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Cancer gene panel

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https://www.readbyqxmd.com/read/28430642/immunocompetent-mouse-allograft-models-for-development-of-therapies-to-target-breast-cancer-metastasis
#1
Yuan Yang, Howard H Yang, Ying Hu, Peter H Watson, Huaitian Liu, Thomas R Geiger, Miriam R Anver, Diana C Haines, Philip Martin, Jeffrey E Green, Maxwell P Lee, Kent W Hunter, Lalage M Wakefield
Effective drug development to combat metastatic disease in breast cancer would be aided by the availability of well-characterized preclinical animal models that (a) metastasize with high efficiency, (b) metastasize in a reasonable time-frame, (c) have an intact immune system, and (d) capture some of the heterogeneity of the human disease. To address these issues, we have assembled a panel of twelve mouse mammary cancer cell lines that can metastasize efficiently on implantation into syngeneic immunocompetent hosts...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427360/association-of-novel-polymorphisms-in-tmem39a-gene-with-systemic-lupus-erythematosus-in-a-chinese-han-population
#2
Xinze Cai, Wenyue Huang, Xudong Liu, Lining Wang, Yi Jiang
BACKGROUND: This study aimed to assess the association between 14 single nucleotide polymorphisms (SNPs) in six genes (IRF8, TMEM39A, IKZF3, ORMDL3, GSDMB, and ZPBP2) and systemic lupus erythematosus (SLE) in a Chinese Han population sample. METHODS: We carried out a case-control study of 415 patients with SLE and 470 healthy controls without autoimmune disease or cancer. DNA for genetic analysis was isolated from the blood of all subjects using standard phenol-chloroform method...
April 20, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28424414/integrated-analysis-of-promoter-methylation-and-expression-of-telomere-related-genes-in-breast-cancer
#3
Jianfu Heng, Fan Zhang, Xinwu Guo, Lili Tang, Limin Peng, Xipeng Luo, Xunxun Xu, Shouman Wang, Lizhong Dai, Jun Wang
Telomeres at the ends of eukaryotic chromosomes play a critical role in tumorgenesis. Using microfluidic PCR and next-generation bisulfite sequencing technology, we investigated the promoter methylation of 29 telomere related genes in paired tumor and normal tissues from 184 breast cancer patients. The expression of significantly differentially methylated genes was quantified using qPCR method.We observed that the average methylation level of the 29 telomere related genes was significant higher in tumor than that in normal tissues (P = 4...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424201/pik3ca-mutations-contribute-to-acquired-cetuximab-resistance-in-metastatic-colorectal-cancer-patients
#4
Jian Ming Xu, Yan Wang, You-Liang Wang, Yan Wang, Tao Liu, Ming Ni, Man-Sheng Li, Li Lin, Fei-Jiao Ge, Chun Gong, Jun-Yan Gu, Ru Jia, He-Fei Wang, Yu Ling Chen, Rong-Rui Liu, Chuan-Hua Zhao, Zhao-Li Tan, Yang Jin, Yunping Zhu, Shuji Ogino, Zhi Rong Qian
<p>Mutations in KRAS are considered to be the main drivers of acquired resistance to epidermal growth factor receptor (EGFR) blockade in patients with metastatic colorectal cancer (mCRC). However, the potential roles of other genes downstream of the EGFR signaling pathway in conferring acquired resistance has not been extensively investigated.</p> <br /><br />Experimental Design: <p>Using circulating tumor DNA (ctDNA) from patients with mCRC and with acquired cetuximab resistance, we developed a targeted amplicon ultra-deep sequencing method to screen for low-abundance somatic mutations in a panel of genes that encode components of the EGFR signaling pathway...
