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https://www.readbyqxmd.com/read/28917852/bio-responsive-alginate-keratin-composite-nanogels-with-enhanced-drug-loading-efficiency-for-cancer-therapy
#1
Zhe Sun, Zeng Yi, Huaiying Zhang, Xiaomin Ma, Wen Su, Xiaoyu Sun, Xudong Li
This article presents a novel dual-stimuli responsive nanogel prepared from human hair keratin and alginate through simple crosslinking method. Keratin offer the crosslinking structure and bio-responsive ability and alginate ameliorated properties of nanogels including particle size, stability and drug loading capacity. The resultant keratin-alginate nanogels (KSA-NGs) could function as promising vectors for doxorubicin hydrochloride (DOX) with a super-high drug-loading rate of 52.9% (w/w) and dual-stimuli responsive behavior to GSH and trypsin...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28915716/implementation-and-utilization-of-the-molecular-tumor-board-to-guide-precision-medicine
#2
REVIEW
Shuko Harada, Rebecca Arend, Qian Dai, Jessica A Levesque, Thomas S Winokur, Rongjun Guo, Martin J Heslin, Lisle Nabell, L Burt Nabors, Nita A Limdi, Kevin A Roth, Edward E Partridge, Gene P Siegal, Eddy S Yang
BACKGROUND: With rapid advances in genomic medicine, the complexity of delivering precision medicine to oncology patients across a university health system demanded the creation of a Molecular Tumor Board (MTB) for patient selection and assessment of treatment options. The objective of this report is to analyze our progress to date and discuss the importance of the MTB in the implementation of personalized medicine. MATERIALS AND METHODS: Patients were reviewed in the MTB for appropriateness for comprehensive next generation sequencing (NGS) cancer gene set testing based on set criteria that were in place...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915579/microrna-profiling-associated-with-non-small-cell-lung-cancer-next-generation-sequencing-detection-experimental-validation-and-prognostic-value
#3
Sandra Gallach, Eloisa Jantus-Lewintre, Silvia Calabuig-Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
BACKGROUND: The average five-year survival for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs (miRNAs) constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified dysregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#4
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28905136/highly-sensitive-detection-of-esr1-mutations-in-cell-free-dna-from-patients-with-metastatic-breast-cancer-using-molecular-barcode-sequencing
#5
Nanae Masunaga, Naofumi Kagara, Daisuke Motooka, Shota Nakamura, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR)...
September 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28904972/evaluation-of-the-bacterial-diversity-in-the-human-tongue-coating-based-on-genus-specific-primers-for-16s-rrna-sequencing
#6
Beili Sun, Dongrui Zhou, Jing Tu, Zuhong Lu
The characteristics of tongue coating are very important symbols for disease diagnosis in traditional Chinese medicine (TCM) theory. As a habitat of oral microbiota, bacteria on the tongue dorsum have been proved to be the cause of many oral diseases. The high-throughput next-generation sequencing (NGS) platforms have been widely applied in the analysis of bacterial 16S rRNA gene. We developed a methodology based on genus-specific multiprimer amplification and ligation-based sequencing for microbiota analysis...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#7
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28891048/identifying-actionable-variants-using-next-generation-sequencing-in-patients-with-a-historical-diagnosis-of-undifferentiated-pleomorphic-sarcoma
#8
Jeremy Lewin, Swati Garg, Beatrice Y Lau, Brendan C Dickson, Frank Traub, Nalan Gokgoz, Anthony M Griffin, Peter C Ferguson, Irene L Andrulis, Hao-Wen Sim, Suzanne Kamel-Reid, Tracy L Stockley, Lillian Siu, Jay S Wunder, Albiruni Ra Razak
There are limited data regarding the molecular characterization of undifferentiated pleomorphic sarcomas (UPS; formerly malignant fibrous histiocytoma). This study aimed to investigate the utility of next generation sequencing (NGS) in UPS to identify subsets of patients who harbour actionable mutations. Patients diagnosed with UPS underwent pathological re-evaluation by a pathologist specializing in sarcoma. Tumor DNA was isolated from archived fresh frozen tissue samples and genotyped using NGS with the Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons)...
September 10, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28882180/high-performance-of-targeted-next-generation-sequencing-on-variance-detection-in-clinical-tumor-specimens-in-comparison-with-current-conventional-methods
#9
Dan Su, Dadong Zhang, Kaiyan Chen, Jing Lu, Junzhou Wu, Xinkai Cao, Lisha Ying, Qihuang Jin, Yizhou Ye, Zhenghua Xie, Lei Xiong, Weimin Mao, Fugen Li
BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis...
