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https://www.readbyqxmd.com/read/28330019/facial-nerve-tractography-a-new-tool-to-detect-perineural-invasion-in-parotid-cancers
#1
René-Charles Rouchy, Arnaud Attyé, Irène Troprès, Maud Medici, Adrian Kastler, Christian Righini, Alexandre Krainik
PURPOSE: To determine whether magnetic resonance (MR) tractography of facial nerve (VIIn) is useful to detect perineural invasion in case of parotid cancers. MATERIALS AND METHODS: Thirty patients, aged 18 or over, were enrolled in this prospective study between December 2013 and March 2016 (IRB 5891), with a diagnosis of parotid tumors (15 malignant, 15 benign). They have undergone preoperative MR scans (3.0-T) before surgical management. The parameters of the diffusion-weighted (DW) sequence were b-value of 1000s/mm(2); 32 directions; voxel size: 2mm isotropic; scan time: 9' The post-processing generates whole-neck constrained spherical deconvolution (CSD)-based tractography data and super-resolution track-weighted imaging (TWI) technique...
March 2017: Journal of Neuroradiology. Journal de Neuroradiologie
https://www.readbyqxmd.com/read/28329645/frequent-somatic-mutations-of-chromatin-remodeling-genes-in-metastatic-cutaneous-squamous-cell-carcinoma
#2
Amanda Ewart Toland
Exome and targeted sequencing studies have identified potential driver mutations for a variety of tumor types. Cutaneous squamous cell carcinoma (cSCC) is one of the most highly mutated cancers but is typically correlated with high survival rates and low rates of metastasis. Nevertheless, metastatic cSCC is a significant health threat; up to 8800 individuals are estimated to die yearly from this disease. As it is difficult to predict which cSCCs are more likely to metastasize, and because there are no targeted therapies specifically designated for metastatic cSCC, we performed exome and targeted sequencing of 18 metastatic and 10 primary cSCCs to identify mutations with potential therapeutic benefit...
September 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28327999/comprehensive-genomic-profiling-of-salivary-mucoepidermoid-carcinomas-reveals-frequent-bap1-pik3ca-and-other-actionable-genomic-alterations
#3
K Wang, J D McDermott, A B Schrock, J A Elvin, L Gay, S D Karam, D Raben, H Somerset, S M Ali, J S Ross, D W Bowles
Background: We sought to identify genomic alterations (GAs) in salivary mucoepidermoid carcinomas. Patients and methods: DNA was extracted from 48 mucoepidermoid carcinomas. Comprehensive genomic profiling (CGP) including the calculation to tumor mutational burden (TMB) was performed on hybridization-captured adaptor ligation-based libraries of 315 cancer-related genes plus introns from 28 genes frequently rearranged for cancer and evaluated for all classes of GAs...
January 16, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327987/pssmhcpan-a-novel-pssm-based-software-for-predicting-class-i-peptide-hla-binding-affinity
#4
Geng Liu, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng-Chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Le Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Background: Predicting peptides binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401 and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#5
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327949/resection-of-navigated-transcranial-magnetic-stimulation-positive-prerolandic-motor-areas-causes-permanent-impairment-of-motor-function
#6
Tobias Moser, Lucia Bulubas, Jamil Sabih, Neal Conway, Noémie Wildschutz, Nico Sollmann, Bernhard Meyer, Florian Ringel, Sandro M Krieg
BACKGROUND: Navigated transcranial magnetic stimulation (nTMS) helps to determine the distribution of motor eloquent areas prior to brain surgery. Yet, the eloquence of primary motor areas frontal to the precentral gyrus identified via nTMS is unclear. OBJECTIVE: To investigate the resection of nTMS-positive prerolandic motor areas and its correlation with postsurgical impairment of motor function. METHODS: Forty-three patients with rolandic or prerolandic gliomas (WHO grade I-IV) underwent nTMS prior to surgery...
