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https://www.readbyqxmd.com/read/29456732/two-protein-coding-genes-act-as-a-novel-clinical-signature-to-predict-prognosis-in-patients-with-ovarian-serous-cystadenocarcinoma
#1
Jue Zhang, Meng Xu, Han Gao, Jin-Chen Guo, Yu-Lin Guo, Miao Zou, Xu-Feng Wu
Ovarian cancer is the seventh most common type of cancer and the eighth most common cause of cancer-associated mortality among women. A number of studies have hypothesized that the expression status of certain genes may be used to predict prognosis in ovarian cancer. In the present study, the RNA expression data from next-generation sequencing and the clinical information of 413 patients from The Cancer Genome Atlas dataset was downloaded to identify the association between gene-expression level and the survival time of the patients with ovarian serous cystadenocarcinoma...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29454261/frequency-of-somatic-tp53-mutations-in-combination-with-known-pathogenic-mutations-in-colon-adenocarcinoma-non-small-cell-lung-carcinoma-and-gliomas-as-identified-by-next-generation-sequencing
#2
Zahra Shajani-Yi, Francine B de Abreu, Jason D Peterson, Gregory J Tsongalis
The tumor suppressor gene TP53 is the most frequently mutated gene in human cancer. It encodes p53, a DNA-binding transcription factor that regulates multiple genes involved in DNA repair, metabolism, cell cycle arrest, apoptosis, and senescence. TP53 is associated with human cancer by mutations that lead to a loss of wild-type p53 function as well as mutations that confer alternate oncogenic functions that enable them to promote invasion, metastasis, proliferation, and cell survival. Identifying the discrete TP53 mutations in tumor cells may help direct therapies that are more effective...
February 13, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29453630/somatic-brca1-mutations-in-clinically-sporadic-breast-cancer-with-medullary-histological-features
#3
Markus Rechsteiner, Konstantin Dedes, Daniel Fink, Bernhard Pestalozzi, Bettina Sobottka, Holger Moch, Peter Wild, Zsuzsanna Varga
BACKGROUND: The role of somatic BRCA1/2 gene mutations in breast cancer is getting increasing attention in view of hereditary disease. The medullary phenotype and triple negative intrinsic subtypes are often, but not exclusively encountered in BRCA1 germline mutated breast cancer, whilst for BRCA2, no association to specific histological features are known. In this study, we addressed the relationship between morphological medullary phenotype and BRCA1/2 somatic mutations in breast cancer without known positive family anamnesis...
February 17, 2018: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/29452859/evaluation-of-liquid-biopsies-for-detection-of-emerging-mutated-genes-in-metastatic-colorectal-cancer
#4
Hiroyasu Furuki, Takeshi Yamada, Goro Takahashi, Takuma Iwai, Michihiro Koizumi, Seiichi Shinji, Yasuyuki Yokoyama, Kohki Takeda, Nobuhiko Taniai, Eiji Uchida
BACKGROUND: Detection of gene mutations is important for planning molecular targeted therapy. Although most gene mutations are concordant between primary colon cancers and their liver metastases, new mutations can emerge in metastases. The liquid biopsy is a newly developed, gene analytic method to detect mutations in metastatic tumors. In this prospective study, we evaluated the applicability of liquid biopsies in the detection of mutations in primary and metastatic tumors. METHODS: We included 22 patients with liver metastases from colorectal cancer and extracted DNA from primary colorectal tumors, metastatic liver tumors, and peripheral blood (liquid biopsy)...
February 2, 2018: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29451897/selective-identification-of-somatic-mutations-in-pancreatic-cancer-cells-through-a-combination-of-next-generation-sequencing-of-plasma-dna-using-molecular-barcodes-and-a-bioinformatic-variant-filter
#5
Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya Kato
The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more...
