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https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#1
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545024/an-unusual-intragenic-promoter-of-piwil2-contributes-to-aberrant-activation-of-oncogenic-pl2l60
#2
Shan-Shan Liu, Ning Liu, Meng-Yao Liu, Lei Sun, Wu-Yan Xia, Hong-Min Lu, Yu-Jie Fu, Guo-Liang Yang, Juan-Jie Bo, Xiao-Xing Liu, Haizhong Feng, Hailong Wu, Lin-Feng Li, Jian-Xin Gao
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28545022/a-high-throughput-method-to-detect-rna-profiling-by-integration-of-rt-mlpa-with-next-generation-sequencing-technology
#3
Jing Wang, Xue Yang, Haofeng Chen, Xuewei Wang, Xiangyu Wang, Yi Fang, Zhenyu Jia, Jidong Gao
RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544575/analysis-of-physical-characteristics-of-tumor-treating-fields-for-human-glioblastoma
#4
Edwin Lok, Pyay San, Van Hua, Melissa Phung, Eric T Wong
Tumor Treating Fields (TTFields) therapy is an approved treatment that has known clinical efficacy against recurrent and newly diagnosed glioblastoma. However, the distribution of the electric fields and the corresponding pattern of energy deposition in the brain are poorly understood. To evaluate the physical parameters that may influence TTFields, postacquisition MP-RAGE, T1 and T2 MRI sequences from a responder with a right parietal glioblastoma were anatomically segmented and then solved using finite-element method to determine the distribution of the electric fields and rate of energy deposition at the gross tumor volume (GTV) and other intracranial structures...
May 23, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28543693/somatic-driver-mutations-in-melanoma
#5
REVIEW
Bobby Y Reddy, David M Miller, Hensin Tsao
Melanoma has one of the highest somatic mutational burdens among solid malignancies. Although the rapid progress in genomic research has contributed immensely to our understanding of the pathogenesis of melanoma, the clinical significance of the vast array of genomic alterations discovered by next-generation sequencing is far from being fully characterized. Most mutations prevalent in melanoma are simply neutral "passengers," which accompany functionally significant "drivers" under transforming conditions. The delineation of driver mutations from passenger mutations is critical to the development of targeted therapies...
June 1, 2017: Cancer
https://www.readbyqxmd.com/read/28543390/the-effect-of-ebv-on-wif1-nlk-and-apc-gene-methylation-and-expression-in-gastric-carcinoma-and-nasopharyngeal-cancer
#6
Zhenzhen Zhao, Wen Liu, Jincheng Liu, Jiayi Wang, Bing Luo
Epstein-Barr virus (EBV) is an important DNA tumor virus that is associated with approximately 10% of gastric carcinomas and 99% of nasopharyngeal cancers. DNA methylation and microRNAs (miRNAs) are the most studied epigenetic mechanisms that can prompt disease susceptibility. This study aimed to detect the effect of EBV on Wnt inhibitory factor 1 (WIF1), Nemo-like kinase (NLK), and adenomatous polyposis coli (APC) gene methylation and expression in gastric carcinoma and nasopharyngeal cancer. METHODS: The WIF1, NLK, and APC gene mRNA expression levels were measured by real-time quantitative RT-PCR in four EBV-positive cell lines and four EBV-negative cell lines...
May 23, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28543364/diffusion-weighted-mri-with-minimal-distortion-in-head-and-neck-radiotherapy-using-a-turbo-spin-echo-acquisition-method
#7
Tim Schakel, Johannes M Hoogduin, Chris H J Terhaard, Marielle E P Philippens
PURPOSE: Diffusion weighted (DW) MRI, showing high contrast between tumor and background tissue, is a promising technique in radiotherapy for tumor delineation. However, its use for head-and-neck patients is hampered by poor geometric accuracy in conventional echo planar imaging (EPI) DW-MRI. An alternative turbo spin echo sequence, DW-SPLICE, is implemented and demonstrated in patients. METHODS: The DW-SPLICE sequence was implemented on a 3.0T system and evaluated in 10 patients...
May 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28542371/whole-genome-sequencing-of-spermatocytic-tumors-provides-insights-into-the-mutational-processes-operating-in-the-male-germline
#8
Eleni Giannoulatou, Geoffrey J Maher, Zhihao Ding, Ad J M Gillis, Lambert C J Dorssers, Alexander Hoischen, Ewa Rajpert-De Meyts, Gilean McVean, Andrew O M Wilkie, Leendert H J Looijenga, Anne Goriely
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases...
