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Breast cancer genomic testing

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https://www.readbyqxmd.com/read/29145865/the-endonuclease-eepd1-mediates-synthetic-lethality-in-rad52-depleted-brca1-mutant-breast-cancer-cells
#1
Robert Hromas, Hyun-Suk Kim, Gurjit Sidhu, Elizabeth Williamson, Aruna Jaiswal, Taylor A Totterdale, Jocelyn Nole, Suk-Hee Lee, Jac A Nickoloff, Kimi Y Kong
BACKGROUND: Proper repair and restart of stressed replication forks requires intact homologous recombination (HR). HR at stressed replication forks can be initiated by the 5' endonuclease EEPD1, which cleaves the stalled replication fork. Inherited or acquired defects in HR, such as mutations in breast cancer susceptibility protein-1 (BRCA1) or BRCA2, predispose to cancer, including breast and ovarian cancers. In order for these HR-deficient tumor cells to proliferate, they become addicted to a bypass replication fork repair pathway mediated by radiation repair protein 52 (RAD52)...
November 16, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29128582/budget-impact-analysis-of-gene-expression-tests-to-aid-therapy-decisions-for-breast-cancer-patients-in-germany
#2
M P Lux, N Nabieva, T Hildebrandt, H Rebscher, S Kümmel, J-U Blohmer, M G Schrauder
OBJECTIVES: Many women with early-stage, hormone receptor-positive breast cancer may not benefit from adjuvant chemotherapy. Gene expression tests can reduce chemotherapy over- and undertreatment by providing prognostic information on the likelihood of recurrence and, with Oncotype DX, predictive information on chemotherapy benefit. These tests are currently not reimbursed by German healthcare payers. An analysis was conducted to evaluate the budget impact of gene expression tests in Germany...
November 9, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/29109393/scalable-whole-exome-sequencing-of-cell-free-dna-reveals-high-concordance-with-metastatic-tumors
#3
Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah C Reed, Denisse Rotem, Justin Rhoades, Denis Loginov, Dimitri Livitz, Daniel Rosebrock, Ignaty Leshchiner, Jaegil Kim, Chip Stewart, Mara Rosenberg, Joshua M Francis, Cheng-Zhong Zhang, Ofir Cohen, Coyin Oh, Huiming Ding, Paz Polak, Max Lloyd, Sairah Mahmud, Karla Helvie, Margaret S Merrill, Rebecca A Santiago, Edward P O'Connor, Seong H Jeong, Rachel Leeson, Rachel M Barry, Joseph F Kramkowski, Zhenwei Zhang, Laura Polacek, Jens G Lohr, Molly Schleicher, Emily Lipscomb, Andrea Saltzman, Nelly M Oliver, Lori Marini, Adrienne G Waks, Lauren C Harshman, Sara M Tolaney, Eliezer M Van Allen, Eric P Winer, Nancy U Lin, Mari Nakabayashi, Mary-Ellen Taplin, Cory M Johannessen, Levi A Garraway, Todd R Golub, Jesse S Boehm, Nikhil Wagle, Gad Getz, J Christopher Love, Matthew Meyerson
Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29100455/clinical-validation-of-genetic-variants-associated-with-in-vitro-chemotherapy-related-lymphoblastoid-cell-toxicity
#4
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...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29100405/gene-network-inherent-in-genomic-big-data-improves-the-accuracy-of-prognostic-prediction-for-cancer-patients
#5
Yun Hak Kim, Dae Cheon Jeong, Kyoungjune Pak, Tae Sik Goh, Chi-Seung Lee, Myoung-Eun Han, Ji-Young Kim, Liu Liangwen, Chi Dae Kim, Jeon Yeob Jang, Wonjae Cha, Sae-Ock Oh
Accurate prediction of prognosis is critical for therapeutic decisions regarding cancer patients. Many previously developed prognostic scoring systems have limitations in reflecting recent progress in the field of cancer biology such as microarray, next-generation sequencing, and signaling pathways. To develop a new prognostic scoring system for cancer patients, we used mRNA expression and clinical data in various independent breast cancer cohorts (n=1214) from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and Gene Expression Omnibus (GEO)...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29100044/a-plea-for-appraisal-and-appreciation-of-immunohistochemistry-in-the-assessment-of-prognostic-and-predictive-markers-in-invasive-breast-cancer
#6
Mieke Van Bockstal, Giuseppe Floris, Christine Galant, Kathleen Lambein, Louis Libbrecht
This viewpoint is a personal reflection on the values and merits of immunohistochemistry in current breast cancer diagnosis. Immunohistochemistry is a validated mainstay in molecular subtyping of invasive breast cancer. Immunohistochemical assessment of hormone receptor status and HER2 expression is used to determine the clinico-pathological surrogate of breast cancer intrinsic subtypes, which guide neoadjuvant and adjuvant therapy. The advent of genomic prognostic signatures and qualitative mRNA-based assays makes some clinicians and researchers wonder whether immunohistochemistry should be abandoned...