February 24, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#7
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28327926/genomic-characterisation-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#8
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 ( ERBB2 ) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference [1]. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
February 21, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#9
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28326610/dose-and-temporal-evaluation-of-ethylene-oxide-induced-mutagenicity-in-the-lungs-of-male-big-blue-mice-following-inhalation-exposure-to-carcinogenic-concentrations
#10
Mugimane G Manjanatha, Sharon D Shelton, Ying Chen, Barbara L Parsons, Meagan B Myers, Karen L McKim, B Bhaskar Gollapudi, Nigel P Moore, Lynne T Haber, Bruce Allen, Martha M Moore
Ethylene oxide (EO) is a direct acting alkylating agent; in vitro and in vivo studies indicate that it is both a mutagen and a carcinogen. However, it remains unclear whether the mode of action (MOA) for cancer for EO is a mutagenic MOA, specifically via point mutation. To investigate the MOA for EO-induced mouse lung tumors, male Big Blue (BB) B6C3F1 mice (10/group) were exposed to EO by inhalation, 6 hr/day, 5 days/week for 4 (0, 10, 50, 100, or 200 ppm EO), 8, or 12 weeks (0, 100, or 200 ppm EO). Lung DNA samples were analyzed for cII mutant frequency (MF) at 4, 8 and 12 weeks of exposure; the mutation spectrum was analyzed for mutants from control and 200 ppm EO treatments...
March 22, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28325666/development-of-novel-patient-derived-preclinical-models-from-malignant-effusions-in-patients-with-tyrosine-kinase-inhibitor-resistant-clear-cell-renal-cell-carcinoma
#11
Jiryeon Jang, Oliver Rath, Julia Schueler, Hyun Hwan Sung, Hwang Gyun Jeon, Byong Chang Jeong, Seong Il Seo, Seong Soo Jeon, Hyun Moo Lee, Han-Yong Choi, Ghee-Young Kwon, Woong Yang Park, Jeeyun Lee, Se Hoon Park
PURPOSE: Although targeting angiogenesis with tyrosine kinase inhibitors (TKIs) has become standard of care in the treatment of clear cell renal cell carcinoma (RCC), resistance mechanism are not fully understood, and there is a need to develop new therapeutic options overcoming them. METHODS AND MATERIALS: To develop a preclinical model that predicts clinical activity of novel agents in 19 RCC patients, we established patient-derived cell (PDC) and xenograft (PDX) models derived from malignant effusions or surgical specimen...
March 15, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28323992/quantification-of-thyroid-cancer-and-multinodular-goiter-risk-in-the-dicer1-syndrome-a-family-based-cohort-study
#12
Nicholas E Khan, Andrew J Bauer, Kris Ann P Schultz, Leslie Doros, Rosamma M Decastro, Alexander Ling, Maya B Lodish, Laura A Harney, Ron G Kase, Ann G Carr, Christopher T Rossi, Amanda Field, Anne K Harris, Gretchen M Williams, Louis P Dehner, Yoav H Messinger, D Ashley Hill, Douglas R Stewart
Context: The risk of thyroid cancer and multinodular goiter (MNG) in the DICER1 syndrome, a rare tumor-predisposition disorder, is unknown. Objective: To quantify the risk of thyroid cancer and MNG in individuals with the DICER1 syndrome. Design: Family-based cohort study. Setting: National Institutes of Health (NIH) Clinical Center (CC). Participants: The National Cancer Institute DICER1 syndrome cohort consisted of 145 individuals with a DICER1 germline mutation and 135 family controls from 48 families...
February 2, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323658/changing-face-of-metastatic-prostate-cancer-the-law-of-diminishing-returns-holds-true
#13
Ulka N Vaishampayan
PURPOSE OF REVIEW: Prostate cancer presents with a multitude of faces. It ranges from localized cancers staying quiescent for many years during active surveillance to the raging diffuse liver metastases causing terminal disease. The incidence of metastatic disease is increasing. This review will highlight some of the recent developments as well as ongoing challenges of managing advanced prostate cancer. RECENT FINDINGS: Significant strides are being made in managing metastatic prostate cancer...
March 18, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28323522/detection-of-cytosine-and-cpg-density-in-proto-oncogenes-and-tumor-suppressor-genes-in-promoter-sequences-of-acute-myeloid-leukemia
#14
Senol Dogan, Anis Cilic, Damir Marjanovic, Amina Kurtovic-Kozaric
Aberrant methylation is one of the driving forces of cancer genome development. Although the rate of methylation appears massively variable across the genome, it is mainly observed in histone modification, chromatin organization, DNA accessibility, or promoter sequence. Methylation of promoter sequence occurs mostly to cytosine nucleotides, which can affect transcription factors' binding affinities. In this study, we demonstrated that cytosine repeats (C types density), consisting of CC, CCC, CCCC, CCCCC, CCCCCC, CCCCCCC motifs and CpG islands density in 25 proto-oncogenes, tumor suppressor genes and control genes may play a role in the pathogenesis of acute myeloid leukemia...