2018: PloS One
https://www.readbyqxmd.com/read/29451745/detection-of-ros1-positive-non-small-cell-lung-cancer-on-cytological-specimens-using-immunocytochemistry
#6
Tatjana Vlajnic, Spasenija Savic, Audrey Barascud, Betty Baschiera, Michel Bihl, Bruno Grilli, Michelle Herzog, Julien Rebetez, Lukas Bubendorf
BACKGROUND: Rearrangements of the ROS1 oncogene are found in 1% to 2% of non-small cell lung cancers (NSCLC) and are regarded as mutually exclusive oncogenic driver mutations. Since the approval of targeted therapy for ROS1-positive NSCLC, ROS1 testing has become a part of the diagnostic routine. Fluorescence in situ hybridization (FISH), optionally selected for by immunohistochemistry on histological material, is a common practice for the detection of ROS1 rearrangements. However, NSCLC often is diagnosed by cytology alone, requiring predictive marker testing on cytological specimens...
February 16, 2018: Cancer Cytopathology
https://www.readbyqxmd.com/read/29445031/the-perils-of-single-site-genetic-testing-for-hereditary-cancer-syndromes-in-the-era-of-next-generation-sequencing
#7
Nicole Casasanta, Elizabeth Stark, Allison McHenry, Tara Biagi, Rebecca Kaltman
A challenge in counseling patients with a family history suggesting a hereditary cancer syndrome is deciding which genetic tests or panels to order. In this article, we discuss the identification of multiple familial mutations through genetic counseling and panel testing. For patients meeting National Comprehensive Cancer Network criteria for clinical genetic testing, providers should consider expanded panels to provide a more complete assessment of one's genetic risk. The continued use of expanded panel testing in the clinical setting will help inform optimal management of cancer patients, as well as the management of their unaffected family members...
February 14, 2018: Oncologist
https://www.readbyqxmd.com/read/29443391/human-papillomavirus-genome-integration-in-squamous-carcinogenesis-what-have-next-generation-sequencing-studies-taught-us
#8
REVIEW
Ian J Groves, Nicholas Coleman
Human papillomavirus (HPV) infection is associated with ~5% of all human cancers, including a range of squamous cell carcinomas (SCCs). Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an integral event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation and further genomic instability...
February 14, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29442275/five-novel-oncogenic-signatures-could-be-utilized-as-afp-related-diagnostic-biomarkers-for-hepatocellular-carcinoma-based-on-next-generation-sequencing
#9
Zheng Yu, Rongchang Wang, Fan Chen, Jianru Wang, Xiaohui Huang
BACKGROUND: Alpha-fetal protein (AFP) is an important conventional clinical diagnostic indicator of hepatocellular carcinoma (HCC). However, the utilization of AFP alone might yield deceptive results due to its limited sensitivity and accuracy. AIMS: Our study was designed to investigate latent diagnostic biomarkers that could function as auxiliary clinical indicators of HCC and enhance the accuracy of joint diagnosis with AFP. METHODS: We analyzed gene expression profiles and clinical data from HCC patients in The Cancer Genome Atlas database...
February 13, 2018: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/29439875/consensus-document-on-the-implementation-of-next-generation-sequencing-in-the-genetic-diagnosis-of-hereditary-cancer
#10
José Luis Soto, Ignacio Blanco, Orland Díez, Javier García Planells, Isabel Lorda, Gert Matthijs, Mercedes Robledo, Erika Souche, Conxi Lázaro
Genetic diagnosis of hereditary cancer syndromes offers the opportunity to establish more effective predictive and preventive measures for the patient and their families. The ultimate objective is to decrease cancer morbidity and mortality in high genetic risk families. Next Generation Sequencing (NGS) offers an important improvement in the efficiency of genetic diagnosis, allowing an increase in diagnostic yield with a substantial reduction in response times and economic costs. Consequently, the implementation of this new technology is a great opportunity for improvement in the clinical management of affected families...