October 31, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/29095543/background-current-role-and-potential-applications-of-radiogenomics
#7
Katja Pinker, Fuki Shitano, Evis Sala, Richard K Do, Robert J Young, Andreas G Wibmer, Hedvig Hricak, Elizabeth J Sutton, Elizabeth A Morris
With the genomic revolution in the early 1990s, medical research has been driven to study the basis of human disease on a genomic level and to devise precise cancer therapies tailored to the specific genetic makeup of a tumor. To match novel therapeutic concepts conceived in the era of precision medicine, diagnostic tests must be equally sufficient, multilayered, and complex to identify the relevant genetic alterations that render cancers susceptible to treatment. With significant advances in training and medical imaging techniques, image analysis and the development of high-throughput methods to extract and correlate multiple imaging parameters with genomic data, a new direction in medical research has emerged...
November 2, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29093017/a-population-of-heterogeneous-breast-cancer-patient-derived-xenografts-demonstrate-broad-activity-of-parp-inhibitor-in-brca1-2-wild-type-tumors
#8
Kurt W Evans, Erkan Yuca, Argun Akcakanat, Stephen M Scott, Natalia Paez Arango, Xiaofeng Zheng, Ken Chen, Coya Tapia, Emily Tarco, Agda K Eterovic, Dalliah M Black, Jennifer K Litton, Timothy A Yap, Debu Tripathy, Gordon B Mills, Funda Meric-Bernstam
Background: Breast cancer patients who do not respond to neoadjuvant therapy have a poor prognosis. There is a pressing need for novel targets and models for preclinical testing. Here we report characterization of breast cancer patient-derived xenografts (PDX) largely generated from residual tumors following neoadjuvant chemotherapy.Experimental Design: PDXs were derived from surgical samples of primary or locally recurrent tumors. Normal and tumor DNA sequencing, RNASeq, and reverse phase protein arrays (RPPA) were performed...
November 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29089811/clinical-utility-of-multigene-profiling-assays-in-early-stage-breast-cancer
#9
M C Chang, L H Souter, S Kamel-Reid, M Rutherford, P Bedard, M Trudeau, J Hart, A Eisen
BACKGROUND: This clinical practice guideline was developed to determine the level of evidence supporting the clinical utility of commercially available multigene profiling assays and to provide guidance about whether certain breast cancer patient populations in Ontario would benefit from alternative tests in addition to Oncotype dx (Genomic Health, Redwood City, CA, U.S.A.). METHODS: A systematic electronic Ovid search of the medline and embase databases sought out systematic reviews and primary literature...
October 2017: Current Oncology
https://www.readbyqxmd.com/read/29080873/-a-bioinformatic-pipeline-for-ngs-data-analysis-and-mutation-calling-in-human-solid-tumors
#10
K Yu Tsukanov, A Yu Krasnenko, D A Plakhina, D O Korostin, A V Churov, O S Druzhilovskaya, D V Rebrikov, V V Ilinsky
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29076877/the-role-of-molecular-testing-in-the-differential-diagnosis-of-salivary-gland-carcinomas
#11
Alena Skálová, Göran Stenman, Roderick H W Simpson, Henrik Hellquist, David Slouka, Tomas Svoboda, Justin A Bishop, Jennifer L Hunt, Ken-Ichi Nibu, Alessandra Rinaldo, Vincent Vander Poorten, Kenneth O Devaney, Petr Steiner, Alfio Ferlito
Salivary gland neoplasms are a morphologically heterogenous group of lesions that are often diagnostically challenging. In recent years, considerable progress in salivary gland taxonomy has been reached by the discovery of tumor type-specific fusion oncogenes generated by chromosome translocations. This review describes the clinicopathologic features of a selected group of salivary gland carcinomas with a focus on their distinctive genomic characteristics. Mammary analog secretory carcinoma is a recently described entity characterized by a t(12;15)(p13;q25) translocation resulting in an ETV6-NTRK3 fusion...
