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https://www.readbyqxmd.com/read/28090632/identification-of-highly-selective-mmp-14-inhibitory-fabs-by-deep-sequencing
#1
Tyler Lopez, Dong Hyun Nam, Evan Kaihara, Zahid Mustafa, Xin Ge
Matrix metalloproteinase (MMP)-14 is an important target for cancer treatment due to its critical roles in tumor invasion and metastasis. Previous failures of all compound-based broad-spectrum MMP inhibitors in clinical trials suggest that selectivity is the key for a successful therapy. With inherent high specificity, monoclonal antibodies (mAbs) therefore arise as attractive inhibitors able to target the particular MMP of interest. As a routine screening method, enzyme-linked immunosorbent assays (ELISA) have been applied to panned phage libraries for the isolation of mAbs inhibiting MMP-14...
January 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28078112/molecular-spectrum-of-kras-nras-braf-pik3ca-tp53-and-apc-somatic-gene-mutations-in-arab-patients-with-colorectal-cancer-determination-of-frequency-and-distribution-pattern
#2
Humaid O Al-Shamsi, Jeremy Jones, Yazan Fahmawi, Ibrahim Dahbour, Aziz Tabash, Reham Abdel-Wahab, Ahmed O S Abousamra, Kenna R Shaw, Lianchun Xiao, Manal M Hassan, Benjamin R Kipp, Scott Kopetz, Amr S Soliman, Robert R McWilliams, Robert A Wolff
BACKGROUND: The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features. METHODS: Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed...
December 2016: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28076841/clonal-evolution-in-therapy-related-neoplasms
#3
Emiliano Fabiani, Giulia Falconi, Luana Fianchi, Marianna Criscuolo, Tiziana Ottone, Laura Cicconi, Stefan Hohaus, Simona Sica, Massimiliano Postorino, Antonino Neri, Marta Lionetti, Giuseppe Leone, Francesco Lo-Coco, Maria Teresa Voso
Therapy-related myeloid neoplasms (t-MN) may occur as a late effect of cytotoxic therapy for a primary malignancy or autoimmune diseases in susceptible individuals. We studied the development of somatic mutations in t-MN, using a collection of follow-up samples from 14 patients with a primary hematologic malignancy, who developed a secondary leukemia (13 t-MN and 1 t-acute lymphoblastic leukemia), at a median latency of 73 months (range 18-108) from primary cancer diagnosis.Using Sanger and next generation sequencing (NGS) approaches we identified 8 mutations (IDH1 R132H, ASXL1 Y591*, ASXL1 S689*, ASXL1 R693*, SRSF2 P95H, SF3B1 K700E, SETBP1 G870R and TP53 Y220C) in seven of thirteen t-MN patients (54%), whereas the t-ALL patient had a t(4,11) translocation, resulting in the KMT2A/AFF1 fusion gene...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28075483/detecting-apc-gene-mutations-in-familial-adenomatous-polyposis-fap
#4
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 coding exons. The mutation spectrum of the APC gene is broad in that 87% of causative mutations are point mutations (including other sequence variants) and around 10% to 15% are intragenic deletions and duplications...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28071743/self-assembly-assisted-fabrication-of-dextran-based-nanohydrogels-with-reduction-cleavable-junctions-for-applications-as-efficient-drug-delivery-systems
#5
Hao Wang, Tingting Dai, Shuyan Zhou, Xiaoxiao Huang, Songying Li, Kang Sun, Guangdong Zhou, Hongjing Dou
In order to overcome the key challenge in improving both fabrication efficiency and their drug delivery capability of anti-cancer drug delivery systems (ACDDS), here polyacrylic acid (PAA) grafted dextran (Dex) nanohydrogels (NGs) with covalent crosslinked structure bearing redox sensitive disulfide crosslinking junctions (Dex-SS-PAA) were synthesized efficiently through a one-step self-assembly assisted methodology (SAA). The Dex-SS-PAA were subsequently conjugated with doxorubicin through an acid-labile hydrazone bond (Dex-SS-PAA-DOX)...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28067034/gadolinium-loaded-poly-n-vinylcaprolactam-nanogels-synthesis-characterization-and-application-for-enhanced-tumor-mr-imaging
#6
Wenjie Sun, Sabrina Thies, Jiulong Zhang, Chen Peng, Guangyu Tang, Mingwu Shen, Andrij Pich, Xiangyang Shi
We report the synthesis of poly(N-vinylcaprolactam) nanogels (PVCL NGs) loaded with gadolinium (Gd) for tumor MR imaging applications. The PVCL NGs were synthesized via precipitation polymerization using the monomer N-vinylcaprolactam (VCL), the comonomer acrylic acid (AAc), and the degradable crosslinker 3,9-divinyl-2,4,8,10-tetraoxaspiro-[5,5]-undecane (VOU) in aqueous solution, followed by covalently binding with 2,2',2''-(10-(4-((2-aminoethyl)amino)-1-carboxy-4-oxobutyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triyl) triacetic acid (NH2-DOTA-GA)/Gd complexes...