2017: PloS One
https://www.readbyqxmd.com/read/28542273/expression-profile-of-epstein-barr-virus-and-human-adenovirus-small-rnas-in-tonsillar-b-and-t-lymphocytes
#9
Farzaneh Assadian, Wael Kamel, Göran Laurell, Catharina Svensson, Tanel Punga, Göran Akusjärvi
We have used high-throughput small RNA sequencing to characterize viral small RNA expression in purified tonsillar B and T lymphocytes isolated from patients tested positive for Epstein-Barr virus (EBV) or human adenovirus (HAdV) infections, respectively. In the small set of patients analyzed, the expression profile of EBV and HAdV miRNAs could not distinguish between patients diagnosed with tonsillar hypertrophy or chronic/recurrent tonsillitis. The EBV miR-BART expression profile among the patients diagnosed with tonsillar diseases resembles most closely the pattern seen in EBV+ tumors (Latency II/I)...
2017: PloS One
https://www.readbyqxmd.com/read/28542229/thermodynamic-framework-to-assess-low-abundance-dna-mutation-detection-by-hybridization
#10
Hanny Willems, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform...
2017: PloS One
https://www.readbyqxmd.com/read/28541743/rarevar-a-framework-for-detecting-low-frequency-single-nucleotide-variants
#11
Yangyang Hao, Xiaoling Xuei, Lang Li, Harikrishna Nakshatri, Howard J Edenberg, Yunlong Liu
Accurate identification of low-frequency somatic point mutations in tumor samples has important clinical utilities. Although high-throughput sequencing technology enables capturing such variants while sequencing primary tumor samples, our ability for accurate detection is compromised when the variant frequency is close to the sequencer error rate. Most current experimental and bioinformatic strategies target mutations with ≥5% allele frequency, which limits our ability to understand the cancer etiology and tumor evolution...
May 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28541631/germline-and-somatic-mutations-in-homologous-recombination-genes-among-chinese-ovarian-cancer-patients-detected-using-next-generation-sequencing
#12
Qianying Zhao, Jiaxin Yang, Lei Li, Dongyan Cao, Mei Yu, Keng Shen
OBJECTIVE: To define genetic profiling of homologous recombination (HR) deficiency in Chinese ovarian cancer patients. METHODS: we have applied next-generation sequencing to detect deleterious mutations through all exons in 31 core HR genes. Paired whole blood and frozen tumor samples from 50 Chinese women diagnosed with epithelial ovarian carcinomas were tested to identify both germline and somatic variants. RESULTS: Deleterious germline HR-mutations were identified in 36% of the ovarian cancer patients...
July 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/28541485/histologically-defined-intratumoral-sequencing-uncovers-evolutionary-cues-into-conserved-molecular-events-driving-gliomagenesis
#13
Antony Prabhu, Pravin Kesarwani, Shiva Kant, Stewart F Graham, Prakash Chinnaiyan
BACKGROUND: Glioblastoma represents an archetypal example of a heterogeneous malignancy. To understand the diverse molecular consequences of this complex tumor ecology, we analyzed RNA-seq data generated from commonly identified intra-tumoral structures in glioblastoma enriched using laser capture microdissection. METHODS: Raw gene-level fragments per kilobase of transcript per million reads mapped (FPKM) values and the associated clinical data were acquired from the publically available Ivy GAP database and analyzed using MetaboAnalyst (v...
May 25, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28540598/parp-inhibitors-in-prostate-cancer
#14
REVIEW
Praveen Ramakrishnan Geethakumari, Matthew J Schiewer, Karen E Knudsen, Wm Kevin Kelly
The genomic landscape of metastatic prostate cancer (mPCa) reveals that up to 90% of patients harbor actionable mutations and >20% have somatic DNA repair gene defects (DRD). This provides the therapeutic rationale of PARP inhibition (PARPi) to achieve "synthetic lethality" in treating this fatal disease. Clinical trials with PARP inhibitors have shown significant response rates up to 88% for PCa patients having DRD like BRCA1/2 or ATM mutations. The FDA has awarded "breakthrough designation" to develop the PARPi olaparib in treating this subset of metastatic PCa patients...
June 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/28540524/changes-in-tumor-biology-during-chemoradiation-of-cervix-cancer-assessed-by-multiparametric-mri-and-hypoxia-pet
#15
Petra Georg, Piotr Andrzejewski, Pascal Baltzer, Michaela Daniel, Wolfgang Wadsak, Markus Mitterhauser, Alina Sturdza, Katarina Majercakova, Georgios Karanikas, Richard Pötter, Marcus Hacker, Thomas Helbich, Dietmar Georg, Katja Pinker
PURPOSE: Imaging biomarkers assessed with magnetic resonance imaging (MRI) and/or positron emission tomography (PET) enable non-invasive tumor characterization in cervix cancer patients. We investigated the spatio-temporal stability of hypoxia, perfusion, and the cell density of tumors over time by repetitive imaging prior to, during, and after radio-chemotherapy. PROCEDURES: Thirteen patients were included in this prospective study. The imaging protocol included the following: [(18)F]fluoromisonidazole ([(18)F]FMISO)-PET/x-ray computed tomography (CT) and multiparametric (mp)-MRI at four time-points (TP): baseline (BL); and weeks 2 (TP1), 5 (TP2), and 19 after treatment start (follow-up FU)...