October 26, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29072371/her2-exon-27-mutations-predict-worse-survival-of-breast-cancer-patients-especially-in-her2-negative-patients
#12
Pilei Si, Tao Chen, Bin Fang, Jiabing Yao, Gaoxiu Liu, Haijun Chen, Baoping Zhai, Wentao Li
The aims of this study were to assess the prognostic value of the HER2 exon 27 mutations in breast cancer patients. Genomic DNA was isolated from peripheral blood leukocytes, and then HER2 exon 27 mutations were detected by direct sequencing. Survival curves were estimated by Kaplan-Meier curves and the differences between the curves were compared by log-rank tests. A total cohort of 892 female patients with operable primary breast cancer was included in this study. The median follow-up was 47 months. Of these 892 patients, 3...
October 26, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/29066719/gene-isoforms-as-expression-based-biomarkers-predictive-of-drug-response-in-vitro
#13
Zhaleh Safikhani, Petr Smirnov, Kelsie L Thu, Jennifer Silvester, Nehme El-Hachem, Rene Quevedo, Mathieu Lupien, Tak W Mak, David Cescon, Benjamin Haibe-Kains
Next-generation sequencing technologies have recently been used in pharmacogenomic studies to characterize large panels of cancer cell lines at the genomic and transcriptomic levels. Among these technologies, RNA-sequencing enable profiling of alternatively spliced transcripts. Given the high frequency of mRNA splicing in cancers, linking this feature to drug response will open new avenues of research in biomarker discovery. To identify robust transcriptomic biomarkers for drug response across studies, we develop a meta-analytical framework combining the pharmacological data from two large-scale drug screening datasets...
October 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/29063981/the-effect-of-genetic-variants-on-the-relationship-between-statins-and-breast-cancer-in-postmenopausal-women-in-the-women-s-health-initiative-observational-study
#14
Cathryn H Bock, Allison M Jay, Gregory Dyson, Jennifer L Beebe-Dimmer, Michele L Cote, Lifang Hou, Barbara V Howard, Pinkal Desai, Kristen Purrington, Ross Prentice, Michael S Simon
PURPOSE: Statins have been postulated to have chemopreventive activity against breast cancer. We evaluated whether germline genetic polymorphisms modified the relationship between statins and breast cancer risk using data from the Women's Health Initiative. We evaluated these interactions using both candidate gene and agnostic genome-wide approaches. METHODS: To identify candidate gene-statin interactions, we tested interactions between 22 SNPS in nine candidate genes implicated in the effect of statins on lipid metabolism in 1687 cases and 1687 controls...
October 24, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29059430/genome-wide-association-study-to-identify-susceptibility-loci-that-modify-radiation-related-risk-for-breast-cancer-after-childhood-cancer
#15
MULTICENTER STUDY
Lindsay M Morton, Joshua N Sampson, Gregory T Armstrong, Ting-Huei Chen, Melissa M Hudson, Eric Karlins, Casey L Dagnall, Shengchao Alfred Li, Carmen L Wilson, Deo Kumar Srivastava, Wei Liu, Guolian Kang, Kevin C Oeffinger, Tara O Henderson, Chaya S Moskowitz, Todd M Gibson, Diana M Merino, Jeannette R Wong, Sue Hammond, Joseph P Neglia, Lucie M Turcotte, Jeremy Miller, Laura Bowen, William A Wheeler, Wendy M Leisenring, John A Whitton, Laurie Burdette, Charles Chung, Belynda D Hicks, Kristine Jones, Mitchell J Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C Strong, Yutaka Yasui, Marilyn Stovall, Rita E Weathers, Susan A Smith, Rebecca Howell, Stella M Davies, Gretchen A Radloff, Kenan Onel, Amy Berrington de González, Peter D Inskip, Preetha Rajaraman, Joseph F Fraumeni, Smita Bhatia, Stephen J Chanock, Margaret A Tucker, Leslie L Robison
Background: Childhood cancer survivors treated with chest-directed radiotherapy have substantially elevated risk for developing breast cancer. Although genetic susceptibility to breast cancer in the general population is well studied, large-scale evaluation of breast cancer susceptibility after chest-directed radiotherapy for childhood cancer is lacking. Methods: We conducted a genome-wide association study of breast cancer in female survivors of childhood cancer, pooling two cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study and St...