March 21, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/28323123/circumventing-intratumoral-heterogeneity-to-identify-potential-therapeutic-targets-in-hepatocellular-carcinoma
#15
Ao Huang, Xin Zhao, Xin-Rong Yang, Fu-Qiang Li, Xin-Lan Zhou, Kui Wu, Xin Zhang, Qi-Man Sun, Ya Cao, Hong-Mei Zhu, Xiang-Dong Wang, Huan-Ming Yang, Jian Wang, Zhao-You Tang, Yong Hou, Jia Fan, Jian Zhou
BACKGROUND AND AIMS: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) in blood could possibly reflect the entire mutation spectrum in certain tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC). METHODS: Thirty-two multi-regional tumor samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS); matched preoperative cfDNAs were sequenced accordingly...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28323122/exome-analysis-of-the-evolutionary-path-of-hepatocellular-adenoma-carcinoma-transition-vascular-invasion-and-brain-dissemination
#16
Sílvia Vilarinho, Zeynep Erson-Omay, Kisha Mitchell-Richards, Charles Cha, Carol Nelson-Williams, Akdes Serin Harmancı, Katsuhito Yasuno, Murat Günel, Tamar H Taddei
Hepatocellular adenoma (HCA) is a rare benign liver tumor, predominantly seen in young women. Its major complications are malignant transformation, spontaneous hemorrhage, and rupture. We describe a case of a young female with no underlying liver disease who presented with acute abdominal pain and was found to have a 17 cm heterogeneous mass in the left lobe of the liver. She underwent left hepatectomy and pathology revealed a 14 cm moderately differentiated hepatocellular carcinoma (HCC) arising in a shell of a HCA...
March 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28321907/systematical-analyses-of-variants-in%C3%A2-dnase-i-hypersensitive-sites-identified-two-novel-hepatocellular-carcinoma-susceptibility-loci-among-chinese-population
#17
Tao Jiang, Fangzhi Du, Na Qin, Qun Lu, Juncheng Dai, Hongbing Shen, Zhibin Hu
BACKGROUND AND AIM: Although several variants located at coding and non-coding regions were evaluated by previous studies, the evidence for associations between variants located in DNase I-hypersensitive sites (DHSs) and hepatocellular carcinoma (HCC) risk was still limited. Recent advances using ENCODE data indicated that genetic variants in DHSs played an important role in carcinogenesis. Therefore, systematically investigate the associations between regulatory variants in DHSs and HCC risk should be put on the agenda...
March 20, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28321903/spin-lock-imaging-of-exogenous-exchange-based-contrast-agents-to-assess-tissue-ph
#18
Zhongliang Zu, Hua Li, Xiaoyu Jiang, John C Gore
PURPOSE: Some X-ray contrast agents contain exchangeable protons that give rise to exchange-based effects on MRI, including chemical exchange saturation transfer (CEST). However, CEST has poor specificity to explicit exchange parameters. Spin-lock sequences at high field are also sensitive to chemical exchange. Here, we evaluate whether spin-locking techniques can detect the contrast agent iohexol in vivo after intravenous administration, and their potential for measuring changes in tissue pH...
March 20, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28321501/visualization-of-tumor-heterogeneity-by-in-situ-padlock-probe-technology-in-colorectal-cancer
#19
Amin El-Heliebi, Karl Kashofer, Julia Fuchs, Stephan W Jahn, Christian Viertler, Andrija Matak, Peter Sedlmayr, Gerald Hoefler
Tumor heterogeneity is considered a major cause for therapy resistance in colorectal cancer. Sub-populations of cells with different genetic alterations may exist in spatially distinct areas. Upon therapy, resistant sub-clones may enrich and ultimately lead to disease progression. Although ample data are available on tumors which are heterogeneous on a morphological level, only little is known about morphologically homogeneous tumors. We aimed to investigate if morphologically homogeneous colorectal cancer can harbor a heterogeneous genetic landscape...
March 20, 2017: Histochemistry and Cell Biology
https://www.readbyqxmd.com/read/28321364/effect-of-method-of-deduplication-on-estimation-of-differential-gene-expression-using-rna-seq
#20
Anna V Klepikova, Artem S Kasianov, Mikhail S Chesnokov, Natalia L Lazarevich, Aleksey A Penin, Maria Logacheva
BACKGROUND: RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. RESULTS: To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI)...
2017: PeerJ
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