February 10, 2018: Medicina Clínica
https://www.readbyqxmd.com/read/29439670/phase-i-study-of-an-active-immunotherapy-for-asymptomatic-phase-lymphoplasmacytic-lymphoma-with-dna-vaccines-encoding-antigen-chemokine-fusion-study-protocol
#11
Sheeba K Thomas, Soung-Chul Cha, D Lynne Smith, Kun Hwa Kim, Sapna R Parshottam, Sheetal Rao, Michael Popescu, Vincent Y Lee, Sattva S Neelapu, Larry W Kwak
BACKGROUND: There is now a renewed interest in cancer vaccines. Patients responding to immune checkpoint blockade usually bear tumors that are heavily infiltrated by T cells and express a high load of neoantigens, indicating that the immune system is involved in the therapeutic effect of these agents; this finding strongly supports the use of cancer vaccine strategies. Lymphoplasmacytic lymphoma (LPL) is a low grade, incurable disease featuring an abnormal proliferation of Immunoglobulin (Ig)-producing malignant cells...
February 13, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29438522/ras-mutation-analysis-in-circulating-tumor-dna-from-patients-with-metastatic-colorectal-cancer-the-ageo-rasanc-prospective-multicenter-study
#12
J B Bachet, O Bouché, J Taieb, O Dubreuil, M L Garcia, A Meurisse, C Normand, J M Gornet, P Artru, S Louafi, F Bonnetain, A Thirot-Bidault, I Baumgaertner, R Coriat, D Tougeron, T Lecomte, F Mary, T Aparicio, L Marthey, V Taly, H Blons, D Vernerey, P Laurent-Puig
Background: RAS mutations are currently sought for in tumor samples, which takes a median of almost 3 weeks in western European countries. This creates problems in clinical situations that require urgent treatment and for inclusion in therapeutic trials that need RAS status for randomization. Analysis of circulating tumor DNA might help to shorten the time required to determine RAS mutational status prior to anti-EGFR antibody therapy for metastatic colorectal cancer. Here we compared plasma versus tissue RAS analysis in a large prospective multicenter cohort...
February 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29436178/microsatellite-instability-status-determined-by-next-generation-sequencing-and-compared-with-pd-l1-and-tumor-mutational-burden-in-11-348-patients
#13
Ari Vanderwalde, David Spetzler, Nianqing Xiao, Zoran Gatalica, John Marshall
Microsatellite instability (MSI) testing identifies patients who may benefit from immune checkpoint inhibitors. We developed an MSI assay that uses data from a commercially available next-generation sequencing (NGS) panel to determine MSI status. The assay is applicable across cancer types and does not require matched samples from normal tissue. Here, we describe the MSI-NGS method and explore the relationship of MSI with tumor mutational burden (TMB) and PD-L1. MSI examined by PCR fragment analysis and NGS was compared for 2189 matched cases...
February 13, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29436103/genomic-hotspots-but-few-recurrent-fusion-genes-in-breast-cancer
#14
Danai Fimereli, Debora Fumagalli, David Brown, David Gacquer, Françoise Rothé, Roberto Salgado, Denis Larsimont, Christos Sotiriou, Vincent Detours
The advent of next generation sequencing technologies has boosted the interest in exploring the role of fusion genes in the development and progression of solid tumors. In breast cancer, most of the detected gene fusions seem to be "passenger" events while the presence of recurrent and driver fusions is still under study. We performed RNA sequencing in 55 well-characterized breast cancer samples and 10 adjacent normal breast tissues, complemented by an analysis of SNP array data. We explored the presence of fusion genes and defined their association with breast cancer subtypes, clinical-pathologic characteristics and copy number aberrations...