November 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29049316/genomic-comparison-of-early-passage-conditionally-reprogrammed-breast-cancer-cells-to-their-corresponding-primary-tumors
#16
Akanksha S Mahajan, Bruna M Sugita, Anju N Duttargi, Francisco Saenz, Ewa Krawczyk, Justine N McCutcheon, Aline S Fonseca, Bhaskar Kallakury, Paula Pohlmann, Yuriy Gusev, Luciane R Cavalli
Conditionally reprogrammed cells (CRCs) are epithelial cells that are directly isolated from patients' specimens and propagated in vitro with feeder cells and a Rho kinase inhibitor. A number of these cells have been generated from biopsies of breast cancer patients, including ductal carcinoma in situ and invasive carcinomas. The characterization of their genomic signatures is essential to determine their ability to reflect the natural biology of their tumors of origin. In this study, we performed the genomic characterization of six newly established invasive breast cancer CRC cultures in comparison to the original patients' primary breast tumors (PBT) from which they derived...
2017: PloS One
https://www.readbyqxmd.com/read/29048660/canonical-and-non-canonical-wnt-signaling-in-cancer-stem-cells-and-their-niches-cellular-heterogeneity-omics-reprogramming-targeted-therapy-and-tumor-plasticity-review
#17
Masaru Katoh
Cancer stem cells (CSCs), which have the potential for self-renewal, differentiation and de-differentiation, undergo epigenetic, epithelial-mesenchymal, immunological and metabolic reprogramming to adapt to the tumor microenvironment and survive host defense or therapeutic insults. Intra-tumor heterogeneity and cancer-cell plasticity give rise to therapeutic resistance and recurrence through clonal replacement and reactivation of dormant CSCs, respectively. WNT signaling cascades cross-talk with the FGF, Notch, Hedgehog and TGFβ/BMP signaling cascades and regulate expression of functional CSC markers, such as CD44, CD133 (PROM1), EPCAM and LGR5 (GPR49)...
September 19, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29044504/a-low-frequency-haplotype-spanning-slx4-fancp-constitutes-a-new-risk-locus-for-early-onset-breast-cancer-60-years-and-is-associated-with-reduced-dna-repair-capacity
#18
Harald Surowy, Dominic Varga, Barbara Burwinkel, Frederik Marmé, Christof Sohn, Manuel Luedeke, Antje Rinckleb, Christiane Maier, Helmut Deissler, Meta Volcic, Lisa Wiesmüller, Annette Hasenburg, Maximilian Klar, Josef Hoegel, Walther Vogel
Only a fraction of breast cancer (BC) cases can be yet explained by mutations in genes or genomic variants discovered in linkage, genome-wide association and sequencing studies. The known genes entailing medium or high risk for BC are strongly enriched for a function in DNA double strand repair. Thus, aiming at identifying low frequency variants conferring an intermediate risk, we here investigated 17 variants (MAF: 0.01-0.1) in 10 candidate genes involved in DNA repair or cell cycle control. In an exploration cohort of 437 cases and 1189 controls we show the variant rs3810813 in the SLX4/FANCP gene to be significantly associated with both BC (≤60 years; OR=2...
October 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29029636/gene-expression-modules-in-primary-breast-cancers-as-risk-factors-for-organotropic-patterns-of-first-metastatic-spread-a-case-control-study
#19
Katherine Lawler, Efterpi Papouli, Cristina Naceur-Lombardelli, Anca Mera, Kayleigh Ougham, Andrew Tutt, Siker Kimbung, Ingrid Hedenfalk, Jun Zhan, Hongquan Zhang, Richard Buus, Mitch Dowsett, Tony Ng, Sarah E Pinder, Peter Parker, Lars Holmberg, Cheryl E Gillett, Anita Grigoriadis, Arnie Purushotham
BACKGROUND: Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited. METHODS: A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis...
October 13, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28993799/genetic-characterization-of-brain-metastases-in-the-era-of-targeted-therapy
#20
REVIEW
Catherine H Han, Priscilla K Brastianos
In the current era of molecularly targeted therapies and precision medicine, choice of cancer treatment has been increasingly tailored according to the molecular or genomic characterization of the cancer the individual has. Previously, the clinical observation of inadequate control of brain metastases was widely attributed to a lack of central nervous system (CNS) penetration of the anticancer drugs. However, more recent data have suggested that there are genetic explanations for such observations. Genomic analyses of brain metastases and matching primary tumor and other extracranial metastases have revealed that brain metastases can harbor potentially actionable driver mutations that are unique to them...
2017: Frontiers in Oncology
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