January 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28061482/genomic-mutation-driven-metastatic-breast-cancer-therapy-a-single-center-experience
#7
Yuan Yuan, Susan E Yost, Yate-Ching Yuan, Nicola M Solomon, Isa Mambetsariev, Sumanta Pal, Paul Frankel, Ravi Salgia, Susan L Neuhausen, Joanne Mortimer
BACKGROUND: Next-Generation Sequencing (NGS) has made genomic mutation-driven therapy feasible for metastatic breast cancer (MBC) patients. We frequently submit tumor tissue from MBC patients for targeted NGS of tumor using the Illumina HiSeq 2000 platform (FoundationOne®, Foundation Medicine, MA). Herein, we report the results and clinical impact of this test in MBC patients. PATIENTS AND METHODS: We identified patients with MBC treated at City of Hope from January 2014 to May 2016 who underwent NGS...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060956/technical-insights-into-highly-sensitive-isolation-and-molecular-characterization-of-fixed-and-live-circulating-tumor-cells-for-early-detection-of-tumor-invasion
#8
Sophie Laget, Lucile Broncy, Katia Hormigos, Dalia M Dhingra, Fatima BenMohamed, Thierry Capiod, Magne Osteras, Laurent Farinelli, Stephen Jackson, Patrizia Paterlini-Bréchot
Circulating Tumor Cells (CTC) and Circulating Tumor Microemboli (CTM) are Circulating Rare Cells (CRC) which herald tumor invasion and are expected to provide an opportunity to improve the management of cancer patients. An unsolved technical issue in the CTC field is how to obtain highly sensitive and unbiased collection of these fragile and heterogeneous cells, in both live and fixed form, for their molecular study when they are extremely rare, particularly at the beginning of the invasion process. We report on a new protocol to enrich from blood live CTC using ISET® (Isolation by SizE of Tumor/Trophoblastic Cells), an open system originally developed for marker-independent isolation of fixed tumor cells...
2017: PloS One
https://www.readbyqxmd.com/read/28051113/a-comprehensive-custom-panel-design-for-routine-hereditary-cancer-testing-preserving-control-improving-diagnostics-and-revealing-a-complex-variation-landscape
#9
Elisabeth Castellanos, Bernat Gel, Inma Rosas, Eva Tornero, Sheila Santín, Raquel Pluvinet, Juan Velasco, Lauro Sumoy, Jesús Del Valle, Manuel Perucho, Ignacio Blanco, Matilde Navarro, Joan Brunet, Marta Pineda, Lidia Feliubadaló, Gabi Capellá, Conxi Lázaro, Eduard Serra
We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set...
January 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049581/validation-of-a-next-generation-sequencing-panel-for-detection-of-hotspot-cancer-mutations-in-a-clinical-laboratory
#10
Reza Shahsiah, Jenefer DeKoning, Saeed Samie, Seyed Ziaeddin Latifzadeh, Zahra Mehdizadeh Kashi
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform...
December 16, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28045747/next-generation-sequencing-reveals-pathway-activations-and-new-routes-to-targeted-therapies-in-cutaneous-metastatic-melanoma
#11
J Andrew Carlson, Jose Candido Caldeira Xavier, Ashley Tarasen, Christine E Sheehan, Geoff Otto, Vincent A Miller, Philip J Stephens, Julia A Elvin, Jo-Anne Vergilio, James Suh, Laurie M Gay, Jeffrey S Ross
BACKGROUND: Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test. METHODS: NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements...
