receptor (PR), and HER2.Methods: We genotyped 1,764 breast cancer patients and 1,400 controls from the California Teachers Study cohort using the Infinium HumanExome Beadchip. Individual variant and gene-based analyses were conducted for overall breast cancer and by individual tumor marker subtype.Results: No exonic variants or gene-based analyses were statistically significantly associated with breast cancer overall or by ER-, PR-, or HER2-defined subtype...
September 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28863725/clinical-practice-recommendations-based-on-an-updated-review-of-breast-cancer-risk-among-women-treated-for-childhood-cancer
#9
Yael E Derman
Breast cancer is the most common secondary malignancy among women treated for childhood cancer. This review highlights interacting etiologies contributing to development of secondary breast cancer to complement guidelines for surveillance and survivorship care and make recommendations for clinical practice. Treatment exposures determine Children's Oncology Group breast cancer surveillance guidelines; those treated with cumulative doses ≥20 Gy chest irradiation should undergo annual magnetic resonance imaging and mammography after age 25 years or 8 years after exposure, whichever comes last...
September 1, 2017: Journal of Pediatric Oncology Nursing: Official Journal of the Association of Pediatric Oncology Nurses
https://www.readbyqxmd.com/read/28863385/tumour-radiosensitivity-is-associated-with-immune-activation-in-solid-tumours
#10
Tobin Strom, Louis B Harrison, Anna R Giuliano, Michael J Schell, Steven A Eschrich, Anders Berglund, William Fulp, Ram Thapa, Domenico Coppola, Sungjune Kim, Jessica Frakes, John Foekens, James J Mulé, Javier F Torres-Roca
PURPOSE: Our goal was to determine whether tumour radiosensitivity is associated with activation of the immune system across all tumour types as measured by two gene expression signatures (GESs). METHODS: We identified 10,240 genomically profiled distinct solid primary tumours with gene expression analysis available from an institutional de-identified database. Two separate GESs were included in the analysis, the radiosensitivity index (RSI) GES (a 10-gene GES as a measure of radiosensitivity) and the 12-chemokine (12-CK) signature (a 12-gene GES as a measure of immune activation)...
August 29, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28858535/implementation-of-surgeon-initiated-gene-expression-profile-testing-onco-type-dx-among-patients-with-early-stage-breast-cancer-to-reduce-delays-in-chemotherapy-initiation
#11
Katya Losk, Rachel A Freedman, Nancy U Lin, Mehra Golshan, Stephen M Pochebit, Susan C Lester, Kelsey Natsuhara, Kristen Camuso, Tari R King, Craig A Bunnell
PURPOSE: Delays to adjuvant chemotherapy initiation in breast cancer may adversely affect clinical outcomes and patient satisfaction. We previously identified an association between genomic testing (Onco type DX) and delayed chemotherapy initiation. We sought to reduce the interval between surgery and adjuvant chemotherapy initiation by developing standardized criteria and workflows for Onco type DX testing. METHODS: Criteria for surgeon-initiated reflex Onco type DX testing, workflows for communication between surgeons and medical oncologists, and a streamlined process for receiving and processing Onco type DX requests in pathology were established by multidisciplinary consensus...
September 2017: Journal of Oncology Practice
https://www.readbyqxmd.com/read/28856074/utilizing-tumor-and-plasma-liquid-biopsy-in-treatment-decision-making-for-an-estrogen-receptor-positive-advanced-breast-cancer-patient
#12
Bing Xu, Amy Krie, Pradip De, Casey Williams, Rachel Elsey, Jessica Klein, Brian Leyland-Jones
Breast cancer affects 12% of females in the United States and is the leading cause of cancer death in the female population. Personalized therapy is being used in clinical practice to treat breast cancer based on tumor molecular profiling, which can be obtained from tissue biopsy or plasma liquid biopsy as circulating tumor deoxyribonucleic acid (ctDNA). The available ctDNA tests provide a non-invasive way to monitor the cancer genome in a real-time manner. In this case report, a 38-year-old female with recurrent estrogen receptor (ER) positive breast cancer is treated with letrozole, everolimus, and palbociclib...