April 19, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28423508/annexin-a13-promotes-tumor-cell-invasion-in-vitro-and-is-associated-with-metastasis-in-human-colorectal-cancer
#5
Guozhong Jiang, Pengju Wang, Weiwei Wang, Wencai Li, Liping Dai, Kuisheng Chen
PURPOSE: Aberrantly upregulated expression of selected members of annexin, a group of calcium- and membrane-binding proteins, have been found to be associated with metastasis, poor prognosis, and other clinical characteristics in colorectal cancer (CRC), the third most diagnosed cancer. However, ANXA13 (encoding protein annexin A13), the original founder gene of the annexin A family, has not been studied carefully as a potential prognostic biomarker in CRC. METHODS: The protein level of annexin A13 was determined by western blot in a panel of CRC cell lines...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423363/multiple-gene-panel-analysis-in-a-case-series-of-255-women-with-hereditary-breast-and-ovarian-cancer
#6
Gianluca Tedaldi, Michela Tebaldi, Valentina Zampiga, Rita Danesi, Valentina Arcangeli, Mila Ravegnani, Ilaria Cangini, Francesca Pirini, Elisabetta Petracci, Andrea Rocca, Fabio Falcini, Dino Amadori, Daniele Calistri
As new genes predisposing to breast (BC) and ovarian cancer (OC) are constantly emerging, the use of panels of genes analyzed by Next-Generation Sequencing (NGS) is increasing in clinical diagnostics. The identification of a large number of new germline mutations allows for deeper knowledge of cancer predisposition, although raising many questions about patient management.BC and OC patients recruited by our counseling service between 2012-2015 were included in this study. DNA was extracted from peripheral blood and a panel of 94 genes involved in hereditary tumors was analyzed by NGS...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423360/tiam1-variants-improve-clinical-outcome-in-neuroblastoma
#7
Elena Sanmartín, Yania Yáñez, Victoria Fornés-Ferrer, José L Zugaza, Adela Cañete, Victoria Castel, Jaime Font de Mora
Identification of tumor driver mutations is crucial for improving clinical outcome using a personalized approach to the treatment of cancer. Neuroblastoma is a tumor of the peripheral sympathetic nervous system for which only a few driver alterations have been described including MYCN amplification and ALK mutations. We assessed 106 primary neuroblastoma tumors by next generation sequencing using a customized amplicon-based gene panel. Our results reveal that genetic variants in TIAM1 gene associate with better clinical outcome, suggesting a role for these TIAM1 variants in preventing progression of this disease...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423358/characterization-of-fusion-genes-in-common-and-rare-epithelial-ovarian-cancer-histologic-subtypes
#8
Madalene A Earp, Rama Raghavan, Qian Li, Junqiang Dai, Stacey J Winham, Julie M Cunningham, Yanina Natanzon, Kimberly R Kalli, Xiaonan Hou, S John Weroha, Paul Haluska, Kate Lawrenson, Simon A Gayther, Chen Wang, Ellen L Goode, Brooke L Fridley
Gene fusions play a critical role in some cancers and can serve as important clinical targets. In epithelial ovarian cancer (EOC), the contribution of fusions, especially by histological type, is unclear. We therefore screened for recurrent fusions in a histologically diverse panel of 220 EOCs using RNA sequencing. The Pipeline for RNA-Sequencing Data Analysis (PRADA) was used to identify fusions and allow for comparison with The Cancer Genome Atlas (TCGA) tumors. Associations between fusions and clinical prognosis were evaluated using Cox proportional hazards regression models...