January 2017: American Journal of Dermatopathology
https://www.readbyqxmd.com/read/28034454/comprehensive-genomic-sequencing-and-the-molecular-profiles-of-clinically-advanced-breast-cancer
#12
Jeffrey S Ross, Laurie M Gay
Targeting specific mutations that have arisen within a tumour is a promising means of increasing the efficacy of treatments, and breast cancer is no exception to this new paradigm of personalised medicine. Traditional DNA sequencing methods used to characterise clinical cancer specimens and impact treatment decisions are highly sensitive, but are often limited in their scope to known mutational hot spots. Next-generation sequencing (NGS) technologies can also test for these well-known hot spots, as well as identifying insertions and deletions, copy number changes such as ERBB2 (HER2) gene amplification, and a wide array of fusion or rearrangement events...
December 26, 2016: Pathology
https://www.readbyqxmd.com/read/28031426/molecular-profiling-to-determine-clonality-of-serial-magnetic-resonance-imaging-ultrasound-fusion-biopsies-from-men-on-active-surveillance-for-low-risk-prostate-cancer
#13
Ganesh S Palapattu, Simpa S Salami, Andi K Cani, Daniel H Hovelson, Lorena Lazo de la Vega, Kelly R Vandenberg, Jarred V Bratley, Chia-Jen Liu, Lakshmi P Kunju, Jeffery S Montgomery, Todd M Morgan, Shyam Natarajan, Jiaoti Huang, Scott A Tomlins, Leonard S Marks
PURPOSE: To determine whether MRI/ultrasound (MRI/US) fusion biopsy facilitates longitudinal resampling of the same clonal focus of prostate cancer and to determine whether high-grade cancers can evolve from low-grade clones. EXPERIMENTAL DESIGN: All men on active surveillance who underwent tracking MRI/US fusion biopsy of Gleason 6 prostate cancer, on at least two distinct occasions, between 2012 and 2014 were enrolled. MRI/US fusion was used to track and resample specific cancer foci...
October 7, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28031175/adjuvant-folfox-cetuximab-in-full-ras-and-braf-wildtype-stage-iii-colon-cancer-patients
#14
J Taieb, R Balogoun, K Le Malicot, J Tabernero, E Mini, G Folprecht, J-L Van Laethem, J-F Emile, C Mulot, S Fratté, C-B Levaché, L Saban-Roche, J Thaler, L N Petersen, J Bridgewater, G Perkins, C Lepage, E Van Cutsem, A Zaanan, P Laurent-Puig
BACKGROUND: RAS mutations have been shown to confer resistance to anti-EGFR treatment. We analyzed the results of the PETACC8 trial (cetuximab + FOLFOX vs FOLFOX) in full RAS and BRAF wildtype (WT) patients (pts) with resected stage III colon cancer. METHODS: Exons 2, 3 and 4 of KRAS and NRAS, and BRAF exons 11 and 15, were sequenced using the Ampliseq colon-lung cancer panel version 2, in PETACC8 trial pts who consented to translational research. The impact of cetuximab on time to recurrence (TTR), disease-free survival (DFS) and overall survival (OS) was investigated in pts with tumors harboring RAS & BRAF WT and RAS mutations...
December 28, 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28029553/somatic-mutation-detection-using-various-targeted-detection-assays-in-paired-samples-of-circulating-tumor-dna-primary-tumor-and-metastases-from-patients-undergoing-resection-of-colorectal-liver-metastases
#15
Nick Beije, Jean C Helmijr, Marjolein J A Weerts, Corine M Beaufort, Matthew Wiggin, Andre Marziali, Cornelis Verhoef, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens
Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally-invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell-free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor-adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR)...
October 10, 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28028034/rapamycin-insensitive-companion-of-mtor-rictor-amplification-defines-a-subset-of-advanced-gastric-cancer-and-is-sensitive-to-azd2014-mediated-mtorc1-2-inhibition
#16
S T Kim, S Y Kim, S J Klempner, J Yoon, N Kim, S Ahn, H Bang, K-M Kim, W Park, S H Park, J O Park, Y S Park, H Y Lim, S H Lee, K Park, W K Kang, J Lee
PURPOSE: Targeting oncogenic genomic aberrations is an established therapeutic strategy in multiple tumor types. Molecular classification has uncovered a number of novel targets, and rapamycin-insensitive companion of mTOR (RICTOR) amplification has been identified in lung cancer. Further investigation assessing the therapeutic potential of RICTOR amplification as a novel target across advanced cancers is needed. PATIENTS AND METHODS: Tumor samples from 640 patients with metastatic solid tumors, primarily gastrointestinal and lung cancers were prospectively subjected to a next-generation sequencing (NGS) assay to identify molecular targets...