June 29, 2017: Curēus
https://www.readbyqxmd.com/read/28855612/functional-proteomics-outlines-the-complexity-of-breast-cancer-molecular-subtypes
#13
Angelo Gámez-Pozo, Lucía Trilla-Fuertes, Julia Berges-Soria, Nathalie Selevsek, Rocío López-Vacas, Mariana Díaz-Almirón, Paolo Nanni, Jorge M Arevalillo, Hilario Navarro, Jonas Grossmann, Francisco Gayá Moreno, Rubén Gómez Rioja, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Paloma Main, Jaime Feliú, Purificación Martínez Del Prado, Pilar Zamora, Eva Ciruelos, Enrique Espinosa, Juan Ángel Fresno Vara
Breast cancer is a heterogeneous disease comprising a variety of entities with various genetic backgrounds. Estrogen receptor-positive, human epidermal growth factor receptor 2-negative tumors typically have a favorable outcome; however, some patients eventually relapse, which suggests some heterogeneity within this category. In the present study, we used proteomics and miRNA profiling techniques to characterize a set of 102 either estrogen receptor-positive (ER+)/progesterone receptor-positive (PR+) or triple-negative formalin-fixed, paraffin-embedded breast tumors...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851423/the-brca1ness-signature-is-associated-significantly-with-response-to-parp-inhibitor-treatment-versus-control-in-the-i-spy-2-randomized-neoadjuvant-setting
#14
Tesa M Severson, Denise M Wolf, Christina Yau, Justine Peeters, Diederik Wehkam, Philip C Schouten, Suet-Feung Chin, Ian J Majewski, Magali Michaut, Astrid Bosma, Bernard Pereira, Tycho Bismeijer, Lodewyk Wessels, Carlos Caldas, René Bernards, Iris M Simon, Annuska M Glas, Sabine Linn, Laura van 't Veer
BACKGROUND: Patients with BRCA1-like tumors correlate with improved response to DNA double-strand break-inducing therapy. A gene expression-based classifier was developed to distinguish between BRCA1-like and non-BRCA1-like tumors. We hypothesized that these tumors may also be more sensitive to PARP inhibitors than standard treatments. METHODS: A diagnostic gene expression signature (BRCA1ness) was developed using a centroid model with 128 triple-negative breast cancer samples from the EU FP7 RATHER project...
August 25, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28831439/clinical-overestimation-of-her2-positivity-in-early-estrogen-and-progesterone-receptor-positive-breast-cancer-and-the-value-of-molecular-subtyping-using-blueprint
#15
Ettienne J Myburgh, Lizanne Langenhoven, Kathleen A Grant, Lize van der Merwe, Maritha J Kotze
PURPOSE: Human epidermal growth factor receptor 2 (HER2) positivity is an important prognostic and predictive indicator in breast cancer. HER2 status is determined by immunohistochemistry and fluorescent in situ hybridization (FISH), which are potentially inaccurate techniques as a result of several technical factors, polysomy of chromosome 17, and amplification or overexpression of CEP17 (centromeric probe for chromosome 17) and/or HER2. In South Africa, HER2-positive tumors are excluded from a MammaPrint (MP; Agendia BV, Amsterdam, Netherlands) pretest algorithm...
August 2017: Journal of Global Oncology
https://www.readbyqxmd.com/read/28830573/assessment-of-the-prognostic-role-of-a-94-single-nucleotide-polymorphisms-risk-score-in-early-breast-cancer-in-the-signal-phare-prospective-cohort-no-correlation-with-clinico-pathological-characteristics-and-outcomes
#16
Elsa Curtit, Xavier Pivot, Julie Henriques, Sophie Paget-Bailly, 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, Pierre Kerbrat, Céline Faure-Mercier, Hélène Blanché, Mourad Sahbatou, Anne Boland, Delphine Bacq, Céline Besse, Gilles Thomas, Jean-François Deleuze, Iris Pauporté, Gilles Romieu, David G Cox
BACKGROUND: Genome-wide association studies (GWAS) have to date identified 94 genetic variants (single nucleotide polymorphisms (SNPs)) associated with risk of developing breast cancer. A score based on the combined effect of the 94 risk alleles can be calculated to measure the global risk of breast cancer. We aimed to test the hypothesis that the 94-SNP-based risk score is associated with clinico-pathological characteristics, breast cancer subtypes and outcomes in early breast cancer...
August 22, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28814081/monitoring-genetic-population-biomarkers-for-wastewater-based-epidemiology
#17
Zhugen Yang, Gaolian Xu, Julien Reboud, Barbara Kasprzyk-Hordern, Jonathan M Cooper
We report a rapid "sample-to-answer" platform that can be used for the quantitative monitoring of genetic biomarkers within communities through the analysis of wastewater. The assay is based on the loop-mediated isothermal amplification (LAMP) of nucleic acid biomarkers 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...
August 29, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28811643/overexpressed-somatic-alleles-are-enriched-in-functional-elements-in-breast-cancer
#18
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
#19
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
#20
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
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