February 13, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29435133/elucidating-mechanisms-of-sunitinib-resistance-in-renal-cancer-an-integrated-pathological-molecular-analysis
#15
Henriett Butz, Qiang Ding, Roy Nofech-Mozes, Zsuzsanna Lichner, Heyu Ni, George M Yousef
Upon sunitinib treatment of metastatic renal cell carcinoma patients eventually acquire resistance. Our aim was to investigate microRNAs behind sunitinib resistance. We developed an in vivo xenograft and an in vitro model and compared morphological, immunhistochemical, transcriptomical and miRNome data changes during sunitinib response and resistance by performing next-generation mRNA and miRNA sequencing. Complex bioinformatics (pathway, BioFunction and network) analysis were performed. Results were validated by in vitro functional assays...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29435039/characterization-of-mutations-in-brca1-2-and-the-relationship-with-clinic-pathological-features-of-breast-cancer-in-a-hereditarily-high-risk-sample-of-chinese-population
#16
Min Fang, Li Zhu, Hengyu Li, Xizhou Li, Yanmei Wu, Kainan Wu, Jian Lin, Yuan Sheng, Yue Yu
The database of BRCA1/2 mutations in Chinese population remains incomplete at present. Therefore, the present study aimed to report specific harmful BRCA1/2 mutations in the Chinese population and discuss the clinicopathological features in mutation carriers. BRCA1/2 germline mutation tests for 71 patients with breast cancer from a hereditarily high-risk Chinese population were performed using next-generation sequencing for identification of deleterious mutations. Furthermore, the clinicopathological features between BRCA1/2 mutation carriers and non-carriers were compared...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434979/lats2-promoter-hypermethylation-and-its-effect-on-gene-expression-in-human-breast-cancer
#17
Saki Matsui, Naofumi Kagara, Chieko Mishima, Yasuto Naoi, Masafumi Shimoda, Atsushi Shimomura, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
Tumor-specific promoter hypermethylation of large tumor suppressor, homolog 2 (LATS2), a tumor suppressor gene, has been investigated using methylation-specific polymerase chain reaction (MSP) assays in different types of human cancer producing conflicting results. The aim of the present study was to evaluate the methylation status of the LATS2 promoter region using bisulfite sequencing with a next generation sequencer for breast cancer. In the 11 patients enrolled in the present study, the LATS2 promoter methylation index (MI) was uniformly high in tumor and normal tissues of the breast (median, 84...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434452/-pik3ca-and-tp53-mutations-predict-overall-survival-of-stage-ii-iii-colorectal-cancer-patients
#18
A-Jian Li, Hua-Guang Li, Er-Jiang Tang, Wei Wu, Ying Chen, Hui-Hong Jiang, Mou-Bin Lin, Lu Yin
AIM: To investigate the predictive value of PIK3CA and TP53 mutation status in colorectal cancer (CRC) patients treated with 5-fluorouracil-based chemotherapy. METHODS: In this study, a total of 315 patients with histologically proven CRC were enrolled from Yangpu Hospital affiliated to Shanghai Tongji University between 2007 and 2011. Of these patients, 241 with stage II/III CRC received 5-fluorouracil-based adjuvant chemotherapy. Formalin-fixed paraffin-embedded lesion samples of the patients with curatively resected CRC were collected...
February 7, 2018: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29433585/characterization-and-validation-of-potential-therapeutic-targets-based-on-the-molecular-signature-of-patient-derived-xenografts-in-gastric-cancer
#19
Zuhua Chen, Wenwen Huang, Tiantian Tian, Wanchun Zang, Jingyuan Wang, Zhentao Liu, Zhongwu Li, Yumei Lai, Zhi Jiang, Jing Gao, Lin Shen
BACKGROUND: Patient-derived xenograft (PDX) models with definite molecular signature are attractive preclinical models for development of novel targeted drugs. Here, we profiled and explored potential therapeutic targets based on characterized PDX models for advanced gastric cancer (AGC). METHODS: The genomic variation and molecular profile of 50 PDX models from AGC patients were analyzed by targeted next-generation sequencing, in situ hybridization, and immunohistochemistry...
February 13, 2018: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/29433547/finite-size-effects-in-transcript-sequencing-count-distribution-its-power-law-correction-necessarily-precedes-downstream-normalization-and-comparative-analysis
#20
Wing-Cheong Wong, Hong-Kiat Ng, Erwin Tantoso, Richie Soong, Frank Eisenhaber
BACKGROUND: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i...
February 12, 2018: Biology Direct
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