April 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422739/diagnostic-role-of-wnt-pathway-gene-promoter-methylation-in-non-small-cell-lung-cancer
#9
Shunlin Liu, Xiaoying Chen, Ruhua Chen, Jinzhi Wang, Guoliang Zhu, Jianzhong Jiang, Hongwei Wang, Shiwei Duan, Jianan Huang
Wnt signal pathway genes are known to be involved with cancer development. Here we tested the hypothesis whether DNA methylation of genes part of the Wnt signaling pathway could help the diagnosis of non-small cell lung cancer (NSCLC). The methylation levels of SFRP1, SFRP2, WIF1 and PRKCB in 111 NSCLC patients were evaluated by quantitative methylation-specific PCR (qMSP). Promoter methylation levels of four candidate genes were significantly higher in tumor tissues compared with the adjacent tissues. SFRP1, SFRP2 and PRKCB genes were all shown to be good predictors of NSCLC risk (SFRP1: AUC = 0...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422736/identification-of-map-kinase-pathways-as-therapeutic-targets-in-gallbladder-carcinoma-using-targeted-parallel-sequencing
#10
Mengdan Li, Lihong Chen, Yiping Qu, Fang Sui, Qi Yang, Meiju Ji, Bingyin Shi, Mingwei Chen, Peng Hou
The aim of this study was to profile somatic mutation spectrum in gallbladder cancers (GBCs), and determine the role of MAP kinase pathway in GBC by a series of in vitro and in vivo studies. We performed targeted massively parallel sequencing of DNA isolated from GBCs and matched blood from 14 GBC patients to search for mutations in 504 genes commonly altered in human cancers. We identified recurrent mutations enriched in several major signaling pathways including MAP kinase, Wnt/β-catenin and NF-κB pathways...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419837/identification-and-molecular-cloning-of-novel-transcripts-of-the-human-kallikrein-related-peptidase-10-klk10-gene-using-next-generation-sequencing
#11
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Kallikreins (KLKs) form the largest group of serine proteases in the human genome sharing many structural and functional characteristics. Multiple alternative transcripts have been reported for most human KLKs, while many of them have been found aberrantly expressed in various human malignancies, thus possessing significant prognostic or/and diagnostic value. Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity, as it affects cell cycle control, proliferation, apoptosis, invasion, and metastasis...
April 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28418920/complementary-utility-of-targeted-next-generation-sequencing-and-immunohistochemistry-panels-as-a-screening-platform-to-select-targeted-therapy-for-advanced-gastric-cancer
#12
Hyo Song Kim, Hanna Lee, Su-Jin Shin, Seung-Hoon Beom, Minkyu Jung, Sujin Bae, Eun Young Lee, Kyu Hyun Park, Yoon Young Choi, Taeil Son, Hyoung-Il Kim, Jae-Ho Cheong, Woo Jin Hyung, Jun Chul Park, Sung Kwan Shin, Sang Kil Lee, Yong Chan Lee, Woong Sub Koom, Joon Seok Lim, Hyun Cheol Chung, Sung Hoon Noh, Sun Young Rha, Hyunki Kim, Soonmyung Paik
We tested the clinical utility of combined profiling of Ion Torrent PGM based next-generation sequencing (NGS) and immunohistochemistry (IHC) for assignment to molecularly targeted therapies. A consecutive cohort of 93 patients with advanced/metastatic GC who underwent palliative chemotherapy between March and December 2015 were prospectively enrolled. Formalin fixed paraffin embedded tumor biopsy specimens were subjected to a 10 GC panels [Epstein Barr virus encoding RNA in-situ hybridization, IHC for mismatch repair proteins (MMR; MLH1, PMS2, MSH2, and MSH6), receptor tyrosine kinases (HER2, EGFR, and MET), PTEN, and p53 protein], and a commercial targeted NGS panel of 52 genes (Oncomine Focus Assay)...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418867/early-detection-of-gastric-cancer-using-global-genome-wide-and-irf4-elmo1-clip4-and-msc-dna-methylation-in-endoscopic-biopsies
#13
Francesca Pirini, Sassan Noazin, Martha H Jahuira-Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Gloria Vargas, William Prado, Ethan Soudry, Jimena Pérez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili-Gangas, Priscilla Brebi-Mieville, Douglas E Berg, Masamichi Hayashi, David Sidransky, Robert H Gilman, Rafael Guerrero-Preston
Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings.We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project ("TCGA")...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418444/associations-between-cancer-predisposition-testing-panel-genes-and-breast-cancer
#14
Fergus J Couch, Hermela Shimelis, Chunling Hu, Steven N Hart, Eric C Polley, Jie Na, Emily Hallberg, Raymond Moore, Abigail Thomas, Jenna Lilyquist, Bingjian Feng, Rachel McFarland, Tina Pesaran, Robert Huether, Holly LaDuca, Elizabeth C Chao, David E Goldgar, Jill S Dolinsky
Importance: Germline pathogenic variants in BRCA1 and BRCA2 predispose to an increased lifetime risk of breast cancer. However, the relevance of germline variants in other genes from multigene hereditary cancer testing panels is not well defined. Objective: To determine the risks of breast cancer associated with germline variants in cancer predisposition genes. Design, Setting, and Participants: A study population of 65 057 patients with breast cancer receiving germline genetic testing of cancer predisposition genes with hereditary cancer multigene panels...