May 24, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28540464/comparison-of-lesion-enhancement-between-bb-cube-and-3d-spgr-images-for-brain-tumors-with-1-5-t-magnetic-resonance-imaging
#16
Hirokazu Hasegawa, Ryuichiro Ashikaga, Kaoru Okajima, Tetsuya Wakayama, Mitsuharu Miyoshi, Yasumasa Nishimura, Takamichi Murakami
PURPOSE: This study aimed to compare the detectability of neoplastic lesion enhancement after gadolinium-based contrast media injection in three-dimensional T1-weighted black blood Cube (3D-T1W BB Cube) and three-dimensional T1-weighted fast spoiled gradient-echo (3D-T1W fast SPGR) images obtained with 1.5-T magnetic resonance imaging (MRI). MATERIALS AND METHODS: Phantom and clinical studies were performed to compare the lesion detectability and contrast ratio (CR) between 3D-T1W BB Cube and 3D-T1W fast SPGR pulse sequences...
May 24, 2017: Japanese Journal of Radiology
https://www.readbyqxmd.com/read/28540122/presurgical-role-of-mri-tractography-in-a-case-of-extensive-cervicothoracic-spinal-ependymoma
#17
Francesca Granata, Sergio Racchiusa, Enricomaria Mormina, Valeria Barresi, Giada Garufi, Giovanni Grasso, Francesco Maria Salpietro, Marcello Longo, Concetta Alafaci
BACKGROUND: Intramedullary spinal ependymoma is a tumor, hardly characterizable with conventional magnetic resonance (MR) imaging only. MR diffusion tensor imaging (DTI) with three-dimensional fiber-tracking reconstructions allows the evaluation of the relationship between neoplasm and white matter fiber tracts, being a powerful tool in presurgical planning. We present DTI findings in a case of a young female with an extensive cervicothoracic spinal ependymoma. CASE DESCRIPTION: The patient complained of a 2-month history of acute urinary retention, weakness and numbness on the lower limbs and the upper left limb...
2017: Surgical Neurology International
https://www.readbyqxmd.com/read/28539559/simultaneous-visualization-of-vessels-and-brain-tumor-with-contrast-enhanced-three-dimensional-phase-contrast-mr-imaging
#18
Yutaka Shigenaga, Masato Sasaki, Takeshi Ishimoto, Keiko Ama
The sequence for concurrently depicting engulfed vessels and a well-enhanced tumor in once-off scanning has never been reported for preoperative magnetic resonance imaging for brain tumor resection. Multimodal fusion techniques have been recently developed, but the risks of misregistration still remain. Here a case is reported where contrast-enhanced three-dimensional phase contrast sequence concurrently depicted an engulfed vessel and metastatic brain tumor in once-off scanning and related technical aspects are discussed...
May 24, 2017: Magnetic Resonance in Medical Sciences: MRMS
https://www.readbyqxmd.com/read/28539465/utility-of-genomic-assessment-of-blood-derived-circulating-tumor-dna-ctdna-in-patients-with-advanced-lung-adenocarcinoma
#19
Maria Schwaederle, Sandip P Patel, Hatim Husain, Megumi Ikeda, Richard Lanman, Kimberly C Banks, AmirAli Talasaz, Lyudmila Bazhenova, Razelle Kurzrock
<p>Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with non-small cell lung adenocarcinoma (NSCLC) were ascertained and correlated with clinical characteristics and therapeutic outcomes.</p> <br /><br />Experimental Design: Comprehensive plasma ctDNA testing was performed in 88 consecutive patients; 34 also had tissue next generation sequencing; 29, other forms of genotyping; and 25 (28.4%) had no tissue molecular tests because of inadequate tissue or biopsy contraindications...
May 24, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28539123/multilevel-genomics-of-colorectal-cancers-with-microsatellite-instability-clinical-impact-of-jak1-mutations-and-consensus-molecular-subtype-1
#20
Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A Danielsen, Ina A Eilertsen, Guro E Lind, Kaja C G Berg, Edward Leithe, Leonardo A Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I Skotheim, Ragnhild A Lothe
BACKGROUND: Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations-the microsatellite instability (MSI) phenotype. We investigated molecular heterogeneity and tumor immunogenicity in relation to clinical endpoints within this distinct subtype of colorectal cancers. METHODS: A total of 333 primary MSI+ colorectal tumors from multiple cohorts were analyzed by multilevel genomics and computational modeling-including mutation profiling, clonality modeling, and neoantigen prediction in a subset of the tumors, as well as gene expression profiling for consensus molecular subtypes (CMS) and immune cell infiltration...
May 24, 2017: Genome Medicine
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