September 7, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28875369/-personalized-oncology
#10
REVIEW
C Heining, P Horak, S Gröschel, H Glimm, S Fröhling
CLINICAL ISSUE: Innovative next generation sequencing (NGS) technologies and comprehensive sequencing investigations in large patient cohorts have paved the way for very promising personalized treatment strategies based on the molecular characteristics of individual tumors. STANDARD TREATMENT: Targeted therapies, such as tyrosine kinase inhibitors, antibodies and modern immunotherapeutic approaches are well established as monotherapy and combination therapy for many hematological and oncological malignancies...
September 5, 2017: Der Radiologe
https://www.readbyqxmd.com/read/28868023/next-generation-sequencing-in-order-to-better-characterize-a-brca-variant-of-uncertain-significance
#11
Steven Sorscher, Shakti Ramkissoon
BRCA germline mutations are the most common predisposing factor in familial breast-ovarian cancer syndrome families. However, many screened patients are identified as harboring BRCA variants of uncertain significance (VUS), rather than carrying deleterious germline mutations [Calo et al.: Cancers 2010; 2:1644-1660]. While such VUSs are typically reclassified as benign polymorphisms, this may occur years after the VUS is first identified [Murray et al.: Genet Med 2011; 13; 998-1005]. Loss of heterozygosity (LOH) of BRCA is nearly always the gatekeeper event in inherited BRCA-related breast cancer and LOH of BRCA is rare in sporadic cancers [Osorio et al...
May 2017: Case Reports in Oncology
https://www.readbyqxmd.com/read/28866070/next-generation-sequencing-a-novel-approach-to-distinguish-multifocal-primary-lung-adenocarcinomas-from-intrapulmonary-metastases
#12
Snehal B Patel, Wendy Kadi, Ann E Walts, Alberto M Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, Jean Lopategui
Distinguishing between multiple lung primaries and intrapulmonary metastases is imperative for accurate staging. The American Joint Committee on Cancer (AJCC) criteria are routinely used for this purpose but can yield equivocal conclusions. We evaluated whether next generation sequencing (NGS) using the 50 gene AmpliSeq Cancer Hotspot Panel v2 can be used to facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). Primary-metastatic pairs showed high mutational concordance: Seven pairs shared mutations, and 1 was concordant for having no mutations...
August 30, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28860410/next-generation-sequencing-for-patients-with-sarcoma-a-single-center-experience
#13
Gregory M Cote, Jie He, Edwin Choy
BACKGROUND: Sarcomas comprise over 50 subtypes of mesenchymal cancers. For the majority of sarcomas, the driver mutations remain unknown. In this article, we describe our experience with a targeted next-generation sequencing (NGS) platform in clinic patients. MATERIALS AND METHODS: We retrospectively analyzed results of NGS using 133 tumor samples from patients diagnosed with a variety of sarcomas that were analyzed with targeted NGS covering over 400 cancer-related genes (405 DNA, 265 RNA) on a commercially available platform...
August 31, 2017: Oncologist
https://www.readbyqxmd.com/read/28859058/preoperative-chemoradiation-with-capecitabine-irinotecan-and-cetuximab-in-rectal-cancer-significance-of-pre-treatment-and-post-resection-ras-mutations
#14
Simon Gollins, Nick West, David Sebag-Montefiore, Arthur Sun Myint, Mark Saunders, Shabbir Susnerwala, Phil Quirke, Sharadah Essapen, Leslie Samuel, Bruce Sizer, Jane Worlding, Katie Southward, Gemma Hemmings, Emma Tinkler-Hundal, Morag Taylor, Daniel Bottomley, Philip Chambers, Emma Lawrie, Andre Lopes, Sandy Beare
BACKGROUND: The influence of EGFR pathway mutations on cetuximab-containing rectal cancer preoperative chemoradiation (CRT) is uncertain. METHODS: In a prospective phase II trial (EXCITE), patients with magnetic resonance imaging (MRI)-defined non-metastatic rectal adenocarinoma threatening/involving the surgical resection plane received pelvic radiotherapy with concurrent capecitabine, irinotecan and cetuximab. Resection was recommended 8 weeks later. The primary endpoint was histopathologically clear (R0) resection margin...