April 13, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28418352/-fatty-acid-synthase-in-the-diagnosis-of-prostate-neoplasms
#15
D O Allina, Yu Yu Andreeva, L E Zavalishina, L V Moskvina, G A Frank
The differential diagnosis of benign and malignant changes in the prostate presents still definite difficulties; the antibody panel existing for these purposes is imperfect. Fatty acid synthase (FASN) is an androgen-regulated enzyme required for de novo lipogenesis. A number of studies have noted increased expression of the gene encoding this protein in tumors and precancerous lesions of different locations. AIM: Тo estimate the diagnostic value of analyzing the expression of FASN in prostate neoplasias...
2017: Arkhiv Patologii
https://www.readbyqxmd.com/read/28416823/-identification-of-a-new-pro-invasion-factor-in-tumor-microenvironment-progress-in-function-and-mechanism-of-extracellular-atp
#16
W G Fang, X X Tian
Up to 90% of all cancer related morbidity and mortality can be attributed to metastasis. In recent years the study of tumor microenvironment, its cellular and molecular components, and how they can affect neoplastic progression toward metastasis, has become a hot focus in cancer research. Accumulated evidence shows that the formation of metastasis is a multi-step sequential process, in which, the tumor cells continuously interact with the host microenvironment. Host derived factors, i.e. growth factors/inhibitors, angiogenic factors, chemokines, etc...
April 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/28416665/hippo-pathway-mediates-resistance-to-cytotoxic-drugs
#17
Taranjit S Gujral, Marc W Kirschner
Chemotherapy is widely used for cancer treatment, but its effectiveness is limited by drug resistance. Here, we report a mechanism by which cell density activates the Hippo pathway, which in turn inactivates YAP, leading to changes in the regulation of genes that control the intracellular concentrations of gemcitabine and several other US Food and Drug Administration (FDA)-approved oncology drugs. Hippo inactivation sensitizes a diverse panel of cell lines and human tumors to gemcitabine in 3D spheroid, mouse xenografts, and patient-derived xenograft models...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28416604/oncogenic-characterization-and-pharmacologic-sensitivity-of-activating-fibroblast-growth-factor-receptor-fgfr-genetic-alterations-to-the-selective-fgfr-inhibitor-erdafitinib
#18
Jayaprakash D Karkera, Gabriela Martinez Cardona, Katherine Bell, Dana Gaffney, Joseph C Portale, Ademi Santiago-Walker, Christopher Moy, Peter King, Michael Sharp, Rastilav Bahleda, Feng R Luo, John D Alvarez, Matthew V Lorenzi, Suso J Platero
Fibroblast growth factor receptor (FGFR) genetic alterations are frequently observed in cancer, suggesting that FGFR inhibition may be a promising therapy in patients harboring these lesions.  Identification of predictive and pharmacodynamic biomarkers to select and monitor patients most likely to respond to FGFR inhibition will be the key to clinical development of this class of agents.  Sensitivity to FGFR inhibition and correlation with FGFR pathway activation status were determined in molecularly annotated panels of cancer cell lines and xenograft models...
April 17, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28415793/clinical-framework-for-next-generation-sequencing-based-analysis-of-treatment-predictive-mutations-and-multiplexed-gene-fusion-detection-in-non-small-cell-lung-cancer
#19
Kajsa Ericson Lindquist, Anna Karlsson, Per Levéen, Hans Brunnström, Christel Reuterswärd, Karolina Holm, Mats Jönsson, Karin Annersten, Frida Rosengren, Karin Jirström, Jaroslaw Kosieradzki, Lars Ek, Åke Borg, Maria Planck, Göran Jönsson, Johan Staaf
Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients)...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415743/survival-differences-of-cimp-subtypes-integrated-with-cna-information-in-human-breast-cancer
#20
Huihan Wang, Weili Yan, Shumei Zhang, Yue Gu, Yihan Wang, Yanjun Wei, Hongbo Liu, Fang Wang, Qiong Wu, Yan Zhang
CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation...
March 14, 2017: Oncotarget
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