December 27, 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28027945/next-generation-assessment-of-erbb2-human%C3%A2-epidermal-growth-factor-receptor-2-amplification-status-clinical-validation-in-the-context-of-a-hybrid-capture-based-comprehensive-solid-tumor-genomic-profiling-assay
#17
Dara S Ross, Ahmet Zehir, Donavan T Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F Hechtman, Yelena Y Janjigian, Britta Weigelt, Pedram Razavi, David M Hyman, José Baselga, Michael F Berger, Marc Ladanyi, Maria E Arcila
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to patients' treatment plans. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling...
December 24, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28027320/genomic-analysis-of-uterine-lavage-fluid-detects-early-endometrial-cancers-and-reveals-a-prevalent-landscape-of-driver-mutations-in-women-without-histopathologic-evidence-of-cancer-a-prospective-cross-sectional-study
#18
Navya Nair, Olga Camacho-Vanegas, Dmitry Rykunov, Matthew Dashkoff, Sandra Catalina Camacho, Cassie A Schumacher, Jonathan C Irish, Timothy T Harkins, Elijah Freeman, Isaac Garcia, Elena Pereira, Sviatoslav Kendall, Rachel Belfer, Tamara Kalir, Robert Sebra, Boris Reva, Peter Dottino, John A Martignetti
BACKGROUND: Endometrial cancer is the most common gynecologic malignancy, and its incidence and associated mortality are increasing. Despite the immediate need to detect these cancers at an earlier stage, there is no effective screening methodology or protocol for endometrial cancer. The comprehensive, genomics-based analysis of endometrial cancer by The Cancer Genome Atlas (TCGA) revealed many of the molecular defects that define this cancer. Based on these cancer genome results, and in a prospective study, we hypothesized that the use of ultra-deep, targeted gene sequencing could detect somatic mutations in uterine lavage fluid obtained from women undergoing hysteroscopy as a means of molecular screening and diagnosis...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/28027313/base-position-error-rate-analysis-of-next-generation-sequencing-applied-to-circulating-tumor-dna-in-non-small-cell-lung-cancer-a-prospective-study
#19
Nicolas Pécuchet, Eleonora Zonta, Audrey Didelot, Pierre Combe, Constance Thibault, Laure Gibault, Camille Lours, Yves Rozenholc, Valérie Taly, Pierre Laurent-Puig, Hélène Blons, Elizabeth Fabre
BACKGROUND: Circulating tumor DNA (ctDNA) is an approved noninvasive biomarker to test for the presence of EGFR mutations at diagnosis or recurrence of lung cancer. However, studies evaluating ctDNA as a noninvasive "real-time" biomarker to provide prognostic and predictive information in treatment monitoring have given inconsistent results, mainly due to methodological differences. We have recently validated a next-generation sequencing (NGS) approach to detect ctDNA. Using this new approach, we evaluated the clinical usefulness of ctDNA monitoring in a prospective observational series of patients with non-small cell lung cancer (NSCLC)...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/28024622/synthesis-of-a-novel-thermo-ph-sensitive-nanogel-based-on-salep-modified-graphene-oxide-for-drug-release
#20
Ghasem Rezanejade Bardajee, Zari Hooshyar, Maryam Farsi, Akram Mobini, Golnaz Sang
Nanogels (NGs) are three-dimensional water soluble cross-linked hydrogel materials in the nanoscale size range with a high loading capacity for guest molecules and act as drug carrier systems. In the present work, a new type of thermo/pH sensitive NG comprising salep modified graphene oxide (SMGO) with branched N-isopropylacrylamide (NIPAM) and acrylic acid (AA) was prepared. The SMGO/P(NIPAM-co-AA) NGs exhibited nanoporous structure and spherical particles with diameters about 82nm as characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and dynamic light scattering (DLS)...
March 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
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