August 31, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28852913/cancer-patients-intentions-towards-receiving-unsolicited-genetic-information-obtained-using-next-generation-sequencing
#15
Rhodé M Bijlsma, Hester Wessels, Roel H P Wouters, Anne M May, Margreet G E M Ausems, Emile E Voest, Annelien L Bredenoord
Next-generation sequencing (NGS) can be used to generate information about a patient's tumour and personal genome. This powerful diagnostic tool provides solicited and unsolicited hereditary genetic (risk) information that could have consequences for cancer patients and their quality of life. A well-defined approach for returning appropriate genetic risk information is needed in personalized cancer care. A qualitative design with semi-structured interviews was used. We conducted interviews with 24 Dutch patients with different types of cancer, both NGS-experienced and NGS-inexperienced, to learn their intentions, needs and preferences towards receiving unsolicited genetic information obtained using NGS...
August 29, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28842574/using-the-new-cellcollector-to-capture-circulating-tumor-cells-from-blood-in-different-groups-of-pulmonary-disease-a-cohort-study
#16
Yutong He, Jin Shi, Gaofeng Shi, Xiaoli Xu, Qingyi Liu, Congmin Liu, Zhaoyu Gao, Jiaoteng Bai, Baoen Shan
Circulating tumor cells (CTCs) are promising biomarkers for clinical application. Cancer screening with Low-Dose Computed Tomography (LDCT) and CTC detections in pulmonary nodule patients has never been reported. The aim of this study was to explore the effectiveness of the combined methods to screen lung cancer. Out of 8313 volunteers screened by LDCT, 32 ground-glass nodules (GGNs) patients and 19 healthy volunteers were randomly selected. Meanwhile, 15 lung cancer patients also enrolled. CellCollector, a new CTC capturing device, was applied for CTCs detection...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28842178/variance-in-estimated-pairwise-genetic-distance-under-high-versus-low-coverage-sequencing-the-contribution-of-linkage-disequilibrium
#17
Max Shpak, Yang Ni, Jie Lu, Peter Müller
The mean pairwise genetic distance among haplotypes is an estimator of the population mutation rate θ and a standard measure of variation in a population. With the advent of next-generation sequencing (NGS) methods, this and other population parameters can be estimated under different modes of sampling. One approach is to sequence individual genomes with high coverage, and to calculate genetic distance over all sample pairs. The second approach, typically used for microbial samples or for tumor cells, is sequencing a large number of pooled genomes with very low individual coverage...
August 24, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28838384/cell-free-circulating-tumor-dna-supplementing-tissue-biopsies-for-identification-of-targetable-mutations-implications-for-precision-medicine-and-considerations-for-reconciling-results
#18
J Kevin Hicks, James Saller, Emilie Wang, Theresa Boyle, Jhanelle E Gray
Cell-free circulating tumor DNA (ctDNA) next-generation sequencing (NGS) is emerging as a noninvasive technique for detecting targetable mutations. We describe two lung adenocarcinoma cases that show the clinical utility of supplementing tumor biopsy molecular interrogation with ctDNA NGS. For both cases, ctDNA NGS identified actionable mutations that were previously not reported by molecular interrogation of tissue. Explanations are provided for the observed differences between ctDNA and tumor biopsy genomic results along with considerations for reconciling findings...
September 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28835367/fgfr2-amplification-in-colorectal-adenocarcinoma
#19
Jamal H Carter, Catherine E Cottrell, Samantha McNulty, Katinka A Vingh-Conrad, Stephen Lamp, Jonathan W Heusel, Eric J Duncavage
FGFR2 is recurrently amplified in 5% of gastric cancers and 1-4% of breast cancers; however, this molecular alteration has never been reported in a primary colorectal cancer specimen. Preclinical studies indicate that several FGFR tyrosine-kinase inhibitors (TKI), such as AZD4547, have in vitro activity against the FGFR2-amplified colorectal cell line, NCI-H716. The efficacy of these inhibitors is currently under investigation in clinical trials for breast and gastric cancer. Thus, better characterizing colorectal tumors for FGFR2 amplification could identify a subset of patients who may benefit from FGFR TKI therapies...
August 23, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28835206/an-optimised-protocol-for-isolation-of-rna-from-small-sections-of-laser-capture-microdissected-ffpe-tissue-amenable-for-next-generation-sequencing
#20
Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon, Enni Markkanen
BACKGROUND: Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA-protein crosslinking and RNA fragmentation, both of which heavily impact on RNA quantity and quality for downstream analysis. With very small sample sizes, e.g. when performing Laser-capture microdissection (LCM) to isolate specific subpopulations of cells, recovery of sufficient RNA for analysis with reverse-transcription quantitative PCR (RT-qPCR) or next-generation sequencing (NGS) becomes very cumbersome and difficult...
August 23, 2017: BMC Molecular Biology
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